From 6f58309c941ef1db89ac366cc040653b67d4e941 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 25 Oct 2024 15:02:07 +0000 Subject: [PATCH 01/48] Automatic readme update --- README.md | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index bb195c5..5dfac19 100644 --- a/README.md +++ b/README.md @@ -5,33 +5,34 @@ -# {{ packagename }} +# packagetemplate [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/) -[![R-CMD-check](https://github.com/%7B%7B%20gh_repo%20%7D%7D/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/%7B%7B%20gh_repo%20%7D%7D/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml) [![Codecov test -coverage](https://codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D/branch/main/graph/badge.svg)](https://app.codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D?branch=main) +coverage](https://codecov.io/gh/epiverse-trace/epiparameterDB/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameterDB?branch=main) [![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept) -{{ packagename }} provides functions to …. +packagetemplate provides functions to …. -{{ packagename }} is developed at the CENTER at the UNIVERSITY as part -of the [Epiverse-TRACE program](https://data.org/initiatives/epiverse/). +packagetemplate is developed at the [CENTER\|similar](url) at the +[UNIVERSITY\|similar](url) as part of the [Epiverse-TRACE +program](https://data.org/initiatives/epiverse/). ## Installation -You can install the development version of {{ packagename }} from +You can install the development version of packagetemplate from [GitHub](https://github.com/) with: ``` r # install.packages("pak") -pak::pak("{{ gh_repo }}") +pak::pak("epiverse-trace/epiparameterDB") ``` ## Example @@ -50,18 +51,16 @@ package is not ready for use outside of the development team. ### Contributions Contributions are welcome via [pull -requests](https://github.com/%7B%7B%20gh_repo%20%7D%7D/pulls). +requests](https://github.com/epiverse-trace/epiparameterDB/pulls). ### Related projects This project is related to other existing projects in R or other languages, but also differs from them in the following aspects: -- - ### Code of Conduct -Please note that the {{ packagename }} project is released with a +Please note that the packagetemplate project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. From 1b9a3343af3abdcfabfd022304069a048157300d Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:46:55 +0000 Subject: [PATCH 02/48] write DESCRIPTION for {epiparameterDB} --- DESCRIPTION | 37 +++++++++++++++++-------------------- 1 file changed, 17 insertions(+), 20 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ec9436a..c1a15dd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,29 +1,26 @@ -Package: packagetemplate -Title: Your Package Title in Titlecase -Version: 0.0.1 +Package: epiparameterDB +Title: Database of epidemiological parameters +Version: 0.0.0.9000 Authors@R: c( - person("James M.", "Azam", , "james.azam@lshtm.ac.uk", role = "aut", - comment = c(ORCID = "0000-0001-5782-7330")), - person("Hugo", "Gruson", , "hugo@data.org", role = c("aut", "cre"), - comment = c(ORCID = "0000-0002-4094-1476")), - person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = "aut", - comment = c(ORCID = "0000-0001-5294-7819")), - person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = "aut", + person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = c("cre", "aut", "cph"), comment = c(ORCID = "0000-0001-5218-3046")), - person("Karim", "Mané", , "karim.mane@lshtm.ac.uk", role = "aut", - comment = c(ORCID = "0000-0002-9892-2999")), - person("Jaime A.", "Pavlich-Mariscal", , "jpavlich@javeriana.edu.co", role = "ctb", - comment = c(ORCID = "0000-0002-3892-6680")), - person("Chris", "Hartgerink", , "chris@data.org", role = "ctb", - comment = c(ORCID = "0000-0003-1050-6809")) + person("Adam", "Kucharski", , "adam.kucharski@lshtm.ac.uk", role = "aut", + comment = c(ORCID = "0000-0001-8814-9421")), + person("Carmen", "Tamayo", , "carmen.tamayo-cuartero@lshtm.ac.uk", role = "aut", + comment = c(ORCID = "0000-0003-4184-2864")) ) Description: Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) . -License: MIT + file LICENSE +License: CC0 + file LICENSE +URL: https://github.com/epiverse-trace/epiparameterDB/, + https://epiverse-trace.github.io/epiparameterDB/ +BugReports: https://github.com/epiverse-trace/epiparameterDB/issues Depends: R (>= 4.0.0) -Suggests: +Suggests: + DT, + jsonlite, knitr, rmarkdown, spelling, @@ -32,8 +29,8 @@ VignetteBuilder: knitr Config/Needs/website: epiverse-trace/epiversetheme Config/testthat/edition: 3 -Config/testthat/parallel: true Encoding: UTF-8 Language: en-GB +LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 From 4754a774d7712fe72f3c0c02b5cdba4283d4665d Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:47:20 +0000 Subject: [PATCH 03/48] update LICENSE and LICENSE.md to CC0 --- LICENSE | 4 ++-- LICENSE.md | 64 ++++++++++++++++++++++++++++++++++++------------------ 2 files changed, 45 insertions(+), 23 deletions(-) diff --git a/LICENSE b/LICENSE index 3c3fc0e..ae90a21 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2022 -COPYRIGHT HOLDER: the package authors +YEAR: 2024 +COPYRIGHT HOLDER: epiparameterDB authors diff --git a/LICENSE.md b/LICENSE.md index 6599f3f..139c68e 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,21 +1,43 @@ -# MIT License - -Copyright (c) 2022 the package authors - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +## creative commons + +# CC0 1.0 Universal + +CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER. + +### Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. 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Copyright and Related Rights include, but are not limited to, the following: + + i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; + + ii. moral rights retained by the original author(s) and/or performer(s); + + iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; + + iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; + + v. rights protecting the extraction, dissemination, use and reuse of data in a Work; + + vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and + + vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. + +2. __Waiver.__ To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose. + +3. __Public License Fallback.__ Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. + +4. __Limitations and Disclaimers.__ + + a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. + + b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. + + c. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. + + d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work. From 7d8ed22ccbcbec4d370217c8ae4a4cba5770749e Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:47:45 +0000 Subject: [PATCH 04/48] write README for {epiparameterDB} --- README.Rmd | 61 ++++++++++++++++++++------------ README.md | 100 +++++++++++++++++++++++++++++++++++++++++------------ 2 files changed, 116 insertions(+), 45 deletions(-) diff --git a/README.Rmd b/README.Rmd index 6ed6f51..2b6113b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,55 +18,70 @@ knitr::opts_chunk$set( ) ``` -# {{ packagename }} +# `{epiparameterDB}` [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/) -[![R-CMD-check](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml) -[![Codecov test coverage](https://codecov.io/gh/{{ gh_repo }}/branch/main/graph/badge.svg)](https://app.codecov.io/gh/{{ gh_repo }}?branch=main) -[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept) +[![R-CMD-check](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/epiverse-trace/epiparameterDB/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameterDB?branch=main) +[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -{{ packagename }} provides functions to .... +`{epiparameterDB}` provides a database of epidemiological parameters. It stores the data for the `{epiparameter}` R package. - -{{ packagename }} is developed at the [CENTER|similar](url) at the [UNIVERSITY|similar](url) as part of the [Epiverse-TRACE program](https://data.org/initiatives/epiverse/). +We recommend reading the epidemiological parameters via the `epiparameter::epiparameter_db()` function rather than +using this package. `epiparameter::epiparameter_db()` function formats the epidemiological parameters into `` objects and organises the object elements (e.g. into R classes like `` and ``), whereas reading the parameter database (`parameters.json`) in this package will provide a list of information. + +`{epiparameterDB}` is developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the [London School of Hygiene and Tropical Medicine](https://www.lshtm.ac.uk/) as part of [Epiverse-TRACE](https://data.org/initiatives/epiverse/). ## Installation -You can install the development version of {{ packagename }} from +You can install the development version of `{epiparameterDB}` from [GitHub](https://github.com/) with: ``` r # install.packages("pak") -pak::pak("{{ gh_repo }}") +pak::pak("epiverse-trace/epiparameterDB") ``` -## Example +## Usage + +```{r} +library(epiparameterDB) +data(package = "epiparameterDB") +``` + +## Contributing to library of epidemiological parameters + +Parameters can be added to the [JSON file holding the data](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/parameters.json) base directly via a Pull Request. -These examples illustrate some of the current functionalities +You can find explanation of accepted entries for each column in the [data dictionary](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/data_dictionary.json). +There are simpler ways to add to the epidemiological parameter database outlined in the `README` of the `{epiparameter}` package. -## Development +## Help -### Lifecycle +To report a bug please open an [issue](https://github.com/epiverse-trace/epiparameterDB/issues/new/choose) -This package is currently a *concept*, as defined by the [RECON software -lifecycle](https://www.reconverse.org/lifecycle.html). This means that essential -features and mechanisms are still being developed, and the package is not ready -for use outside of the development team. +## Contributions -### Contributions +Contributions to `{epiparameterDB}` are welcomed. [package contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md). -Contributions are welcome via [pull requests](https://github.com/{{ gh_repo }}/pulls). +Contributions are welcome via [pull requests](https://github.com/epiverse-trace/epiparameterDB/pulls). + +## Code of Conduct + +Please note that the `{epiparameterDB}` project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms. ### Related projects This project is related to other existing projects in R or other languages, but also differs from them in the following aspects: +- `{epireview}`: An R package containing epidemiological parameters for a range of priority pathogens (e.g. Ebola, Lassa SARS). These can be read into R as tabular data. To fully utilise data stored in `{epireview}` we recommend converting the epidemiological parameter of choice into an `` object using `epiparameter::as_epiparameter()`, see [`data_from_epireview` vignette](https://epiverse-trace.github.io/epiparameter/articles/data_from_epireview.html). -### Code of Conduct +## Citing this package + +```{r message=FALSE, warning=FALSE} +citation("epiparameterDB") +``` -Please note that the {{ packagename }} project is released with a -[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). -By contributing to this project, you agree to abide by its terms. diff --git a/README.md b/README.md index 5dfac19..7a36d69 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ -# packagetemplate +# `{epiparameterDB}` @@ -14,20 +14,31 @@ MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.or [![R-CMD-check](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epiverse-trace/epiparameterDB/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameterDB?branch=main) -[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept) +[![Lifecycle: +experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -packagetemplate provides functions to …. +`{epiparameterDB}` provides a database of epidemiological parameters. It +stores the data for the `{epiparameter}` R package. - +We recommend reading the epidemiological parameters via the +`epiparameter::epiparameter_db()` function rather than using this +package. `epiparameter::epiparameter_db()` function formats the +epidemiological parameters into `` objects and organises +the object elements (e.g. into R classes like `` and +``), whereas reading the parameter database +(`parameters.json`) in this package will provide a list of information. -packagetemplate is developed at the [CENTER\|similar](url) at the -[UNIVERSITY\|similar](url) as part of the [Epiverse-TRACE -program](https://data.org/initiatives/epiverse/). +`{epiparameterDB}` is developed at the [Centre for the Mathematical +Modelling of Infectious +Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) +at the [London School of Hygiene and Tropical +Medicine](https://www.lshtm.ac.uk/) as part of +[Epiverse-TRACE](https://data.org/initiatives/epiverse/). ## Installation -You can install the development version of packagetemplate from +You can install the development version of `{epiparameterDB}` from [GitHub](https://github.com/) with: ``` r @@ -35,32 +46,77 @@ You can install the development version of packagetemplate from pak::pak("epiverse-trace/epiparameterDB") ``` -## Example +## Usage -These examples illustrate some of the current functionalities +``` r +library(epiparameterDB) +data(package = "epiparameterDB") +``` + +## Contributing to library of epidemiological parameters + +Parameters can be added to the [JSON file holding the +data](https://github.com/epiverse-trace/epiparameter/blob/main/inst/extdata/parameters.json) +base directly via a Pull Request. + +You can find explanation of accepted entries for each column in the +[data +dictionary](https://github.com/epiverse-trace/epiparameterDB/blob/main/inst/extdata/data_dictionary.json). -## Development +There are simpler ways to add to the epidemiological parameter database +outlined in the `README` of the `{epiparameter}` package. -### Lifecycle +## Help -This package is currently a *concept*, as defined by the [RECON software -lifecycle](https://www.reconverse.org/lifecycle.html). This means that -essential features and mechanisms are still being developed, and the -package is not ready for use outside of the development team. +To report a bug please open an +[issue](https://github.com/epiverse-trace/epiparameterDB/issues/new/choose) -### Contributions +## Contributions + +Contributions to `{epiparameterDB}` are welcomed. [package contributing +guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md). Contributions are welcome via [pull requests](https://github.com/epiverse-trace/epiparameterDB/pulls). +## Code of Conduct + +Please note that the `{epiparameterDB}` project is released with a +[Contributor Code of +Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). +By contributing to this project, you agree to abide by its terms. + ### Related projects This project is related to other existing projects in R or other languages, but also differs from them in the following aspects: -### Code of Conduct +- `{epireview}`: An R package containing epidemiological parameters for + a range of priority pathogens (e.g. Ebola, Lassa SARS). These can be + read into R as tabular data. To fully utilise data stored in + `{epireview}` we recommend converting the epidemiological parameter of + choice into an `` object using + `epiparameter::as_epiparameter()`, see [`data_from_epireview` + vignette](https://epiverse-trace.github.io/epiparameter/articles/data_from_epireview.html). -Please note that the packagetemplate project is released with a -[Contributor Code of -Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). -By contributing to this project, you agree to abide by its terms. +## Citing this package + +``` r +citation("epiparameterDB") +#> +#> To cite package 'epiparameterDB' in publications use: +#> +#> Lambert J, Kucharski A, Tamayo C (????). _epiparameterDB: Database of +#> epidemiological parameters_. +#> https://github.com/epiverse-trace/epiparameterDB/, +#> https://epiverse-trace.github.io/epiparameterDB/. +#> +#> A BibTeX entry for LaTeX users is +#> +#> @Manual{, +#> title = {epiparameterDB: Database of epidemiological parameters}, +#> author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo}, +#> note = {https://github.com/epiverse-trace/epiparameterDB/, +#> https://epiverse-trace.github.io/epiparameterDB/}, +#> } +``` From d2ea6f68735964f3656943f815a9dabd11e0df17 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:54:25 +0000 Subject: [PATCH 05/48] draft NEWS.md for initial release --- NEWS.md | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index d342220..8c2a2e2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,16 @@ -# 0.1.0 +# epiparameterDB (development version) -* This project now includes a - [`NEWS.md`](https://r-pkgs.org/other-markdown.html#sec-news) file to inform - users about changes and new features. +This is the first minor release of the `{epiparameterDB}` R package. It contains the epidemiological parameter database originally part of the `{epiparameter}` R package. + +## New features + +* The first release contains the parameter database (`parameters.json`) from the `{epiparameter}` package v0.3.0. +* Functionality to read the JSON file (`parameters.json`), render the database as a vignette (`database.Rmd`), and validate the JSON database with a data dictionary (`data_dictionary.json`) using a GitHub actions workflow (`validate-json.yaml`) have been copied from the original `{epiparameter}` implementation. + +## Bug fixes + +* None + +## Deprecated and defunct + +* None From 1753ae07335068f36e0e666ab68d2dc1d2b5c1cd Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:54:45 +0000 Subject: [PATCH 06/48] write _pkgdown.yml for {epiparameterDB} --- _pkgdown.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index bfd72c7..387754d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,12 +1,12 @@ -# FIXME: The url field needs to be updated to contain the URL of the website -# where the package documentation is hosted -# (e.g., https://epiverse-trace.github.io/pkg). -url: ~ +url: https://epiverse-trace.github.io/epiparameterDB template: package: epiversetheme -# It is recommended to add a pkgdown reference index, grouping the different -# function into logical sections (e.g., modules). -# It is also recommended to rely on selector such as `starts_with()` or -# `ends_with()` to create this index as it is a good way to force yourself into -# using a consistent naming convention for your functions. +development: + mode: unreleased + +reference: + - title: Package data + desc: Data stored in the package + contents: + - epiparameterDB From 34e32c8dbf4f817379391cb01602f864c2099c4a Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:55:03 +0000 Subject: [PATCH 07/48] add data-raw script --- data-raw/parameters.R | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 data-raw/parameters.R diff --git a/data-raw/parameters.R b/data-raw/parameters.R new file mode 100644 index 0000000..20f51e4 --- /dev/null +++ b/data-raw/parameters.R @@ -0,0 +1,10 @@ +usethis::use_data(parameters, overwrite = TRUE) + +## code to prepare `parameters` dataset goes here + +epiparameterDB <- epiparameterDB:::.read_db() +usethis::use_data( + epiparameterDB, + overwrite = TRUE, + version = 3 +) From 04e35c7339edd587a2a0fb1c18fe58772ce88d62 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:55:26 +0000 Subject: [PATCH 08/48] add data/epiparameterDB.rda --- data/epiparameterDB.rda | Bin 0 -> 19517 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 data/epiparameterDB.rda diff --git a/data/epiparameterDB.rda b/data/epiparameterDB.rda new file mode 100644 index 0000000000000000000000000000000000000000..6cb6a76d2903d030afcb364b6fd46c7553f5f7fe GIT binary patch literal 19517 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za^)_<6M>ZEACelxq;z}kvQhaBCxCEZ2cp_dg; z7_pv2ftlxhmFYGO=jA#--P$R$4b%1D9ueq040pppAn zOok-#@}5*uJLBGbzQCXN3A-iGlGK7==NfhWwr4c|nLQ1Uy07_K@MN~y44ACP% Zq)0Z}2iwpU5V!yFcO+AV2?4%kO)y!M5lR36 literal 0 HcmV?d00001 From 2fe3e3fea67ae1db040cdbaf992b17f7748591fb Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:55:38 +0000 Subject: [PATCH 09/48] add data documentation --- R/data.R | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 R/data.R diff --git a/R/data.R b/R/data.R new file mode 100644 index 0000000..f713bd7 --- /dev/null +++ b/R/data.R @@ -0,0 +1,9 @@ +#' A list of epidemiological parameters. +#' +#' @format ## `epiparameterDB` +#' A `list` of epidemiological parameters read from `extdata/parameters.json` +#' with `r length(epiparameterDB::epiparameterDB)` database entries. The object +#' is tagged with the class attribute `` to validate the +#' parameter library has been loaded using the `{epiparameterDB}` package. +#' +"epiparameterDB" From 666f81cef180bacf3b01d4364e35ca850ab93195 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:55:56 +0000 Subject: [PATCH 10/48] add .read_db and .is_pkg_installed functions --- R/read.R | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 R/read.R diff --git a/R/read.R b/R/read.R new file mode 100644 index 0000000..8681f48 --- /dev/null +++ b/R/read.R @@ -0,0 +1,45 @@ +#' Reads in parameter library from JSON +#' +#' @description +#' Read epidemiological parameter database from JSON using +#' [jsonlite::read_json()] and returns the list with a `` +#' class attribute to validate it has been read using this function. +#' +#' @return `list`. +#' @keywords internal +.read_db <- function() { + + if (!.is_pkg_installed("jsonlite")) { + stop( + "Cannot use this internal function without {jsonlite} installed", + call. = FALSE + ) + } + + params_json <- jsonlite::read_json( + path = system.file( + "extdata", + "parameters.json", + package = "epiparameter", + mustWork = TRUE + ) + ) + + # tag with class + class(params_json) <- "epiparameterDB" + + return(params_json) +} + +#' Check whether a package is installed +#' +#' @details This functions allows testing for when a suggested package +#' dependency is not installed to check if conditional code can be run. +#' +#' @inheritParams base::requireNamespace +#' +#' @return Invisibly returns a boolean `logical`. +#' @keywords internal +.is_pkg_installed <- function(package) { + requireNamespace(package, quietly = TRUE) +} From fbd64cf75fb87c95bf48ee3030a0291c0e2f66be Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:56:07 +0000 Subject: [PATCH 11/48] add .cite_author function --- R/utils.R | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 R/utils.R diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 0000000..68f523f --- /dev/null +++ b/R/utils.R @@ -0,0 +1,28 @@ +#' Format author names for short citation from epidemiological parameter +#' database +#' +#' @param x A single `list` entry from the list of epidemiological parameter +#' database. +#' +#' @return A `character` string with the short citation. +#' @keywords internal +.cite_author <- function(x) { + aut <- x$citation$author + num_author <- length(aut) + # check if first author is an organisation + is_org_author <- is.null(aut[[1]]$family) + # this covers single author entries + if (is_org_author) { + # organisation name stored in $given + cit <- aut[[1]]$given + } else { + cit <- aut[[1]]$family + } + # append second author or et al for multi-author entries + if (num_author == 2) { + cit <- paste(cit, "&", aut[[2]]$family) + } else if (num_author > 2) { + cit <- paste(cit, "et al.") + } + return(cit) +} From bad9a101732419a68c33cb99d941faf3c338e267 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:56:32 +0000 Subject: [PATCH 12/48] add parameters.json and data_dictionary.json to extdata --- inst/extdata/data_dictionary.json | 457 ++ inst/extdata/parameters.json | 11553 ++++++++++++++++++++++++++++ 2 files changed, 12010 insertions(+) create mode 100644 inst/extdata/data_dictionary.json create mode 100644 inst/extdata/parameters.json diff --git a/inst/extdata/data_dictionary.json b/inst/extdata/data_dictionary.json new file mode 100644 index 0000000..f0a3077 --- /dev/null +++ b/inst/extdata/data_dictionary.json @@ -0,0 +1,457 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "title": "epiparameter data", + "description": "The database of epidemiological distributions for a variety of infectious diseases and pathogens. Last modified 11/05/2023.", + "type": "array", + "items": { + "type": "object", + "properties": { + "disease": { + "description": "The infectious disease specified in the study.", + "examples": ["ebola", "measles"], + "type": "string" + }, + "pathogen": { + "description": "Causative agent of disease specified in study. NA if not specified in study.", + "examples": ["SARS-CoV-2", "monkeypox virus"], + "type": ["string", "null"] + }, + "epi_name": { + "description": "The name of the epidemiological parameter type. Names should be whitespace separated within each string.", + "examples": ["incubation period", "serial interval", "offspring distribution"], + "type": "string", + "enum": ["incubation period", "onset to hospitalisation", "onset to death", "serial interval", "generation time", "offspring distribution", "hospitalisation to death", "hospitalisation to discharge", "notification to death", "notification to discharge", "onset to discharge", "onset to ventilation", "case fatality risk"] + }, + "probability_distribution": { + "description": "An object containing the name of the probability distribution and its porameters if available.", + "type": "object", + "properties": { + "prob_distribution": { + "description": "The name of the probability distribution, following R language distribution naming. A probability distribution can be null in cases when summary statistics are reported by a distribution is not given.", + "examples": ["lnorm", "gamma"], + "type": ["string", "null"], + "enum": ["lnorm", "gamma", "weibull", "nbinom", "geom", "pois", "norm", null] + }, + "parameters": { + "type": "object", + "propertyNames": { + "enum": ["shape", "shape_ci_limits", "shape_ci", "scale", "scale_ci_limits", "scale_ci", "meanlog", "meanlog_ci_limits", "meanlog_ci", "sdlog", "sdlog_ci_limits", "sdlog_ci", "dispersion", "dispersion_ci_limits", "dispersion_ci", "precision", "precision_ci_limits", "precision_ci", "mean", "mean_ci_limits", "mean_ci", "sd", "sd_ci_limits", "sd_ci"] + }, + "properties": { + "shape": { + "description": "The shape parameter of either the gamma or Weibull distribution.", + "examples": [2.0, 4.5], + "type": "number" + }, + "shape_ci_limits": { + "description": "The confidence interval of the distribution's shape parameter, specified by two numbers in an array.", + "examples": [[0.3, 3.2],[0.5, 0.7]], + "type": "array", + "items": { + "type": "number" + } + }, + "shape_ci": { + "description": "The interval of the uncertainty around the shape parameter of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": "number" + }, + "scale": { + "description": "The scale parameter of either the gamma or Weibull distribution.", + "examples": [0.9, 1.1], + "type": "number" + }, + "scale_ci_limits": { + "description": "The confidence interval of the distribution's scale parameter, specified by two numbers in an array.", + "examples": [[0.2, 0.5], [1.1, 1.7]], + "type": "array", + "items": { + "type": "number" + } + }, + "scale_ci": { + "description": "The interval of the uncertainty around the scale parameter of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": "number" + }, + "meanlog": { + "description": "The meanlog parameter of the lognormal distribution.", + "examples": [4.3, 7], + "type": "number" + }, + "meanlog_ci_limits": { + "description": "The confidence interval of the distribution's meanlog parameter, specified by two numbers in an array.", + "examples": [[0.4, 0.9], [1.5, 3.2]], + "type": "array", + "items": { + "type": "number" + } + }, + "meanlog_ci": { + "description": "The interval of the uncertainty around the meanlog parameter of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": "number" + }, + "sdlog": { + "description": "The sdlog parameter of the lognormal distribution.", + "examples": [1.2, 1.4], + "type": "number" + }, + "sdlog_ci_limits": { + "description": "The confidence interval of the distribution's sdlog parameter, specified by two numbers in an array.", + "examples": [[0.3, 0.8], [1.4, 1.45]], + "type": "array", + "items": { + "type": "number" + } + }, + "sdlog_ci": { + "description": "The interval of the uncertainty around the sdlog parameter of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + }, + "dispersion": { + "description": "The dispersion parameter of the distribution. This is often used for negative binomial distributions and is often represented as k. This is distinct from the dispersion for a lognormal distribution, which is considered a summary statistic.", + "examples": [1.2, 1.4], + "type": "number" + }, + "dispersion_ci_limits": { + "description": "The confidence interval of the distribution's dispersion, specified by two numbers in an array.", + "examples": [[0.3, 0.8], [1.4, 1.45]], + "type": ["array", "null"], + "items": { + "type": "number" + } + }, + "dispersion_ci": { + "description": "The interval of the uncertainty around the dispersion of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": "number" + }, + "precision": { + "description": "The precision parameter of a distribution. It is common to parameterise a distribution using the precision parameter in Bayesian inference.", + "examples": [1.2, 1.4], + "type": ["number", "null"] + }, + "precision_ci_limits": { + "description": "The confidence interval of the distribution's precision parameter, specified by two numbers in an array.", + "examples": [[0.3, 0.8], [1.4, 1.45]], + "type": ["array", "null"], + "items": { + "type": "number" + } + }, + "precision_ci": { + "description": "The interval of the uncertainty around the precision parameter, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + }, + "mean": { + "description": "The mean of the distribution. Only applies to normal and negative binomial distributions (checked by schema below), for other probability distributions the mean should be included in the summary statistics.", + "examples": [1.0, 2.5], + "type": ["number", "null"] + }, + "mean_ci_limits": { + "description": "The confidence interval of the distribution's mean, specified by two numbers in an array.", + "examples": [[0.3, 0.8], [1.4, 1.45]], + "type": ["array", "null"], + "items": { + "type": "number" + } + }, + "mean_ci": { + "description": "The interval of the uncertainty around the mean, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + }, + "sd": { + "description": "The standard deviation of the distribution. Only applies to normal distributions (checked by schema below), for other probability distributions the standard deviation should be included in the summary statistics.", + "examples": [1.0, 2.5], + "type": ["number", "null"] + }, + "sd_ci_limits": { + "description": "The confidence interval of the distribution's standard deviation, specified by two numbers in an array.", + "examples": [[0.3, 0.8], [1.4, 1.45]], + "type": ["array", "null"], + "items": { + "type": "number" + } + }, + "sd_ci": { + "description": "The interval of the uncertainty around the standard deviation, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + } + } + } + }, + "required": ["prob_distribution"], + "if": { + "properties": { + "prob_distribution": { "const": "norm" } + } + }, + "then": { + "properties": { + "parameters": { + "type": "object", + "anyOf": [ + { "required": ["mean"] }, + { "required": ["sd"] } + ] + } + } + }, + "else": { + "if": { + "properties": { + "prob_distribution": { "const": "nbinom" } + } + }, + "then": { + "properties": { + "parameters": { + "type": "object", + "anyOf": [ + { "required": ["mean"] }, + { "required": ["dispersion"] } + ] + } + } + }, + "else": { + "properties": { + "parameters": { + "type": "object", + "not": { + "anyOf": [ + { "required": ["mean"] }, + { "required": ["sd"] }, + { "required": ["dispersion"] } + ] + } + } + } + } + } + }, + "summary_statistics": { + "type": "object", + "propertyNames": { + "enum": ["mean", "mean_ci_limits", "mean_ci", "sd", "sd_ci_limits", "sd_ci", "median", "median_ci_limits", "median_ci", "dispersion", "dispersion_ci_limits", "dispersion_ci", "quantile_values", "quantile_names", "lower_range", "upper_range"] + }, + "properties": { + "mean": { + "description": "The mean value (expectation) of the distribution. If the mean is not reported put NA.", + "examples": [5, 3.2], + "type": "number" + }, + "mean_ci_limits": { + "description": "The confidence interval of the distribution mean specified by two numbers in an array.", + "examples": [[3.1, 5.5], [2, 4.2]], + "type": "array", + "items": { + "type": "number" + } + }, + "mean_ci": { + "description": "The interval of the uncertainty around the mean of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + }, + "sd": { + "description": "The standard deviation of the distribution.", + "examples": [2.3, 0.5], + "type": "number" + }, + "sd_ci_limits": { + "description": "The confidence interval of the distribution standard deviation specified by two numbers in an array.", + "examples": [[0.2, 0.9], [0.8, 1.2]], + "type": "array", + "items": { + "type": "number" + } + }, + "sd_ci": { + "description": "The interval of the uncertainty around the standard deviation of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": "number" + }, + "median": { + "description": "The 50th quantile (or median) of the distribution.", + "examples": [1.7, 2.5], + "type": ["number", "null"] + }, + "median_ci_limits": { + "description": "The confidence interval of the distribution median specified by two numbers in an array.", + "examples": [[2.1, 2.2], [4.5, 5.1]], + "type": "array", + "items": { + "type": "number" + } + }, + "median_ci": { + "description": "The interval of the uncertainty around the median of the distribution, for example 95% confidence interval would be 95.", + "examples": [95, 90, 80], + "type": ["number", "null"] + }, + "quantile_values": { + "description": "The values at the quantiles of the distribution.", + "examples": [[2.1, 5.5], [4.3, 9.2]], + "type": "array", + "items": { + "type": "number" + } + }, + "quantile_names": { + "description": "The names of the quantiles of the distribution, for example 50 is the median and 95 is the 95th quantile of the distribution. These names need to correspond to the quantile values. The first element in quantile_values is named by the first element in quantile_names, etc.", + "examples": [["2.5", "97.5"], ["25", "75"]], + "type": "array", + "items": { + "type": "string" + } + }, + "lower_range": { + "description": "The lower bound of the range of the data which is used to infer the parameters of the distribution when they are not specified.", + "examples": [0.2, 0.4], + "type": "number" + }, + "upper_range": { + "description": "The upper bound of the range of the data which is used to infer the parameters of the distribution when they are not specified.", + "examples": [4.5, 6.7], + "type": "number" + } + } + }, + "citation": { + "type": "object", + "properties": { + "author": { + "type": "array", + "items": { + "type": "object", + "properties": { + "given": { + "description": "A character string with the given name(s) of the author. Middle name, initialised or not, should be included in the given name, not the family name. This is combined with the family name field to create the full name. Give all authors of the publication as separate authors. Following R's person class, give teams, institutes and companies in the given name and not in the family name.", + "examples": ["John", "Amy", "WHO Team"], + "type": "string" + }, + "family": { + "description": "A character string with the family name(s) of the author. Middle name, initialised or not, should be included in the given name, not the family name. This is combined with the given name field to create the full name. When organisations or teams are supplied as a given name, the family name is null.", + "examples": ["Smith", "Jones"], + "type": ["string", "null"] + } + }, + "required": ["given", "family"] + } + }, + "title": { + "description": "The title of the article that published the epidemiological parameters.", + "examples": ["Incubation period of COVID-19", "Serial interval of Ebola"], + "type": "string" + }, + "journal": { + "description": "The name of the journal that published the article that published the epidemiological parameters. This can also be a pre-print server, e.g., medRxiv.", + "examples": ["The Lancet", "PLoS One", "medRxiv"], + "type": "string" + }, + "year": { + "description": "The year the paper or report was published.", + "examples": ["2019", "2020"], + "type": "number", + "exclusiveMinimum": 0 + }, + "pmid": { + "description": "A PubMed unique identifier number assigned to papers to give them a unique identifier within PubMed.", + "examples": [18183754, 23749571], + "type": ["number", "null"] + }, + "doi": { + "description": "A Digital Object Identifier (DOI) assigned to papers which are unique to each paper.", + "examples": ["doi:10.1080/02626667.2018.1560449", "https://doi.org/10.1111/hex.12487", "https://dx.doi.org/10.1080/02626667.2018.1560449", "https://doi.org/10.1016/j.jpsychires.2017.11.014"], + "type": "string" + } + }, + "required": ["author", "title", "journal", "year", "doi"] + }, + "metadata": { + "type": "object", + "properties": { + "units": { + "description": "The units of the epidemiological parameter.", + "examples": ["days", "No units", "percentage"], + "type": ["string"] + }, + "sample_size": { + "description": "The sample of the data used to fit the delay distribution. This is usually the number of people with data on a primary and possibly secondary event of interest. In cases where the sample size is not stated NA can be used.", + "examples": [25, 150], + "type": ["number", "null"] + }, + "region": { + "description": "The geographical location the data was collected. This can either be given at sub-national, national, continental. Multiple nested regions can be given and are comma separated. When the region is not specified NA can be given.", + "examples": ["England", "Wuhan, China"], + "type": ["string", "null"] + }, + "transmission_mode": { + "description": "A character string defining the mode of transmission of the infectious agent, specific to the data used in the study. The defines whether a pathogen is vector-borne (i.e. is transmitted between humans through a intermediate vector), is transmitted from human-to-human ( natural_human_to_human) or other. If multiple modes of transmission are recorded then mixed can be given. In cases where no mode of transmission if known or given in the study unknown can be stated.", + "examples": ["vector_borne", "natural_human_to_human", "unknown"], + "type": "string" + }, + "vector": { + "description": "The name of the vector transmitting the vector-borne disease. This can be a common name, or a latin binomial name of a specific vector species (see examples). Both the common name and taxonomic name can be given with one given in parentheses. When a disease is not vector-borne NA should be given.", + "examples": ["mosquito", "Aedes aegypti", "mosquito (Aedes aegypti)", "Aedes aegypti (mosquito)"], + "type": "string" + }, + "extrinsic": { + "description": "A boolean value defining whether the data entry is an extrinsic delay distribution, such as the extrinsic incubation period. This field is required because intrinsic and extrinsic delay distributions are stored as separate entries in the database and can be linked. When the disease is not vector-borne FALSE should be given.", + "examples": [true, false], + "type": "boolean" + }, + "inference_method": { + "description": "The type of inference used to fit the delay distribution to the data. Abbreviations of model fitting techniques can be specified as long as they are non-ambiguous. This field is only used to determine whether the uncertainty intervals possibly specified in the other fields are: confidence intervals (in the case of maximum likelihood), or credible intervals (in the case of bayesian inference). Uncertainty bounds for another types of inference methods, or if the inference method is unstated are assumed to be confidence intervals. When the inference method is unknown or a disease does not have a probability distribution NA can be given.", + "examples": ["bayesian", "maximum likelihood", "mle"], + "type": ["string", "null"], + "enum": ["mle", "bayesian", null] + } + } + }, + "method_assessment": { + "type": "object", + "properties": { + "truncation": { + "description": "The truncation point for the distribution when right-truncation is used to account for the bias in survival data when fitting the distribution.", + "examples": [10, 15.5], + "type": ["number", "null"] + }, + "discretised": { + "description": "A boolean indicating whether the distribution fit to the data was discretised. If discretisation is not mentioned in the paper it is assumed the distribution fit to the data was continuous.", + "examples": [true, false], + "type": "boolean" + }, + "censored": { + "description": "A boolean indicating whether the distribution fit to the data correctly handled censored data. This is where the timing of events is either not known with precision or is known by recorded to a coarse level.", + "examples": [true, false], + "type": ["boolean", "null"] + }, + "right_truncated": { + "description": "A boolean indicating whether the distribution fit to the data correctly handled right-truncation to account for the fact that people in the cohort that experienced a primary event did not experience a secondary event and so shorter delay times are over-represented in the data.", + "examples": [true, false], + "type": ["boolean", "null"] + }, + "phase_bias_adjusted": { + "description": "A boolean indicating whether the distribution fit took into account whether the outbreak was in a stage of growth or decline which can bias the results.", + "examples": [true, false], + "type": ["boolean", "null"] + } + } + }, + "notes": { + "description": "A notes field to add extra information that can be used to inform the user of the data but could not be recorded in one of the previous fields. When no notes are given use NA.", + "examples": ["No additional notes", "Pooled data from many papers was used to fit distribution"], + "type": ["string", "null"] + } + }, + "required": ["disease", "epi_name", "summary_statistics", "citation", "metadata", "method_assessment", "notes"], + "additionalProperties": false + } +} diff --git a/inst/extdata/parameters.json b/inst/extdata/parameters.json new file mode 100644 index 0000000..4f7dd2d --- /dev/null +++ b/inst/extdata/parameters.json @@ -0,0 +1,11553 @@ +[ + { + "disease": "Adenovirus", + "pathogen": "Adenovirus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [4.8, 6.5], + "quantile_names": ["25", "75"], + "median": 5.6, + "median_ci_limits": [4.8, 6.3], + "median_ci": 95, + "dispersion": 1.26, + "dispersion_ci_limits": [1.13, 1.38], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-6" + }, + "metadata": { + "units": "days", + "sample_size": 14, + "region": "USA", + "transmission_mode": "experimental", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Analysis on data from Commission on Acute Respiratory Disease. Experimental transmission of minor respiratory illness to human volunteers by filter-passing agents. I. Demonstration of two types of illness characterized by long and short incubation periods and diff erent clinical features. J Clin Invest 1947; 26: 957–82." + }, + { + "disease": "Human Coronavirus", + "pathogen": "Human_Cov", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [2.9, 3.5], + "quantile_names": ["25", "75"], + "median": 3.2, + "median_ci_limits": [2.8, 3.7], + "median_ci": 95, + "dispersion": 1.15, + "dispersion_ci_limits": [1.07, 1.34], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-7" + }, + "metadata": { + "units": "days", + "sample_size": 13, + "region": "UK", + "transmission_mode": "experimental", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Analysis on data from Bradburne AF, Bynoe ML, Tyrrell DA. Eff ects of a “new” human respiratory virus in volunteers. Br Med J 1967; 3: 767–69." + }, + { + "disease": "SARS", + "pathogen": "SARS-Cov-1", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [1.5, 2.7, 5.9, 10.6], + "quantile_names": ["5", "25", "75", "95"], + "median": 4, + "median_ci_limits": [3.6, 4.4], + "median_ci": 95, + "dispersion": 1.81, + "dispersion_ci_limits": [1.67, 1.95], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-8" + }, + "metadata": { + "units": "days", + "sample_size": 157, + "region": "Mixed", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.7, 1.1, 1.9, 2.8], + "quantile_names": ["5", "25", "75", "95"], + "median": 1.4, + "median_ci_limits": [1.3, 1.5], + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.43, 1.6], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-9" + }, + "metadata": { + "units": "days", + "sample_size": 151, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [1.4, 1.7, 2.2, 2.7], + "quantile_names": ["5", "25", "75", "95"], + "median": 1.9, + "median_ci_limits": [1.8, 2], + "median_ci": 95, + "dispersion": 1.23, + "dispersion_ci_limits": [1.17, 1.29], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-10" + }, + "metadata": { + "units": "days", + "sample_size": 90, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "These estimates for the incubation period of influenza A from Lessler et al. 2009 are different from the estimates from the complete data, as they remove Henle et al. 1945 J Immunol, as it is an outlier in the dataset (n=61). Values found at the bottom Table 3." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-B", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.3, 0.4, 0.7, 1.1], + "quantile_names": ["5", "25", "75", "95"], + "median": 0.6, + "median_ci_limits": [0.5, 0.6], + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.37, 1.64], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-11" + }, + "metadata": { + "units": "days", + "sample_size": 78, + "region": "USA", + "transmission_mode": "experimental", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Measles", + "pathogen": "Measles Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [8.9, 10.9, 14.4, 17.7], + "quantile_names": ["5", "25", "75", "95"], + "median": 12.5, + "median_ci_limits": [11.8, 13.3], + "median_ci": 95, + "dispersion": 1.23, + "dispersion_ci_limits": [1.18, 1.28], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-12" + }, + "metadata": { + "units": "days", + "sample_size": 55, + "region": "Mixed", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Parainfluenza", + "pathogen": "Parainfluenza Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [2.1, 3.2], + "quantile_names": ["25", "75"], + "median": 2.6, + "median_ci_limits": [2.1, 3.1], + "median_ci": 95, + "dispersion": 1.35, + "dispersion_ci_limits": [1.16, 1.55], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-13" + }, + "metadata": { + "units": "days", + "sample_size": 11, + "region": "Mixed", + "transmission_mode": "experimental", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "RSV", + "pathogen": "RSV", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [3.1, 3.8, 5.1, 6.3], + "quantile_names": ["5", "25", "75", "95"], + "median": 4.4, + "median_ci_limits": [3.9, 4.9], + "median_ci": 95, + "dispersion": 1.24, + "dispersion_ci_limits": [1.13, 1.35], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-14" + }, + "metadata": { + "units": "days", + "sample_size": 24, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Rhinovirus", + "pathogen": "Rhinovirus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.8, 1.3, 2.7, 4.5], + "quantile_names": ["5", "25", "75", "95"], + "median": 1.9, + "median_ci_limits": [1.4, 2.4], + "median_ci": 95, + "dispersion": 1.68, + "dispersion_ci_limits": [1.36, 2.01], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Ron", + "family": "Brookmeyer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Kenrad E.", + "family": "Nelson" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + } + ], + "title": "Incubation periods of acute respiratory viral infections: a systematic review", + "journal": "The Lancet Infectious Diseases", + "year": 2009, + "pmid": 19393959, + "doi": "10.1016/S1473-3099(09)70069-15" + }, + "metadata": { + "units": "days", + "sample_size": 28, + "region": "USA", + "transmission_mode": "experimental", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Pooled analysis on several data sets, see Lessler et al. 2009 for references of datasets" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.73, 2.94], + "quantile_names": ["5", "95"], + "median": 1.46, + "median_ci_limits": [1.35, 1.57], + "median_ci": 95, + "dispersion": 1.53, + "dispersion_ci_limits": [1.44, 1.61], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + }, + { + "given": "Ron", + "family": "Brookmeyer" + } + ], + "title": "Estimating incubation period distributions with coarse data", + "journal": "Statistics in Medicine", + "year": 2009, + "pmid": 19598148, + "doi": "10.1002/sim.3659" + }, + "metadata": { + "units": "days", + "sample_size": 151, + "region": "Mixed", + "transmission_mode": "unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data from Lessler et al 2009 using double interval-censored analysis. Not open source" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.73, 2.83], + "quantile_names": ["5", "95"], + "median": 1.43, + "median_ci_limits": [1.33, 1.54], + "median_ci": 95, + "dispersion": 1.51, + "dispersion_ci_limits": [1.43, 1.6], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + }, + { + "given": "Ron", + "family": "Brookmeyer" + } + ], + "title": "Estimating incubation period distributions with coarse data", + "journal": "Statistics in Medicine", + "year": 2009, + "pmid": 19598148, + "doi": "10.1002/sim.3659" + }, + "metadata": { + "units": "days", + "sample_size": 151, + "region": "Mixed", + "transmission_mode": "unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data from Lessler et al 2009 using single interval-censored analysis. Not open source" +}, +{ + "disease": "RSV", + "pathogen": "RSV", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [3.05, 6.39], + "quantile_names": ["5", "95"], + "median": 4.41, + "median_ci_limits": [3.9, 4.92], + "median_ci": 95, + "dispersion": 1.25, + "dispersion_ci_limits": [1.14, 1.36], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + }, + { + "given": "Ron", + "family": "Brookmeyer" + } + ], + "title": "Estimating incubation period distributions with coarse data", + "journal": "Statistics in Medicine", + "year": 2009, + "pmid": 19598148, + "doi": "10.1002/sim.3659" + }, + "metadata": { + "units": "days", + "sample_size": 24, + "region": "Mixed", + "transmission_mode": "unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data from Lessler et al 2009 using double interval-censored analysis. Not open source" +}, +{ + "disease": "RSV", + "pathogen": "RSV", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [3.11, 6.26], + "quantile_names": ["5", "95"], + "median": 4.41, + "median_ci_limits": [3.89, 4.94], + "median_ci": 95, + "dispersion": 1.24, + "dispersion_ci_limits": [1.12, 1.35], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Derek A. T.", + "family": "Cummings" + }, + { + "given": "Ron", + "family": "Brookmeyer" + } + ], + "title": "Estimating incubation period distributions with coarse data", + "journal": "Statistics in Medicine", + "year": 2009, + "pmid": 19598148, + "doi": "10.1002/sim.3659" + }, + "metadata": { + "units": "days", + "sample_size": 24, + "region": "Mixed", + "transmission_mode": "unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data from Lessler et al 2009 using single interval-censored analysis. Not open source" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { + "shape": 3.27, + "scale": 0.51 + } + }, + "summary_statistics": { + "quantile_values": [3.43], + "quantile_names": ["95"], + "median": 1.51, + "median_ci_limits": [1.47, 1.55], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Hiroshi", + "family": "Nishiura" + }, + { + "given": "Hisashi", + "family": "Inaba" + } + ], + "title": "Estimation of the incubation period of influenza A (H1N1-2009) among imported cases: addressing censoring using outbreak data at the origin of importation", + "journal": "Journal of Theoretical Biology", + "year": 2011, + "pmid": 21168422, + "doi": "10.1016/j.jtbi.2010.12.017" + }, + "metadata": { + "units": "days", + "sample_size": 72, + "region": "Japan", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": true + }, + "notes": "Gamma and weibull distributions had equally good fit to the data. This entry is the gamma distribution. Gamma, exponential. Not open source." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { + "shape": 1.74, + "scale": 1.83 + } + }, + "summary_statistics": { + "quantile_values": [3.18], + "quantile_names": ["95"], + "median": 1.43, + "median_ci_limits": [1.21, 1.65], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Hiroshi", + "family": "Nishiura" + }, + { + "given": "Hisashi", + "family": "Inaba" + } + ], + "title": "Estimation of the incubation period of influenza A (H1N1-2009) among imported cases: addressing censoring using outbreak data at the origin of importation", + "journal": "Journal of Theoretical Biology", + "year": 2011, + "pmid": 21168422, + "doi": "10.1016/j.jtbi.2010.12.017" + }, + "metadata": { + "units": "days", + "sample_size": 72, + "region": "Japan", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": true + }, + "notes": "Gamma and weibull distributions had equally good fit to the data. This entry is the weibull distribution. Weibull, exponential" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H7N9", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { } + }, + "summary_statistics": { + "mean": 3.4, + "mean_ci_limits": [3, 3.7], + "mean_ci": 95, + "sd": 1.7, + "quantile_values": [6.5], + "quantile_names": ["95"] + }, + "citation": { + "author": [ + { + "given": "Victor", + "family": "Virlogeux" + }, + { + "given": "Ming", + "family": "Li" + }, + { + "given": "Tim K.", + "family": "Tsang" + }, + { + "given": "Luzhao", + "family": "Feng" + }, + { + "given": "Vicky J.", + "family": "Fang" + }, + { + "given": "Hui", + "family": "Jiang" + }, + { + "given": "Peng", + "family": "Wu" + }, + { + "given": "Jiandong", + "family": "Zheng" + }, + { + "given": "Eric H. Y.", + "family": "Lau" + }, + { + "given": "Yu", + "family": "Cao" + }, + { + "given": "Ying", + "family": "Qin" + }, + { + "given": "Qiaohong", + "family": "Liao" + }, + { + "given": "Hongjie", + "family": "Yu" + }, + { + "given": "Benjamin J.", + "family": "Cowling" + } + ], + "title": "Estimating the Distribution of the Incubation Periods of Human Avian Influenza A(H7N9) Virus Infections", + "journal": "American Journal of Epidemiology", + "year": 2015, + "pmid": 26409239, + "doi": "10.1093/aje/kwv115" + }, + "metadata": { + "units": "days", + "sample_size": 229, + "region": "China", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This study used an original data set and a modified data set. This weibull distribution was fitted to the modified data set and it is recommended to use this one." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H7N9", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 4.5, + "mean_ci_limits": [2.8, 16.2], + "mean_ci": 95, + "sd": 3.3, + "quantile_values": [11], + "quantile_names": ["95"] + }, + "citation": { + "author": [ + { + "given": "Victor", + "family": "Virlogeux" + }, + { + "given": "Ming", + "family": "Li" + }, + { + "given": "Tim K.", + "family": "Tsang" + }, + { + "given": "Luzhao", + "family": "Feng" + }, + { + "given": "Vicky J.", + "family": "Fang" + }, + { + "given": "Hui", + "family": "Jiang" + }, + { + "given": "Peng", + "family": "Wu" + }, + { + "given": "Jiandong", + "family": "Zheng" + }, + { + "given": "Eric H. Y.", + "family": "Lau" + }, + { + "given": "Yu", + "family": "Cao" + }, + { + "given": "Ying", + "family": "Qin" + }, + { + "given": "Qiaohong", + "family": "Liao" + }, + { + "given": "Hongjie", + "family": "Yu" + }, + { + "given": "Benjamin J.", + "family": "Cowling" + } + ], + "title": "Estimating the Distribution of the Incubation Periods of Human Avian Influenza A(H7N9) Virus Infections", + "journal": "American Journal of Epidemiology", + "year": 2015, + "pmid": 26409239, + "doi": "10.1093/aje/kwv115" + }, + "metadata": { + "units": "days", + "sample_size": 229, + "region": "China", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This study used an original data set and a modified data set. This gamma distribution was fitted to the original data set and it is recommended to use the weibull distribution that was fitted to the modified data set." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H7N9", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { } + }, + "summary_statistics": { + "mean": 3.5, + "mean_ci_limits": [3.2, 3.8], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Victor", + "family": "Virlogeux" + }, + { + "given": "Juan", + "family": "Yang" + }, + { + "given": "Vicky J.", + "family": "Fang" + }, + { + "given": "Luzhao", + "family": "Feng" + }, + { + "given": "Tim K.", + "family": "Tsang" + }, + { + "given": "Hui", + "family": "Jiang" + }, + { + "given": "Peng", + "family": "Wu" + }, + { + "given": "Jiandong", + "family": "Zheng" + }, + { + "given": "Eric H. Y.", + "family": "Lau" + }, + { + "given": "Ying", + "family": "Qin" + }, + { + "given": "Zhibin", + "family": "Peng" + }, + { + "given": "J. S. Malik", + "family": "Peiris" + }, + { + "given": "Hongjie", + "family": "Yu" + }, + { + "given": "Benjamin J.", + "family": "Cowling" + } + ], + "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period", + "journal": "PLoS One", + "year": 2016, + "pmid": 26885816, + "doi": "10.1371/journal.pone.0148506" + }, + "metadata": { + "units": "days", + "sample_size": 395, + "region": "China", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the complete unpartitioned data." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H7N9", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { + "shape": 2.3, + "shape_ci_limits": [1.8, 2.89], + "shape_ci": 95, + "scale": 4.21, + "scale_ci_limits": [3.62, 4.85], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 3.7, + "mean_ci_limits": [3.4, 4.1], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Victor", + "family": "Virlogeux" + }, + { + "given": "Juan", + "family": "Yang" + }, + { + "given": "Vicky J.", + "family": "Fang" + }, + { + "given": "Luzhao", + "family": "Feng" + }, + { + "given": "Tim K.", + "family": "Tsang" + }, + { + "given": "Hui", + "family": "Jiang" + }, + { + "given": "Peng", + "family": "Wu" + }, + { + "given": "Jiandong", + "family": "Zheng" + }, + { + "given": "Eric H. Y.", + "family": "Lau" + }, + { + "given": "Ying", + "family": "Qin" + }, + { + "given": "Zhibin", + "family": "Peng" + }, + { + "given": "J. S. Malik", + "family": "Peiris" + }, + { + "given": "Hongjie", + "family": "Yu" + }, + { + "given": "Benjamin J.", + "family": "Cowling" + } + ], + "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period", + "journal": "PLoS One", + "year": 2016, + "pmid": 26885816, + "doi": "10.1371/journal.pone.0148506" + }, + "metadata": { + "units": "days", + "sample_size": 173, + "region": "China", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the fatal outcome data." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H7N9", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { + "shape": 2.03, + "shape_ci_limits": [1.62, 2.52], + "shape_ci": 95, + "scale": 3.74, + "scale_ci_limits": [3.2, 4.36], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 3.3, + "mean_ci_limits": [2.9, 3.6], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Victor", + "family": "Virlogeux" + }, + { + "given": "Juan", + "family": "Yang" + }, + { + "given":"Vicky J.", + "family": "Fang" + }, + { + "given": "Luzhao", + "family": "Feng" + }, + { + "given": "Tim K.", + "family": "Tsang" + }, + { + "given": "Hui", + "family": "Jiang" + }, + { + "given": "Peng", + "family": "Wu" + }, + { + "given": "Jiandong", + "family": "Zheng" + }, + { + "given": "Eric H. Y.", + "family": "Lau" + }, + { + "given": "Ying", + "family": "Qin" + }, + { + "given": "Zhibin", + "family": "Peng" + }, + { + "given": "J. S. Malik", + "family": "Peiris" + }, + { + "given": "Hongjie", + "family": "Yu" + }, + { + "given": "Benjamin J.", + "family": "Cowling" + } + ], + "title": "Association between the Severity of Influenza A(H7N9) Virus Infections and Length of the Incubation Period", + "journal": "PLoS One", + "year": 2016, + "pmid": 26885816, + "doi": "10.1371/journal.pone.0148506" + }, + "metadata": { + "units": "days", + "sample_size": 222, + "region": "China", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This study fit the weibull distribution to estimate the parameters for the complete data set, those who had a fatal outcome and those with a non-fatal outcome. This is the distribution fit to the non-fatal outcome data." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 4.3, + "mean_ci_limits": [2.6, 6.6], + "mean_ci": 95, + "median": 4 + }, + "citation": { + "author": [ + { + "given": "Ashleigh R.", + "family": "Tuite" + }, + { + "given": "Amy L.", + "family": "Greer" + }, + { + "given": "Michael", + "family": "Whelan" + }, + { + "given": "Anne-Luise", + "family": "Winter" + }, + { + "given": "Brenda", + "family": "Lee" + }, + { + "given": "Ping", + "family": "Yan" + }, + { + "given": "Jianhong", + "family": "Wu" + }, + { + "given": "Seyed", + "family": "Moghadas" + }, + { + "given": "David", + "family": "Buckeridge" + }, + { + "given": "Babak", + "family": "Pourbohloul" + }, + { + "given": "David N.", + "family": "Fisman" + } + ], + "title": "Estimated epidemiologic parameters and morbidity associated with pandemic H1N1 influenza", + "journal": "Canadian Medical Association Journal", + "year": 2010, + "pmid": 19959592, + "doi": "10.1503/cmaj.091807" + }, + "metadata": { + "units": "days", + "sample_size": 316, + "region": "Canada", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The mid-point of the exposure time was used to approximate an exact exposure time instead of interval-censoring. This can lead to a possible bias (overestimation) in incubation times. It was ambiguously reported whether the mean is the mean of the distribution or the meanlog parameter of the lognormal distribution." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1Pdm", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 2.05, + "sd": 0.49 + }, + "citation": { + "author": [ + { + "given": "Azra", + "family": "Ghani" + }, + { + "given": "Marc", + "family": "Baguelin" + }, + { + "given": "Jamie", + "family": "Griffin" + }, + { + "given": "Stefan", + "family": "Flasche" + }, + { + "given": "Albert Jan", + "family": "van Hoek" + }, + { + "given": "Simon", + "family": "Cauchemez" + }, + { + "given": "Christl", + "family": "Donnelly" + }, + { + "given": "Chris", + "family": "Robertson" + }, + { + "given": "Michael", + "family": "White" + }, + { + "given": "James", + "family": "Truscott" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Peter", + "family": "White" + }, + { + "given": "Steve", + "family": "Leach" + }, + { + "given": "Ian", + "family": "Hall" + }, + { + "given": "Helen", + "family": "Jenkins" + }, + { + "given": "Neil", + "family": "Ferguson" + }, + { + "given": "Ben", + "family": "Cooper" + } + ], + "title": "The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom", + "journal": "PLoS Currents", + "year": 2009, + "pmid": 20029668, + "doi": "10.1371/currents.RRN1130" + }, + "metadata": { + "units": "days", + "sample_size": 16, + "region": "UK", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1Pdm", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 2.51, + "sd": 1.55 + }, + "citation": { + "author": [ + { + "given": "Azra", + "family": "Ghani" + }, + { + "given": "Marc", + "family": "Baguelin" + }, + { + "given": "Jamie", + "family": "Griffin" + }, + { + "given": "Stefan", + "family": "Flasche" + }, + { + "given": "Albert Jan", + "family": "van Hoek" + }, + { + "given": "Simon", + "family": "Cauchemez" + }, + { + "given": "Christl", + "family": "Donnelly" + }, + { + "given": "Chris", + "family": "Robertson" + }, + { + "given": "Michael", + "family": "White" + }, + { + "given": "James", + "family": "Truscott" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Peter", + "family": "White" + }, + { + "given": "Steve", + "family": "Leach" + }, + { + "given": "Ian", + "family": "Hall" + }, + { + "given": "Helen", + "family": "Jenkins" + }, + { + "given": "Neil", + "family": "Ferguson" + }, + { + "given": "Ben", + "family": "Cooper" + } + ], + "title": "The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom", + "journal": "PLoS Currents", + "year": 2009, + "pmid": 20029668, + "doi": "10.1371/currents.RRN1130" + }, + "metadata": { + "units": "days", + "sample_size": 58, + "region": "UK", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [0.9, 2.2], + "quantile_names": ["5", "95"], + "median": 1.4, + "median_ci_limits": [1, 1.8], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team", + "family": null + } + ], + "title": "Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School", + "journal": "The New England Journal of Medicine", + "year": 2009, + "pmid": 20042754, + "doi": "10.1056/NEJMoa0906089" + }, + "metadata": { + "units": "days", + "sample_size": 124, + "region": "New York, USA", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes." +}, +{ + "disease": "Influenza", + "pathogen": "Influenza-A-H1N1", + "epi_name": "generation time", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { + "shape": 2.36, + "scale": 3.18 + } + }, + "summary_statistics": { + "quantile_values": [0.9, 5.1], + "quantile_names": ["5", "95"], + "median": 2.7, + "median_ci_limits": [2, 3.5], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Nicholas G.", + "family": "Reich" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team", + "family": null + } + ], + "title": "Outbreak of 2009 Pandemic Influenza A (H1N1) at a New York City School", + "journal": "The New England Journal of Medicine", + "year": 2009, + "pmid": 20042754, + "doi": "10.1056/NEJMoa0906089" + }, + "metadata": { + "units": "days", + "sample_size": 16, + "region": "New York, USA", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The parameters of the weibull are stated without reporting the uncertainty around them. The parameter estimates and sample size is reported in the supplementary appendix." +}, +{ + "disease": "Marburg Virus Disease", + "pathogen": "Marburg Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "lower_range": 2, + "upper_range": 26 + }, + "citation": { + "author": [ + { + "given": "Boris I.", + "family": "Pavlin" + } + ], + "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease", + "journal": "BMC Research Notes", + "year": 2014, + "pmid": 25495697, + "doi": "10.1186/1756-0500-7-906" + }, + "metadata": { + "units": "days", + "sample_size": 76, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This paper did not fit a distribution to the incubation period data and only reported a lower and upper range of the data. This is present in the database as there are no other studies that report the incubation period for Marburg virus. There is another incubation period reported from the same paper for a subset of the data which report the median and interquartile range but again do not fit a distribution to the data." +}, +{ + "disease": "Marburg Virus Disease", + "pathogen": "Marburg Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 7, + "lower_range": 2, + "upper_range": 13 + }, + "citation": { + "author": [ + { + "given": "Boris I.", + "family": "Pavlin" + } + ], + "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease", + "journal": "BMC Research Notes", + "year": 2014, + "pmid": 25495697, + "doi": "10.1186/1756-0500-7-906" + }, + "metadata": { + "units": "days", + "sample_size": 18, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This paper did not fit a distribution to the incubation period data and only reported a median and range for a subset of the data. This is present in the database as there are no other studies that report the incubation period for Marburg virus. This paper also reports the maximum and minimum for the complete data set." +}, +{ + "disease": "Marburg Virus Disease", + "pathogen": "Marburg Virus", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [8, 15], + "quantile_names": ["25", "75"], + "median": 11 + }, + "citation": { + "author": [ + { + "given": "Boris I.", + "family": "Pavlin" + } + ], + "title": "Calculation of incubation period and serial interval from multiple outbreaks of Marburg virus disease", + "journal": "BMC Research Notes", + "year": 2014, + "pmid": 25495697, + "doi": "10.1186/1756-0500-7-906" + }, + "metadata": { + "units": "days", + "sample_size": 38, + "region": "Mixed", + "transmission_mode": "mixed", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This paper did not fit a distribution to the serial interval data and only reported a median and interquartile range. This is present in the database as there are no other studies that report the serial interval for Marburg virus." +}, +{ + "disease": "Marburg Virus Disease", + "pathogen": "Marburg Virus", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 8, + "lower_range": 2, + "upper_range": 16 + }, + "citation": { + "author": [ + { + "given": "Robert", + "family": "Colebunders" + }, + { + "given": "Antoine", + "family": "Tshomba" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Daniel G.", + "family": "Bausch" + }, + { + "given": "Pat", + "family": "Campbell" + }, + { + "given": "Modeste", + "family": "Libande" + }, + { + "given": "Patricia", + "family": "Pirard" + }, + { + "given": "Florimond", + "family": "Tshioko" + }, + { + "given": "Simon", + "family": "Mardel" + }, + { + "given": "Sabue", + "family": "Mulangu" + }, + { + "given": "Hilde", + "family": "Sleurs" + }, + { + "given": "Pierre E.", + "family": "Rollin" + }, + { + "given": "Jean-Jacques", + "family": "Muyembe-Tamfum" + }, + { + "given": "Benjamin", + "family": "Jeffs" + }, + { + "given": "Matthias", + "family": "Borchert" + }, + { + "given": "International Scientific and Technical Committee 'DRC Watsa/Durba 1999 Marburg Outbreak Investigation Group'", + "family": null + } + ], + "title": "Marburg hemorrhagic fever in Durba and Watsa, Democratic Republic of the Congo: clinical documentation, features of illness, and treatment", + "journal": "The Journal of Infectious Diseases", + "year": 2007, + "pmid": 17940943, + "doi": "10.1086/520543" + }, + "metadata": { + "units": "days", + "sample_size": 77, + "region": "DR Congo", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This paper reports the median and range of the symptom onset to death delay but did not fit a parametric distribution to the data. This is included in the database as it is the only reported symptom onset to death reported in the literature" +}, +{ + "disease": "Marburg Virus Disease", + "pathogen": "Marburg Virus", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 9, + "mean_ci_limits": [8.2, 10], + "mean_ci": 95, + "sd": 5.4, + "sd_ci_limits": [3.9, 8.6], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Marco", + "family": "Ajelli" + }, + { + "given": "Stefano", + "family": "Merler" + } + ], + "title": "Transmission Potential and Design of Adequate Control Measures for Marburg Hemorrhagic Fever", + "journal": "PLoS One", + "year": 2012, + "pmid": 23251407, + "doi": "10.1371/journal.pone.0050948" + }, + "metadata": { + "units": "days", + "sample_size": 374, + "region": "Angola", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The generation time is estimated from non-human viral load data. This paper reports the generation time but assumes the generation time and serial interval are the same it is classified as serial interval here based on Van Kerkove et al. 2015 <10.1038/sdata.2015.19>. The sample size is take from Van Kerkove et al. 2015." +}, +{ + "disease": "SARS", + "pathogen": "SARS-Cov-1", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 1.63, + "mean_ci_limits": [0.54, 2.65], + "mean_ci": 90, + "dispersion": 0.16, + "dispersion_ci_limits": [0.11, 0.64], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 57, + "region": "Singapore", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Parameter estimates are retrieved from the supplementary tables." +}, +{ + "disease": "SARS", + "pathogen": "SARS-Cov-1", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 0.94, + "mean_ci_limits": [0.27, 1.51], + "mean_ci": 90, + "dispersion": 0.17, + "dispersion_ci_limits": [0.1, 0.64], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 33, + "region": "Beijing", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Smallpox", + "pathogen": "Smallpox-Variola-Major", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 3.19, + "mean_ci_limits": [1.66, 4.62], + "mean_ci": 90, + "dispersion": 0.37, + "dispersion_ci_limits": [0.26, 0.69], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 32, + "region": "Europe", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Smallpox", + "pathogen": "Smallpox-Variola-Major", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 0.8, + "mean_ci_limits": [0.32, 1.2], + "mean_ci": 90, + "dispersion": 0.32, + "dispersion_ci_limits": [0.16, 1.76], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 25, + "region": "Benin", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Smallpox", + "pathogen": "Smallpox-Variola-Minor", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 1.6, + "mean_ci_limits": [0.88, 2.16], + "mean_ci": 90, + "dispersion": 0.65, + "dispersion_ci_limits": [0.34, 2.32], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 25, + "region": "England", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Smallpox", + "pathogen": "Smallpox-Variola-Minor", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 1.49, + "dispersion": 0.72, + "dispersion_ci_limits": [0.44, 2.05], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 47, + "region": "Pakistan", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Estimate of R0 taken from original study and CI of dispersion calculated mean of Z and proportion of zeros known " +}, +{ + "disease": "Mpox", + "pathogen": "Monkeypox Virus", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 0.32, + "mean_ci_limits": [0.22, 0.40], + "mean_ci": 90, + "dispersion": 0.58, + "dispersion_ci_limits": [0.32, 3.57], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 147, + "region": "Zaire", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "In the model comparison the geometric model was the better fit to the monkeypox data, however, only the parameters of the negative binomial were reported as so are stored in the database." +}, +{ + "disease": "Pneumonic Plague", + "pathogen": "Yersinia Pestis", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 1.32, + "mean_ci_limits": [1.01, 1.61], + "mean_ci": 90, + "dispersion": 1.37, + "dispersion_ci_limits": [0.88, 3.53], + "dispersion_ci": 90 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 74, + "region": "Mixed", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "In the model comparison the geometric model was the better fit to the Pneumonic Plague data, however, only the parameters of the negative binomial were reported as so are stored in the database." +}, +{ + "disease": "Hantavirus Pulmonary Syndrome", + "pathogen": "Hantavirus (Andes Virus)", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 0.7, + "mean_ci_limits": [0.20, 1.05], + "mean_ci": 90, + "dispersion": 1.66 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 20, + "region": "Argentina", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "In the model comparison the geometric model was the better fit to the Hantavirus data, however, only the parameters of the negative binomial were reported as so are stored in the database. The uncertainty for the dispersion parameter is currently not stored in the database as the upper bound for the confidence interval is infinite, and currently infinite values are not supported." +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "offspring distribution", + "probability_distribution": { + "prob_distribution": "nbinom", + "parameters": { + "mean": 1.5, + "mean_ci_limits": [0.85, 2.08], + "mean_ci": 90, + "dispersion": 5.10 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "J. O.", + "family": "Lloyd-Smith" + }, + { + "given": "S. J.", + "family": "Schreiber" + }, + { + "given": "P. E.", + "family": "Kopp" + }, + { + "given": "W. M.", + "family": "Getz" + } + ], + "title": "Superspreading and the effect of individual variation on disease emergence", + "journal": "Nature", + "year": 2005, + "pmid": 16292310, + "doi": "10.1038/nature04153" + }, + "metadata": { + "units": "No units", + "sample_size": 13, + "region": "Uganda", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "In the model comparison the poisson model was the better fit to the Ebola data, however, only the parameters of the negative binomial were reported as so are stored in the database. The uncertainty for the dispersion parameter is currently not stored in the database as the upper bound for the confidence interval is infinite, and currently infinite values are not supported." +}, +{ + "disease": "Dengue", + "pathogen": "Dengue Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 15, + "mean_ci_limits": [10, 20], + "mean_ci": 95, + "quantile_values": [5, 33], + "quantile_names": ["2.5", "97.5"] + }, + "citation": { + "author": [ + { + "given": "Miranda", + "family": "Chan" + }, + { + "given": "Michael A.", + "family": "Johansson" + } + ], + "title": "The Incubation Periods of Dengue Viruses", + "journal": "PLoS One", + "year": 2012, + "pmid": 23226436, + "doi": "10.1371/journal.pone.0050972" + }, + "metadata": { + "units": "days", + "sample_size": 146, + "region": "Mixed", + "transmission_mode": "vector_borne", + "vector": "Aedes aegypti and Aedes albopictus", + "extrinsic": true, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Extrinsic incubation period for data at 25 degrees celcius" +}, +{ + "disease": "Dengue", + "pathogen": "Dengue Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "precision": 4.9, + "precision_ci_limits": [2.8, 7.5], + "precision_ci": 95 + } + }, + "summary_statistics": { + "mean": 6.5, + "mean_ci_limits": [4.8, 8.8], + "mean_ci": 95, + "quantile_values": [2.4, 15], + "quantile_names": ["2.5" ,"97.5"] + }, + "citation": { + "author": [ + { + "given": "Miranda", + "family": "Chan" + }, + { + "given": "Michael A.", + "family": "Johansson" + } + ], + "title": "The Incubation Periods of Dengue Viruses", + "journal": "PLoS One", + "year": 2012, + "pmid": 23226436, + "doi": "10.1371/journal.pone.0050972" + }, + "metadata": { + "units": "days", + "sample_size": 146, + "region": "Mixed", + "transmission_mode": "vector_borne", + "vector": "Aedes aegypti and Aedes albopictus", + "extrinsic": true, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Extrinsic incubation period for data at 30 degrees celcius" +}, +{ + "disease": "Dengue", + "pathogen": "Dengue Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "meanlog": 1.75, + "sdlog": 0.27, + "precision": 13.7, + "precision_ci_limits": [10.9, 16.9], + "precision_ci": 95 + } + }, + "summary_statistics": { + "mean": 5.97, + "mean_ci_limits": [5.5, 6.4], + "mean_ci": 95, + "sd": 1.64, + "quantile_values": [3.4, 10], + "quantile_names": ["2.5", "97.5"] + }, + "citation": { + "author": [ + { + "given": "Miranda", + "family": "Chan" + }, + { + "given": "Michael A.", + "family": "Johansson" + } + ], + "title": "The Incubation Periods of Dengue Viruses", + "journal": "PLoS One", + "year": 2012, + "pmid": 23226436, + "doi": "10.1371/journal.pone.0050972" + }, + "metadata": { + "units": "days", + "sample_size": 153, + "region": "Mixed", + "transmission_mode": "vector_borne", + "vector": "Aedes aegypti and Aedes albopictus", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Standard deviation, meanlog and sdlog is taken from Siraj et al. 2017 <10.1371/journal.pntd.0005797>" +}, +{ + "disease": "Zika Virus Disease", + "pathogen": "Zika Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [3.2, 4.6, 7.6, 11.2], + "quantile_names": ["5" ,"25", "75", "95"], + "median": 5.9, + "median_ci_limits": [4.4, 7.6], + "median_ci": 95, + "dispersion": 1.5, + "dispersion_ci_limits": [1.2, 1.9], + "dispersion_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Justin", + "family": "Lessler" + }, + { + "given": "Cassandra T.", + "family": "Ott" + }, + { + "given": "Andrea C.", + "family": "Carcelen" + }, + { + "given": "Jacob M.", + "family": "Konikoff" + }, + { + "given": "Joe", + "family": "Williamson" + }, + { + "given": "Qifang", + "family": "Bi" + }, + { + "given": "Lauren M.", + "family": "Kucirka" + }, + { + "given": "Derek A. 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This is a subset of data containing only mosquito-transmitted infections" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 9, + "mean_ci_limits": [6.6, 10.9], + "mean_ci": 95, + "quantile_values": [3.6, 4.2, 17.3, 19.9], + "quantile_names": ["2.5", "5", "95", "97.5"], + "median": 8.5, + "median_ci_limits": [6.6, 10.9], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Fuminari", + "family": "Miura" + }, + { + "given": "Catharina E.", + "family": "van Ewijk" + }, + { + "given": "Jantien A.", + "family": "Backer" + }, + { + "given": "Maria", + "family": "Xiridou" + }, + { + "given": "Eelco", + "family": "Franz" + }, + { + "given": "Eline", + "family": "Op de Coul" + }, + { + "given": "Diederik", + "family": "Brandwagt" + }, + { + "given": "Brigitte", + "family": "van Cleef" + }, + { + "given": "Gini", + "family": "van Rijckevorsel" + }, + { + "given": "Corien", + "family": "Swaan" + }, + { + "given": "Susan", + "family": "van den Hof" + }, + { + "given": "Jacco", + "family": "Wallinga" + } + ], + "title": "Estimated incubation period for monkeypox cases confirmed in the Netherlands, May 2022", + "journal": "Eurosurveillance", + "year": 2022, + "pmid": 35713026, + "doi": "10.2807/1560-7917.ES.2022.27.24.2200448" + }, + "metadata": { + "units": "days", + "sample_size": 18, + "region": "Netherlands", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 7.6, + "mean_ci_limits": [6.2, 9.7], + "mean_ci": 95, + "sd": 1.8, + "sd_ci_limits": [1.6, 2.2], + "sd_ci": 95, + "quantile_values": [17.1], + "quantile_names": ["95"], + "median": 6.4, + "median_ci_limits": [5.1, 7.9], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Kelly", + "family": "Charniga" + }, + { + "given": "Nina B.", + "family": "Masters" + }, + { + "given": "Rachel B.", + "family": "Slayton" + }, + { + "given": "Lucas", + "family": "Gosdin" + }, + { + "given": "Faisal S.", + "family": "Minhaj" + }, + { + "given": "David", + "family": "Philpott" + }, + { + "given": "Dallas", + "family": "Smith" + }, + { + "given": "Shannon", + "family": "Gearhart" + }, + { + "given": "Francisco", + "family": "Alvarado-Ramy" + }, + { + "given": "Clive", + "family": "Brown" + }, + { + "given": "Michelle A.", + "family": "Waltenburg" + }, + { + "given": "Christine M.", + "family": "Hughes" + }, + { + "given": "Yoshinori", + "family": "Nakazawa" + } + ], + "title": "Estimating the incubation period of monkeypox virus during the 2022 multi-national outbreak", + "journal": "medRxiv", + "year": 2022, + "pmid": null, + "doi": "10.1101/2022.06.22.22276713" + }, + "metadata": { + "units": "days", + "sample_size": 22, + "region": "USA", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Uses the methods described by Lessler (10.2471/BLT.16.174540) and Reich (10.1002/sim.3659). Estimated from time from exposure to first symptom onset" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { + "shape": 2.42, + "shape_ci_limits": [1.26, 3.62], + "shape_ci": 95, + "scale": 3.75 , + "scale_ci_limits": [2.17, 7.13], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 9.1, + "mean_ci_limits": [6.5, 10.9], + "mean_ci": 95, + "quantile_values": [2, 20], + "quantile_names": ["5", "95"] + }, + "citation": { + "author": [ + { + "given": "Giorgio", + "family": "Guzzetta" + }, + { + "given": "Alessia", + "family": "Mammone" + }, + { + "given": "Federica", + "family": "Ferraro" + }, + { + "given": "Anna", + "family": "Caraglia" + }, + { + "given": "Alessia", + "family": "Rapiti" + }, + { + "given": "Valentina", + "family": "Marziano" + }, + { + "given": "Piero", + "family": "Poletti" + }, + { + "given": "Danilo", + "family": "Cereda" + }, + { + "given": "Francesco", + "family": "Vairo" + }, + { + "given": "Giovanna", + "family": "Mattei" + }, + { + "given": "Francesco", + "family": "Maraglino" + }, + { + "given": "Giovanni", + "family": "Rezza" + }, + { + "given": "Stefano", + "family": "Merler" + } + ], + "title": "Early Estimates of Monkeypox Incubation Period, Generation Time, and Reproduction Number, Italy, May-June 2022", + "journal": "Emerging Infectious Diseases", + "year": 2022, + "pmid": 35994726, + "doi": "10.3201/eid2810.221126" + }, + "metadata": { + "units": "days", + "sample_size": 30, + "region": "Italy", + "transmission_mode": "natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "meanlog": 1.8, + "meanlog_ci_limits": [1.6, 2.1], + "meanlog_ci": 95, + "sdlog": 0.6, + "sdlog_ci_limits": [0.4, 0.8], + "sdlog_ci": 95 + } + }, + "summary_statistics": { + "mean": 7.5, + "mean_ci_limits": [6, 9.8], + "mean_ci": 95, + "sd": 4.9, + "sd_ci_limits": [3.2, 8.8], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Zachary J.", + "family": "Madewell" + }, + { + "given": "Kelly", + "family": "Charniga" + }, + { + "given": "Nina B.", + "family": "Masters" + }, + { + "given": "Jason", + "family": "Asher" + }, + { + "given": "Lily", + "family": "Fahrenwald" + }, + { + "given": "William", + "family": "Still" + }, + { + "given": "Judy", + "family": "Chen" + }, + { + "given": "Naama", + "family": "Kipperman" + }, + { + "given": "David", + "family": "Bui" + }, + { + "given": "Meghan", + "family": "Shea" + }, + { + "given": "Lori", + "family": "Saathoff-Huber" + }, + { + "given": "Shannon", + "family": "Johnson" + }, + { + "given": "Khalil", + "family": "Harbi" + }, + { + "given": "Abby L.", + "family": "Berns" + }, + { + "given": "Taidy", + "family": "Perez" + }, + { + "given": "Emily", + "family": "Gateley" + }, + { + "given": "Ian H.", + "family": "Spicknall" + }, + { + "given": "Yoshinori", + "family": "Nakazawa" + }, + { + "given": "Thomas L.", + "family": "Gift" + }, + { + "given": "2022 Monkeypox Outbreak Response Team", + "family": null + } + ], + "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2022", + "journal": "medRxiv", + "year": 2022, + "pmid": null, + "doi": "10.1101/2022.10.26.22281516" + }, + "metadata": { + "units": "days", + "sample_size": 35, + "region": "USA", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Meanlog, sdlog, and fitted distribution from supplementary material. Uses cases from Charniga 2022 + extra cases. Incubation period as exposure to rash onset." +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "meanlog": 1.5, + "meanlog_ci_limits": [1.2, 1.8], + "meanlog_ci": 95, + "sdlog": 0.7, + "sdlog_ci_limits": [0.5, 1], + "sdlog_ci": 95 + } + }, + "summary_statistics": { + "mean": 5.6, + "mean_ci_limits": [4.3, 7.8], + "mean_ci": 95, + "sd": 4.4, + "sd_ci_limits": [2.8, 8.7], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Zachary J.", + "family": "Madewell" + }, + { + "given": "Kelly", + "family": "Charniga" + }, + { + "given": "Nina B.", + "family": "Masters" + }, + { + "given": "Jason", + "family": "Asher" + }, + { + "given": "Lily", + "family": "Fahrenwald" + }, + { + "given": "William", + "family": "Still" + }, + { + "given": "Judy", + "family": "Chen" + }, + { + "given": "Naama", + "family": "Kipperman" + }, + { + "given": "David", + "family": "Bui" + }, + { + "given": "Meghan", + "family": "Shea" + }, + { + "given": "Lori", + "family": "Saathoff-Huber" + }, + { + "given": "Shannon", + "family": "Johnson" + }, + { + "given": "Khalil", + "family": "Harbi" + }, + { + "given": "Abby L.", + "family": "Berns" + }, + { + "given": "Taidy", + "family": "Perez" + }, + { + "given": "Emily", + "family": "Gateley" + }, + { + "given": "Ian H.", + "family": "Spicknall" + }, + { + "given": "Yoshinori", + "family": "Nakazawa" + }, + { + "given": "Thomas L.", + "family": "Gift" + }, + { + "given": "2022 Monkeypox Outbreak Response Team", + "family": null + } + ], + "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2023", + "journal": "medRxiv", + "year": 2022, + "pmid": null, + "doi": "10.1101/2022.10.26.22281516" + }, + "metadata": { + "units": "days", + "sample_size": 36, + "region": "USA", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Meanlog, sdlog, and fitted distribution from supplementary material. Uses cases from Charniga 2022 + extra cases. Incubation period as exposure to symptom onset." +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { + "shape": 2.9, + "shape_ci_limits": [2, 4.1], + "shape_ci": 95, + "scale": 2.9, + "scale_ci_limits": [2, 4.4], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 8.5, + "mean_ci_limits": [7.3, 9.9], + "mean_ci": 95, + "sd": 5, + "sd_ci_limits": [4, 6.4], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Zachary J.", + "family": "Madewell" + }, + { + "given": "Kelly", + "family": "Charniga" + }, + { + "given": "Nina B.", + "family": "Masters" + }, + { + "given": "Jason", + "family": "Asher" + }, + { + "given": "Lily", + "family": "Fahrenwald" + }, + { + "given": "William", + "family": "Still" + }, + { + "given": "Judy", + "family": "Chen" + }, + { + "given": "Naama", + "family": "Kipperman" + }, + { + "given": "David", + "family": "Bui" + }, + { + "given": "Meghan", + "family": "Shea" + }, + { + "given": "Lori", + "family": "Saathoff-Huber" + }, + { + "given": "Shannon", + "family": "Johnson" + }, + { + "given": "Khalil", + "family": "Harbi" + }, + { + "given": "Abby L.", + "family": "Berns" + }, + { + "given": "Taidy", + "family": "Perez" + }, + { + "given": "Emily", + "family": "Gateley" + }, + { + "given": "Ian H.", + "family": "Spicknall" + }, + { + "given": "Yoshinori", + "family": "Nakazawa" + }, + { + "given": "Thomas L.", + "family": "Gift" + }, + { + "given": "2022 Monkeypox Outbreak Response Team", + "family": null + } + ], + "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2024", + "journal": "medRxiv", + "year": 2022, + "pmid": null, + "doi": "10.1101/2022.10.26.22281516" + }, + "metadata": { + "units": "days", + "sample_size": 57, + "region": "USA", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Shape and scale from supp. material. Serial interval as exposure to symptom onset" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { + "shape": 2.8, + "shape_ci_limits": [1.8, 4.2], + "shape_ci": 95, + "scale": 2.5, + "scale_ci_limits": [2.5, 4], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 7, + "mean_ci_limits": [5.8, 8.4], + "mean_ci": 95, + "sd": 4.2, + "sd_ci_limits": [3.2, 5.6], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Zachary J.", + "family": "Madewell" + }, + { + "given": "Kelly", + "family": "Charniga" + }, + { + "given": "Nina B.", + "family": "Masters" + }, + { + "given": "Jason", + "family": "Asher" + }, + { + "given": "Lily", + "family": "Fahrenwald" + }, + { + "given": "William", + "family": "Still" + }, + { + "given": "Judy", + "family": "Chen" + }, + { + "given": "Naama", + "family": "Kipperman" + }, + { + "given": "David", + "family": "Bui" + }, + { + "given": "Meghan", + "family": "Shea" + }, + { + "given": "Lori", + "family": "Saathoff-Huber" + }, + { + "given": "Shannon", + "family": "Johnson" + }, + { + "given": "Khalil", + "family": "Harbi" + }, + { + "given": "Abby L.", + "family": "Berns" + }, + { + "given": "Taidy", + "family": "Perez" + }, + { + "given": "Emily", + "family": "Gateley" + }, + { + "given": "Ian H.", + "family": "Spicknall" + }, + { + "given": "Yoshinori", + "family": "Nakazawa" + }, + { + "given": "Thomas L.", + "family": "Gift" + }, + { + "given": "2022 Monkeypox Outbreak Response Team", + "family": null + } + ], + "title": "Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May – August 2025", + "journal": "medRxiv", + "year": 2022, + "pmid": null, + "doi": "10.1101/2022.10.26.22281516" + }, + "metadata": { + "units": "days", + "sample_size": 40, + "region": "USA", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Shape and scale from supp. material. Serial interval as exposure to rash onset" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus-Zaire Subtype", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 12.7, + "sd": 4.31 + }, + "citation": { + "author": [ + { + "given": "Martin", + "family": "Eichner" + }, + { + "given": "Scott F.", + "family": "Dowell" + }, + { + "given": "Nina", + "family": "Firese" + } + ], + "title": "Incubation period of ebola hemorrhagic virus subtype zaire", + "journal": "Osong Public Health and Research Perspectives", + "year": 2011, + "pmid": 24159443, + "doi": "10.1016/j.phrp.2011.04.001" + }, + "metadata": { + "units": "days", + "sample_size": 196, + "region": "Kikwit, Democratic Republic of Congo", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The paper reports lower and upper supported ranges for the mean and standard deviation but it is not clear if these are confidence intervals or not so are not included in the database" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus-Zaire Subtype", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { + "shape": 2.4, + "shape_ci_limits": [1.1, 4.5], + "shape_ci": 95, + "scale": 3.3333, + "scale_ci_limits": [2, 10], + "scale_ci": 95 + } + }, + "summary_statistics": { + "mean": 9.3, + "mean_ci_limits": [6.6, 13.6], + "mean_ci": 95, + "sd": 6, + "sd_ci_limits": [4, 11], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "The Ebola Outbreak Epidemiology Team", + "family": null + }, + { + "given": "Ahmadou", + "family": "Barry" + }, + { + "given": "Steve", + "family": "Ahuka-Mundeke" + }, + { + "given": "Yahaya", + "family": "Ali Ahmed" + }, + { + "given": "Yokouide", + "family": "Allarangar" + }, + { + "given": "Julienne", + "family": "Anoko" + }, + { + "given": "Brett Nicholas", + "family": "Archer" + }, + { + "given": "Aaron Aruna", + "family": "Abedi" + }, + { + "given": "Jayshree", + "family": "Bagaria" + }, + { + "given": "Marie Roseline Darnycka", + "family": "Belizaire" + }, + { + "given": "Sangeeta", + "family": "Bhatia" + }, + { + "given": "Théophile", + "family": "Bokenge" + }, + { + "given": "Emanuele", + "family": "Bruni" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Ernest", + "family": "Dabire" + }, + { + "given": "Amadou Mouctar", + "family": "Diallo" + }, + { + "given": "Boubacar", + "family": "Diallo" + }, + { + "given": "Christl Ann", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Tshewang Choden", + "family": "Dorji" + }, + { + "given": "Aura Rocio Escobar Corado", + "family": "Waeber" + }, + { + "given": "Ibrahima Socé", + "family": "Fall" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Richard Gareth", + "family": "FitzJohn" + }, + { + "given": "Gervais Leon Folefack", + "family": "Tengomo" + }, + { + "given": "Pierre Bernard Henri", + "family": "Formenty" + }, + { + "given": "Alpha", + "family": "Forna" + }, + { + "given": "Anne", + "family": "Fortin" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Katy A. M.", + "family": "Gaythorpe" + }, + { + "given": "Celine", + "family": "Gurry" + }, + { + "given": "Esther", + "family": "Hamblion" + }, + { + "given": "Mamoudou Harouna", + "family": "Djingarey" + }, + { + "given": "Christopher", + "family": "Haskew" + }, + { + "given": "Stéphane Alexandre Louis", + "family": "Hugonnet" + }, + { + "given": "Natsuko", + "family": "Imai" + }, + { + "given": "Benido", + "family": "Impouma" + }, + { + "given": "Guylain", + "family": "Kabongo" + }, + { + "given": "Oly Ilunga", + "family": "Kalenga" + }, + { + "given": "Emerencienne", + "family": "Kibangou" + }, + { + "given": "Theresa Min-Hyung", + "family": "Lee" + }, + { + "given": "Charles Okot", + "family": "Lukoya" + }, + { + "given": "Ousmane", + "family": "Ly" + }, + { + "given": "Sheila", + "family": "Makiala-Mandanda" + }, + { + "given": "Augustin", + "family": "Mamba" + }, + { + "given": "Placide", + "family": "Mbala-Kingebeni" + }, + { + "given": "Franck Fortune Roland", + "family": "Mboussou" + }, + { + "given": "Tamayi", + "family": "Mlanda" + }, + { + "given": "Vital Mondonge", + "family": "Makuma" + }, + { + "given": "Oliver", + "family": "Morgan" + }, + { + "given": "Anastasie Mujinga", + "family": "Mulumba" + }, + { + "given": "Patrick Mukadi", + "family": "Kakoni" + }, + { + "given": "Daniel", + "family": "Mukadi-Bamuleka" + }, + { + "given": "Jean-Jaques", + "family": "Muyembe" + }, + { + "given": "Ndjoloko Tambwe", + "family": "Bathé" + }, + { + "given": "Patricia", + "family": "Ndumbi Ngamala" + }, + { + "given": "Roland", + "family": "Ngom" + }, + { + "given": "Guillaume", + "family": "Ngoy" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Justus", + "family": "Nsio" + }, + { + "given": "Kevin Babila", + "family": "Ousman" + }, + { + "given": "Emilie", + "family": "Peron" + }, + { + "given": "Jonathan Aaron", + "family": "Polonsky" + }, + { + "given": "Michael J.", + "family": "Ryan" + }, + { + "given": "Alhassane", + "family": "Touré" + }, + { + "given": "Rodney", + "family": "Towner" + }, + { + "given": "Gaston", + "family": "Tshapenda" + }, + { + "given": "Reinhilde", + "family": "Van De Weerdt" + }, + { + "given": "Maria", + "family": "Van Kerkhove" + }, + { + "given": "Annika", + "family": "Wendland" + }, + { + "given": "N'Da Konan Michel", + "family": "Yao" + }, + { + "given": "Zabulon", + "family": "Yoti" + }, + { + "given": "Etienne", + "family": "Yuma" + }, + { + "given": "Guy", + "family": "Kalambayi Kabamba" + }, + { + "given": "Jean de Dieu Lukwesa", + "family": "Mwati" + }, + { + "given": "Gisele", + "family": "Mbuy" + }, + { + "given": "Leopold", + "family": "Lubula" + }, + { + "given": "Anny", + "family": "Mutombo" + }, + { + "given": "Oscar", + "family": "Mavila" + }, + { + "given": "Yyonne", + "family": "Lay" + }, + { + "given": "Emma", + "family": "Kitenge" + } + ], + "title": "Outbreak of Ebola virus disease in the Democratic Republic of the Congo, April–May, 2018: an epidemiological study", + "journal": "The Lancet", + "year": 2018, + "pmid": 30047375, + "doi": "10.1016/S0140-6736(18)31387-4" + }, + "metadata": { + "units": "days", + "sample_size": 14, + "region": "DR Congo", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data extracted from Appendix. The mean, sd, shape and scale are taken from the paper, the conversion between the two does not match exactly. The data used to estimate the onset-to-death distribution is not from the DRC outbreak but from the west african outbreak." +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 10.3, + "mean_ci_limits": [9.9, 10.7], + "mean_ci": 95, + "sd": 8.2, + "sd_ci_limits": [7.8, 8.6], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 1798, + "region": "West Africa", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Data extracted from Appendix. This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 12.6, + "mean_ci_limits": [9.1, 17.1], + "mean_ci": 95, + "sd": 13.1, + "sd_ci_limits": [9.6, 19.6], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 49, + "region": "Guinea", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This data comes from the entire period of the Guinea ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 10, + "mean_ci_limits": [9.6, 10.5], + "mean_ci": 95, + "sd": 7.6, + "sd_ci_limits": [7.1, 8.1], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 957, + "region": "Liberia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This data comes from the entire period of the Liberia ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). 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The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "notification to discharge", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 10.9, + "mean_ci_limits": [10.5, 11.4], + "mean_ci": 95, + "sd": 8.2, + "sd_ci_limits": [7.8, 8.7], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 1324, + "region": "West Africa", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 8.2, + "mean_ci_limits": [7.9, 8.4], + "mean_ci": 95, + "sd": 6.4, + "sd_ci_limits": [6.1, 6.6], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 2741, + "region": "West Africa", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "Ebola Virus Disease", + "pathogen": "Ebola Virus", + "epi_name": "onset to discharge", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 15.1, + "mean_ci_limits": [14.6, 15.6], + "mean_ci": 95, + "sd": 8.9, + "sd_ci_limits": [8.5, 9.3], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "WHO Ebola Response Team", + "family": null + }, + { + "given": "Junerlyn", + "family": "Agua-Agum" + }, + { + "given": "Archchun", + "family": "Ariyarajah" + }, + { + "given": "Bruce", + "family": "Aylward" + }, + { + "given": "Isobel M.", + "family": "Blake" + }, + { + "given": "Richard", + "family": "Brennan" + }, + { + "given": "Anne", + "family": "Cori" + }, + { + "given": "Christl A.", + "family": "Donnelly" + }, + { + "given": "Ilaria", + "family": "Dorigatti" + }, + { + "given": "Christopher", + "family": "Dye" + }, + { + "given": "Tim", + "family": "Eckmanns" + }, + { + "given": "Neil M.", + "family": "Ferguson" + }, + { + "given": "Pierre", + "family": "Formenty" + }, + { + "given": "Christophe", + "family": "Fraser" + }, + { + "given": "Erika", + "family": "Garcia" + }, + { + "given": "Tini", + "family": "Garske" + }, + { + "given": "Wes", + "family": "Hinsley" + }, + { + "given": "David", + "family": "Holmes" + }, + { + "given": "Stéphane", + "family": "Hugonnet" + }, + { + "given": "Swathi", + "family": "Iyengar" + }, + { + "given": "Thibaut", + "family": "Jombart" + }, + { + "given": "Ravi", + "family": "Krishnan" + }, + { + "given": "Sascha", + "family": "Meijers" + }, + { + "given": "Harriet L.", + "family": "Mills" + }, + { + "given": "Yasmine", + "family": "Mohamed" + }, + { + "given": "Gemma", + "family": "Nedjati-Gilani" + }, + { + "given": "Emily", + "family": "Newton" + }, + { + "given": "Pierre", + "family": "Nouvellet" + }, + { + "given": "Louise", + "family": "Pelletier" + }, + { + "given": "Devin", + "family": "Perkins" + }, + { + "given": "Steven", + "family": "Riley" + }, + { + "given": "Maria", + "family": "Sagrado" + }, + { + "given": "Johannes", + "family": "Schnitzler" + }, + { + "given": "Dirk", + "family": "Schumacher" + }, + { + "given": "Anita", + "family": "Shah" + }, + { + "given": "Maria D.", + "family": "Van Kerkhove" + }, + { + "given": "Olivia", + "family": "Varsaneux" + }, + { + "given": "Niluka Wijekoon", + "family": "Kannangarage" + } + ], + "title": "West African Ebola Epidemic after One Year — Slowing but Not Yet under Control", + "journal": "The New England Journal of Medicine", + "year": 2015, + "pmid": 25539446, + "doi": "10.1056/NEJMc1414992" + }, + "metadata": { + "units": "days", + "sample_size": 1335, + "region": "West Africa", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This data comes from the entire period of the west africa ebola outbreak up to the point the paper was published (Dec 2013 - 25 Nov 2014). The methods fitting are reported in another paper: DOI: 10.1056/NEJMoa1411100" +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [2.2, 12.4], + "quantile_names": ["5", "95"], + "median": 5.2, + "median_ci_limits": [1.9, 14.7], + "median_ci": null + }, + "citation": { + "author": [ + { + "given": "Abdullah", + "family": "Assiri" + }, + { + "given": "Allison", + "family": "McGeer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Connie S.", + "family": "Price" + }, + { + "given": "Abdullah A.", + "family": "Al Rabeeah" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "Zaki N.", + "family": "Alabdullatif" + }, + { + "given": "Maher", + "family": "Assad" + }, + { + "given": "Abdulmohsen", + "family": "Almulhim" + }, + { + "given": "Hatem", + "family": "Makhdoom" + }, + { + "given": "Hossam", + "family": "Madani" + }, + { + "given": "Rafat", + "family": "Alhakeem" + }, + { + "given": "Jaffar A.", + "family": "Al-Tawfiq" + }, + { + "given": "Matthew", + "family": "Cotten" + }, + { + "given": "Simon J.", + "family": "Watson" + }, + { + "given": "Paul", + "family": "Kellam" + }, + { + "given": "Alimuddin I.", + "family": "Zumla" + }, + { + "given": "Ziad A.", + "family": "Memish" + }, + { + "given": "KSA MERSCOV Investigation Team", + "family": null + } + ], + "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus", + "journal": "The New England Journal of Medicine", + "year": 2013, + "pmid": 23782161, + "doi": "10.1056/NEJMoa1306742" + }, + "metadata": { + "units": "days", + "sample_size": 23, + "region": "Saudi Arabia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [3, 19.4], + "quantile_names": ["5", "95"], + "median": 7.6, + "median_ci_limits": [2.5, 23.1], + "median_ci": null + }, + "citation": { + "author": [ + { + "given": "Abdullah", + "family": "Assiri" + }, + { + "given": "Allison", + "family": "McGeer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Connie S.", + "family": "Price" + }, + { + "given": "Abdullah A.", + "family": "Al Rabeeah" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "Zaki N.", + "family": "Alabdullatif" + }, + { + "given": "Maher", + "family": "Assad" + }, + { + "given": "Abdulmohsen", + "family": "Almulhim" + }, + { + "given": "Hatem", + "family": "Makhdoom" + }, + { + "given": "Hossam", + "family": "Madani" + }, + { + "given": "Rafat", + "family": "Alhakeem" + }, + { + "given": "Jaffar A.", + "family": "Al-Tawfiq" + }, + { + "given": "Matthew", + "family": "Cotten" + }, + { + "given": "Simon J.", + "family": "Watson" + }, + { + "given": "Paul", + "family": "Kellam" + }, + { + "given": "Alimuddin I.", + "family": "Zumla" + }, + { + "given": "Ziad A.", + "family": "Memish" + }, + { + "given": "KSA MERSCOV Investigation Team", + "family": null + } + ], + "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus", + "journal": "The New England Journal of Medicine", + "year": 2013, + "pmid": 23782161, + "doi": "10.1056/NEJMoa1306742" + }, + "metadata": { + "units": "days", + "sample_size": 23, + "region": "Saudi Arabia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "onset to hospitalisation", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 5, + "lower_range": 1, + "upper_range": 10 + }, + "citation": { + "author": [ + { + "given": "Abdullah", + "family": "Assiri" + }, + { + "given": "Allison", + "family": "McGeer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Connie S.", + "family": "Price" + }, + { + "given": "Abdullah A.", + "family": "Al Rabeeah" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "Zaki N.", + "family": "Alabdullatif" + }, + { + "given": "Maher", + "family": "Assad" + }, + { + "given": "Abdulmohsen", + "family": "Almulhim" + }, + { + "given": "Hatem", + "family": "Makhdoom" + }, + { + "given": "Hossam", + "family": "Madani" + }, + { + "given": "Rafat", + "family": "Alhakeem" + }, + { + "given": "Jaffar A.", + "family": "Al-Tawfiq" + }, + { + "given": "Matthew", + "family": "Cotten" + }, + { + "given": "Simon J.", + "family": "Watson" + }, + { + "given": "Paul", + "family": "Kellam" + }, + { + "given": "Alimuddin I.", + "family": "Zumla" + }, + { + "given": "Ziad A.", + "family": "Memish" + }, + { + "given": "KSA MERSCOV Investigation Team", + "family": null + } + ], + "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus", + "journal": "The New England Journal of Medicine", + "year": 2013, + "pmid": 23782161, + "doi": "10.1056/NEJMoa1306742" + }, + "metadata": { + "units": "days", + "sample_size": 23, + "region": "Saudi Arabia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "A distribution was not fitted to the data, instead the median and range observed are reported. The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 11, + "lower_range": 5, + "upper_range": 27 + }, + "citation": { + "author": [ + { + "given": "Abdullah", + "family": "Assiri" + }, + { + "given": "Allison", + "family": "McGeer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Connie S.", + "family": "Price" + }, + { + "given": "Abdullah A.", + "family": "Al Rabeeah" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "Zaki N.", + "family": "Alabdullatif" + }, + { + "given": "Maher", + "family": "Assad" + }, + { + "given": "Abdulmohsen", + "family": "Almulhim" + }, + { + "given": "Hatem", + "family": "Makhdoom" + }, + { + "given": "Hossam", + "family": "Madani" + }, + { + "given": "Rafat", + "family": "Alhakeem" + }, + { + "given": "Jaffar A.", + "family": "Al-Tawfiq" + }, + { + "given": "Matthew", + "family": "Cotten" + }, + { + "given": "Simon J.", + "family": "Watson" + }, + { + "given": "Paul", + "family": "Kellam" + }, + { + "given": "Alimuddin I.", + "family": "Zumla" + }, + { + "given": "Ziad A.", + "family": "Memish" + }, + { + "given": "KSA MERSCOV Investigation Team", + "family": null + } + ], + "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus", + "journal": "The New England Journal of Medicine", + "year": 2013, + "pmid": 23782161, + "doi": "10.1056/NEJMoa1306742" + }, + "metadata": { + "units": "days", + "sample_size": 23, + "region": "Saudi Arabia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "A distribution was not fitted to the data, instead the median and range observed are reported. The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "onset to ventilation", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 7, + "lower_range": 3, + "upper_range": 11 + }, + "citation": { + "author": [ + { + "given": "Abdullah", + "family": "Assiri" + }, + { + "given": "Allison", + "family": "McGeer" + }, + { + "given": "Trish M.", + "family": "Perl" + }, + { + "given": "Connie S.", + "family": "Price" + }, + { + "given": "Abdullah A.", + "family": "Al Rabeeah" + }, + { + "given": "Derek A.T.", + "family": "Cummings" + }, + { + "given": "Zaki N.", + "family": "Alabdullatif" + }, + { + "given": "Maher", + "family": "Assad" + }, + { + "given": "Abdulmohsen", + "family": "Almulhim" + }, + { + "given": "Hatem", + "family": "Makhdoom" + }, + { + "given": "Hossam", + "family": "Madani" + }, + { + "given": "Rafat", + "family": "Alhakeem" + }, + { + "given": "Jaffar A.", + "family": "Al-Tawfiq" + }, + { + "given": "Matthew", + "family": "Cotten" + }, + { + "given": "Simon J.", + "family": "Watson" + }, + { + "given": "Paul", + "family": "Kellam" + }, + { + "given": "Alimuddin I.", + "family": "Zumla" + }, + { + "given": "Ziad A.", + "family": "Memish" + }, + { + "given": "KSA MERSCOV Investigation Team", + "family": null + } + ], + "title": "Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus", + "journal": "The New England Journal of Medicine", + "year": 2013, + "pmid": 23782161, + "doi": "10.1056/NEJMoa1306742" + }, + "metadata": { + "units": "days", + "sample_size": 23, + "region": "Saudi Arabia", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "A distribution was not fitted to the data, instead the median and range observed are reported. The sample size is not explicitly stated. The number of confirmed cases is 23 and there are 2 suspected cases, therefore it is not clear whether the 2 suspected cases were included in the estimation, the sample size is assumed to be 23." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 14.6, + "mean_ci_limits": [11.5, 19.5], + "mean_ci": 95, + "sd": 10.4, + "sd_ci_limits": [7.6, 16.2], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Kenji", + "family": "Mizumoto" + }, + { + "given": "Akira", + "family": "Endo" + }, + { + "given": "Gerardo", + "family": "Chowell" + }, + { + "given": "Yuichiro", + "family": "Miyamatsu" + }, + { + "given": "Masaya", + "family": "Saitoh" + }, + { + "given": "Hiroshi", + "family": "Nishiura" + } + ], + "title": "Real-time characterization of risks of death associated with the Middle East respiratory syndrome (MERS) in the Republic of Korea, 2015", + "journal": "BMC Medicine", + "year": 2015, + "pmid": 26420593, + "doi": "10.1186/s12916-015-0468-3" + }, + "metadata": { + "units": "days", + "sample_size": 185, + "region": "South Korea", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The distribution parameters were jointly inferred with the risk factors of mortality." +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 6.7, + "mean_ci_limits": [6.1, 7.3], + "mean_ci": 95, + "median": 6.3, + "median_ci_limits": [5.7, 6.8], + "median_ci": 95, + "quantile_values": [12.1], + "quantile_names": ["95"] + }, + "citation": { + "author": [ + { + "given": "B. J.", + "family": "Cowling" + }, + { + "given": "M.", + "family": "Park" + }, + { + "given": "V. J.", + "family": "Fang" + }, + { + "given": "P.", + "family": "Wu" + }, + { + "given": "G. M.", + "family": "Leung" + }, + { + "given": "J. T.", + "family": "Wu" + } + ], + "title": "Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2015", + "journal": "Eurosurveillance", + "year": 2015, + "pmid": 26132767, + "doi": "10.2807/1560-7917.es2015.20.25.21163" + }, + "metadata": { + "units": "days", + "sample_size": 166, + "region": "South Korea", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "MERS", + "pathogen": "MERS-Cov", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 12.6, + "mean_ci_limits": [12.1, 13.1], + "mean_ci": 95, + "sd": 2.8, + "sd_ci_limits": [2.4, 3.1], + "sd_ci": 95 + }, + "citation": { + "author": [ + { + "given": "B. J.", + "family": "Cowling" + }, + { + "given": "M.", + "family": "Park" + }, + { + "given": "V. J.", + "family": "Fang" + }, + { + "given": "P.", + "family": "Wu" + }, + { + "given": "G. M.", + "family": "Leung" + }, + { + "given": "J. T.", + "family": "Wu" + } + ], + "title": "Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea, May to June 2016", + "journal": "Eurosurveillance", + "year": 2015, + "pmid": 26132767, + "doi": "10.2807/1560-7917.es2015.20.25.21163" + }, + "metadata": { + "units": "days", + "sample_size": 99, + "region": "South Korea", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 5.84, + "mean_ci_limits": [5.07, 6.55], + "mean_ci": 95, + "sd": 2.98, + "sd_ci_limits": [2.31, 3.72], + "sd_ci": 95, + "quantile_values": [2.69, 12.89], + "quantile_names": ["2.5", "97.5"], + "median": 5.01, + "median_ci_limits": [4, 6], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Ke", + "family": "Men" + }, + { + "given": "Xia", + "family": "Wang" + }, + { + "given": "Li", + "family": "Yihao" + }, + { + "given": "Guangwei", + "family": "Zhang" + }, + { + "given": "Jingjing", + "family": "Hu" + }, + { + "given": "Yanyan", + "family": "Gao" + }, + { + "given": "Henry", + "family": "Han" + } + ], + "title": "Estimate the incubation period of coronavirus 2019 (COVID-19)", + "journal": "medRxiv", + "year": 2020, + "pmid": null, + "doi": "10.1101/2020.02.24.20027474" + }, + "metadata": { + "units": "days", + "sample_size": 59, + "region": "China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The estimate of the incubation period is from a non-parametric bootstrap approach that does not fit a parametric distribution." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 5.74, + "mean_ci_limits": [5.18, 6.3], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Balram", + "family": "Rai" + }, + { + "given": "Anandi", + "family": "Shukla" + }, + { + "given": "Laxmi Kant", + "family": "Dwivedi" + } + ], + "title": "Incubation period for COVID-19: a systematic review and meta-analysis", + "journal": "Zeitschrift fur Gesundheitswissenschaften", + "year": 2022, + "pmid": 33643779, + "doi": "10.1007/s10389-021-01478-1" + }, + "metadata": { + "units": "days", + "sample_size": 6241, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This estimated mean incubation period is from a meta-analysis of 15 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 6.5, + "mean_ci_limits": [5.9, 7.1], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Muluneh", + "family": "Alene" + }, + { + "given": "Leltework", + "family": "Yismaw" + }, + { + "given": "Moges Agazhe", + "family": "Assemie" + }, + { + "given": "Daniel Bekele", + "family": "Ketema" + }, + { + "given": "Wodaje", + "family": "Gietaneh" + }, + { + "given": "Tilahun Yemanu", + "family": "Birhan" + } + ], + "title": "Serial interval and incubation period of COVID-19: a systematic review and meta-analysis", + "journal": "BMC Infectious Diseases", + "year": 2021, + "pmid": 33706702, + "doi": "10.1186/s12879-021-05950-x" + }, + "metadata": { + "units": "days", + "sample_size": 1453, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This estimated mean incubation period is from a meta-analysis of 14 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 5.2, + "mean_ci_limits": [4.9, 5.5], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Muluneh", + "family": "Alene" + }, + { + "given": "Leltework", + "family": "Yismaw" + }, + { + "given": "Moges Agazhe", + "family": "Assemie" + }, + { + "given": "Daniel Bekele", + "family": "Ketema" + }, + { + "given": "Wodaje", + "family": "Gietaneh" + }, + { + "given": "Tilahun Yemanu", + "family": "Birhan" + } + ], + "title": "Serial interval and incubation period of COVID-19: a systematic review and meta-analysis", + "journal": "BMC Infectious Diseases", + "year": 2021, + "pmid": 33706702, + "doi": "10.1186/s12879-021-05950-x" + }, + "metadata": { + "units": "days", + "sample_size": 3924, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This estimated mean serial interval is from a meta-analysis of 23 other serial interval estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 4.7, + "mean_ci_limits": [3.7, 6.0], + "mean_ci": 95, + "sd": 2.9, + "sd_ci_limits": [1.9, 4.9], + "sd_ci": 95, + "median": 4.0, + "median_ci_limits": [3.1, 4.9], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Hiroshi", + "family": "Nishiura" + }, + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + } + ], + "title": "Serial interval of novel coronavirus (COVID-19) infections", + "journal": "International Journal of Infectious Diseases", + "year": 2020, + "pmid": 32145466, + "doi": "10.1016/j.ijid.2020.02.060" + }, + "metadata": { + "units": "days", + "sample_size": 28, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": true, + "phase_bias_adjusted": false + }, + "notes": "These estimates are from fitting to the entire dataset of contact pairs, including pairs that are uncertain." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { } + }, + "summary_statistics": { + "mean": 4.8, + "mean_ci_limits": [3.8, 6.1], + "mean_ci": 95, + "sd": 2.3, + "sd_ci_limits": [1.6, 3.5], + "sd_ci": 95, + "median": 4.6, + "median_ci_limits": [3.5, 5.9], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Hiroshi", + "family": "Nishiura" + }, + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + } + ], + "title": "Serial interval of novel coronavirus (COVID-19) infections", + "journal": "International Journal of Infectious Diseases", + "year": 2020, + "pmid": 32145466, + "doi": "10.1016/j.ijid.2020.02.060" + }, + "metadata": { + "units": "days", + "sample_size": 18, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": true, + "phase_bias_adjusted": false + }, + "notes": "These estimates are from fitting to a subset of the dataset of contact pairs, only including pairs that are the most certain." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [1, 1.1, 13.7, 15, 17.8], + "quantile_names": ["2.5", "5", "95", "97.5", "99"], + "median": 5.4, + "median_ci_limits": [4.8, 6.0], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Lin", + "family": "Yang" + }, + { + "given": "Jingyi", + "family": "Dai" + }, + { + "given": "Jun", + "family": "Zhao" + }, + { + "given": "Yunfu", + "family": "Wang" + }, + { + "given": "Pingji", + "family": "Deng" + }, + { + "given": "Jing", + "family": "Wang" + } + ], + "title": "Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China", + "journal": "Epidemiology and Infection", + "year": 2020, + "pmid": 32594928, + "doi": "10.1017/S0950268820001338" + }, + "metadata": { + "units": "days", + "sample_size": 178, + "region": "Hubei province, China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": "norm", + "parameters": { + "mean": 4.6, + "mean_ci_limits": [3.7, 5.5], + "mean_ci": 95, + "sd": 4.4, + "sd_ci_limits": [3.8, 5.0], + "sd_ci": 95 + } + }, + "summary_statistics": { + "quantile_values": [11.8, 14.8], + "quantile_names": ["95", "99"], + "median": 4.6 + }, + "citation": { + "author": [ + { + "given": "Lin", + "family": "Yang" + }, + { + "given": "Jingyi", + "family": "Dai" + }, + { + "given": "Jun", + "family": "Zhao" + }, + { + "given": "Yunfu", + "family": "Wang" + }, + { + "given": "Pingji", + "family": "Deng" + }, + { + "given": "Jing", + "family": "Wang" + } + ], + "title": "Estimation of incubation period and serial interval of COVID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China", + "journal": "Epidemiology and Infection", + "year": 2020, + "pmid": 32594928, + "doi": "10.1017/S0950268820001338" + }, + "metadata": { + "units": "days", + "sample_size": 131, + "region": "Hubei province, China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 6.38, + "mean_ci_limits": [5.79, 6.97], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Christelle", + "family": "Elias" + }, + { + "given": "Abel", + "family": "Sekri" + }, + { + "given": "Pierre", + "family": "Leblanc" + }, + { + "given": "Michel", + "family": "Cucherat" + }, + { + "given": "Philippe", + "family": "Vanhems" + } + ], + "title": "The incubation period of COVID-19: A meta-analysis", + "journal": "International Journal of Infectious Diseases", + "year": 2021, + "pmid": 33548553, + "doi": "10.1016/j.ijid.2021.01.069" + }, + "metadata": { + "units": "days", + "sample_size": 28675, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This estimated mean incubation period is from a meta-analysis of 99 other incubation period estimates. Only the mean is reported and a distribution cannot be specified as the meta-mean is estimated from a random-effects model." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "weibull", + "parameters": { } + }, + "summary_statistics": { + "mean": 6.4, + "mean_ci_limits": [4.89, 8.5], + "mean_ci": 95, + "sd": 3.05, + "sd_ci_limits": [3.05, 5.3], + "sd_ci": 95, + "quantile_values": [1.35, 1.9, 11.9, 13.04], + "quantile_names": ["2.5", "5", "95", "97.5"], + "median": 6.1 + }, + "citation": { + "author": [ + { + "given": "Long V.", + "family": "Bui" + }, + { + "given": "Ha T.", + "family": "Nguyen" + }, + { + "given": "Hagai", + "family": "Levine" + }, + { + "given": "Ha N.", + "family": "Nguyen" + }, + { + "given": "Thu-Anh", + "family": "Nguyen" + }, + { + "given": "Thuy P.", + "family": "Nguyen" + }, + { + "given": "Truong T.", + "family": "Nguyen" + }, + { + "given": "Toan T. T.", + "family": "Do" + }, + { + "given": "Ngoc T.", + "family": "Pham" + }, + { + "given": "My Hanh", + "family": "Bui" + } + ], + "title": "Estimation of the incubation period of COVID-19 in Vietnam", + "journal": "PLoS One", + "year": 2020, + "pmid": 33362233, + "doi": "10.1371/journal.pone.0243889" + }, + "metadata": { + "units": "days", + "sample_size": 19, + "region": "Vietnam", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes" +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "meanlog": 1.66, + "meanlog_ci_limits": [1.55, 1.76], + "meanlog_ci": 95, + "sdlog": 0.48, + "sdlog_ci_limits": [0.42, 0.54], + "sdlog_ci": 95 + } + }, + "summary_statistics": { }, + "citation": { + "author": [ + { + "given": "Conor", + "family": "McAloon" + }, + { + "given": "Áine", + "family": "Collins" + }, + { + "given": "Kevin", + "family": "Hunt" + }, + { + "given": "Ann", + "family": "Barber" + }, + { + "given": "Andrew W.", + "family": "Byrne" + }, + { + "given": "Francis", + "family": "Butler" + }, + { + "given": "Miriam", + "family": "Casey" + }, + { + "given": "John", + "family": "Griffin" + }, + { + "given": "Elizabeth", + "family": "Lane" + }, + { + "given": "David", + "family": "McEvoy" + }, + { + "given": "Patrick", + "family": "Wall" + }, + { + "given": "Martin", + "family": "Green" + }, + { + "given": "Luke", + "family": "O'Grady" + }, + { + "given": "Simon J.", + "family": "More" + } + ], + "title": "Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research", + "journal": "BMJ Open", + "year": 2020, + "pmid": 32801208, + "doi": "10.1136/bmjopen-2020-039652" + }, + "metadata": { + "units": "days", + "sample_size": 1357, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The incubation period parameters are estimated from a meta-analysis of other studies that estimated the incubation period using a lognormal distribution. This is the full set of data (N=9)." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { + "meanlog": 1.63, + "meanlog_ci_limits": [1.51, 1.75], + "meanlog_ci": 95, + "sdlog": 0.5, + "sdlog_ci_limits": [0.46, 0.55], + "sdlog_ci": 95 + } + }, + "summary_statistics": { + "mean": 5.8, + "mean_ci_limits": [5, 6.7], + "mean_ci": 95, + "median": 5.1, + "median_ci_limits": [4.5, 5.8], + "median_ci": 95, + "quantile_values": [11.7], + "quantile_names": ["95"] + }, + "citation": { + "author": [ + { + "given": "Conor", + "family": "McAloon" + }, + { + "given": "Áine", + "family": "Collins" + }, + { + "given": "Kevin", + "family": "Hunt" + }, + { + "given": "Ann", + "family": "Barber" + }, + { + "given": "Andrew W.", + "family": "Byrne" + }, + { + "given": "Francis", + "family": "Butler" + }, + { + "given": "Miriam", + "family": "Casey" + }, + { + "given": "John", + "family": "Griffin" + }, + { + "given": "Elizabeth", + "family": "Lane" + }, + { + "given": "David", + "family": "McEvoy" + }, + { + "given": "Patrick", + "family": "Wall" + }, + { + "given": "Martin", + "family": "Green" + }, + { + "given": "Luke", + "family": "O'Grady" + }, + { + "given": "Simon J.", + "family": "More" + } + ], + "title": "Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research", + "journal": "BMJ Open", + "year": 2020, + "pmid": 32801208, + "doi": "10.1136/bmjopen-2020-039652" + }, + "metadata": { + "units": "days", + "sample_size": 1269, + "region": "Mixed", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "mle" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "The incubation period parameters are estimated from a meta-analysis of other studies that estimated the incubation period using a lognormal distribution. This is the data set with Backer removed as they did not have a defined exposure window (N=8)." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 5, + "mean_ci_limits": [4.2, 6], + "mean_ci": 95, + "sd": 3, + "sd_ci_limits": [2.1, 4.5], + "sd_ci": 95, + "quantile_values": [1.7, 10.6], + "quantile_names": ["5", "95"], + "median": 4.3, + "median_ci_limits": [3.5, 5.1], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Tetsuro", + "family": "Kobayashi" + }, + { + "given": "Yichi", + "family": "Yang" + }, + { + "given": "Katsuma", + "family": "Hayashi" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + }, + { + "given": "Sung-mok", + "family": "Jung" + }, + { + "given": "Baoyin", + "family": "Yuan" + }, + { + "given": "Ryo", + "family": "Kinoshita" + }, + { + "given": "Hiroshi", + "family": "Nishiura" + } + ], + "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data", + "journal": "Journal of Clinical Medicine", + "year": 2020, + "pmid": 32079150, + "doi": "10.3390/jcm9020538" + }, + "metadata": { + "units": "days", + "sample_size": 52, + "region": "China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This dataset excludes Wuhan residents (to have a more precise exposure interval). This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 5.6, + "mean_ci_limits": [5, 6.3], + "mean_ci": 95, + "sd": 2.8, + "sd_ci_limits": [2.2, 3.6], + "sd_ci": 95, + "quantile_values": [2.3, 10.8], + "quantile_names": ["5", "95"], + "median": 5, + "median_ci_limits": [4.4, 5.6], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Tetsuro", + "family": "Kobayashi" + }, + { + "given": "Yichi", + "family": "Yang" + }, + { + "given": "Katsuma", + "family": "Hayashi" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + }, + { + "given": "Sung-mok", + "family": "Jung" + }, + { + "given": "Baoyin", + "family": "Yuan" + }, + { + "given": "Ryo", + "family": "Kinoshita" + }, + { + "given": "Hiroshi", + "family": "Nishiura" + } + ], + "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data", + "journal": "Journal of Clinical Medicine", + "year": 2020, + "pmid": 32079150, + "doi": "10.3390/jcm9020538" + }, + "metadata": { + "units": "days", + "sample_size": 158, + "region": "China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This dataset includes Wuhan residents (which have a less precise exposure interval). This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "onset to hospitalisation", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 3.3, + "mean_ci_limits": [2.7, 4], + "mean_ci": 95, + "sd": 4.2, + "sd_ci_limits": [3.3, 5.4], + "sd_ci": 95, + "quantile_values": [0, 11.6], + "quantile_names": ["5", "95"], + "median": 1.7, + "median_ci_limits": [1.2, 2.2], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Tetsuro", + "family": "Kobayashi" + }, + { + "given": "Yichi", + "family": "Yang" + }, + { + "given": "Katsuma", + "family": "Hayashi" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + }, + { + "given": "Sung-mok", + "family": "Jung" + }, + { + "given": "Baoyin", + "family": "Yuan" + }, + { + "given": "Ryo", + "family": "Kinoshita" + }, + { + "given": "Hiroshi", + "family": "Nishiura" + } + ], + "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data", + "journal": "Journal of Clinical Medicine", + "year": 2020, + "pmid": 32079150, + "doi": "10.3390/jcm9020538" + }, + "metadata": { + "units": "days", + "sample_size": 155, + "region": "China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "onset to hospitalisation", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 6.5, + "mean_ci_limits": [5.2, 8], + "mean_ci": 95, + "sd": 4.3, + "sd_ci_limits": [2.9, 5.6], + "sd_ci": 95, + "quantile_values": [1.9, 13.9], + "quantile_names": ["5", "95"], + "median": 5.1, + "median_ci_limits": [4.1, 6.3], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Natalie M.", + "family": "Linton" + }, + { + "given": "Tetsuro", + "family": "Kobayashi" + }, + { + "given": "Yichi", + "family": "Yang" + }, + { + "given": "Katsuma", + "family": "Hayashi" + }, + { + "given": "Andrei R.", + "family": "Akhmetzhanov" + }, + { + "given": "Sung-mok", + "family": "Jung" + }, + { + "given": "Baoyin", + "family": "Yuan" + }, + { + "given": "Ryo", + "family": "Kinoshita" + }, + { + "given": "Hiroshi", + "family": "Nishiura" + } + ], + "title": "Incubation Period and Other Epidemiological Characteristics of 2019 Novel Coronavirus Infections with Right Truncation: A Statistical Analysis of Publicly Available Case Data", + "journal": "Journal of Clinical Medicine", + "year": 2020, + "pmid": 32079150, + "doi": "10.3390/jcm9020538" + }, + "metadata": { + "units": "days", + "sample_size": 34, + "region": "China", + "transmission_mode": "natural_natural_human_to_human", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "This method does not apply right-truncation, but does compare the gamma, weibull and lognormal distributions." +}, +{ + "disease": "COVID-19", + "pathogen": "SARS-CoV-2", + "epi_name": "onset to death", + "probability_distribution": { + "prob_distribution": "lnorm", + "parameters": { } + }, + "summary_statistics": { + "mean": 14.5, + "mean_ci_limits": [12.5, 17], + "mean_ci": 95, + "sd": 6.7, + "sd_ci_limits": [4.9, 9.4], + "sd_ci": 95, + 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"Zhanwei", + "family": "Du" + } + ], + "title": "Serial intervals and incubation periods of the monkeypox virus clades", + "journal": "Journal of Travel Medicine", + "year": 2022, + "pmid": 36130210, + "doi": "10.1093/jtm/taac105" + }, + "metadata": { + "units": "days", + "sample_size": 16, + "region": "Congo", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Systematic review" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "serial interval", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [8.9, 10.67], + "quantile_names": ["25", "75"], + "median": 9.78 + }, + "citation": { + "author": [ + { + "given": "Shuqi", + "family": "Wang" + }, + { + "given": "Fengdi", + "family": "Zhang" + }, + { + "given": "Zhilu", + "family": "Yuan" + }, + { + "given": "Mingda", + "family": "Xu" + }, + { + "given": "Zhen", + "family": "Wang" + }, + { + "given": "Chao", + "family": "Gao" + }, + { + "given": "Renzhong", + "family": "Guo" + }, + { + "given": "Zhanwei", + "family": "Du" + } + ], + "title": "Serial intervals and incubation periods of the monkeypox virus clades", + "journal": "Journal of Travel Medicine", + "year": 2022, + "pmid": 36130210, + "doi": "10.1093/jtm/taac105" + }, + "metadata": { + "units": "days", + "sample_size": 34, + "region": "Mixed", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Systematic review" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus Clade I", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [8, 12.25], + "quantile_names": ["25", "75"], + "median": 9.5 + }, + "citation": { + "author": [ + { + "given": "Shuqi", + "family": "Wang" + }, + { + "given": "Fengdi", + "family": "Zhang" + }, + { + "given": "Zhilu", + "family": "Yuan" + }, + { + "given": "Mingda", + "family": "Xu" + }, + { + "given": "Zhen", + "family": "Wang" + }, + { + "given": "Chao", + "family": "Gao" + }, + { + "given": "Renzhong", + "family": "Guo" + }, + { + "given": "Zhanwei", + "family": "Du" + } + ], + "title": "Serial intervals and incubation periods of the monkeypox virus clades", + "journal": "Journal of Travel Medicine", + "year": 2022, + "pmid": 36130210, + "doi": "10.1093/jtm/taac105" + }, + "metadata": { + "units": "days", + "sample_size": 16, + "region": "Congo", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Systematic review" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus Clade IIa", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "quantile_values": [11.39, 23.91], + "quantile_names": ["25", "75"], + "median": 16.76 + }, + "citation": { + "author": [ + { + "given": "Shuqi", + "family": "Wang" + }, + { + "given": "Fengdi", + "family": "Zhang" + }, + { + "given": "Zhilu", + "family": "Yuan" + }, + { + "given": "Mingda", + "family": "Xu" + }, + { + "given": "Zhen", + "family": "Wang" + }, + { + "given": "Chao", + "family": "Gao" + }, + { + "given": "Renzhong", + "family": "Guo" + }, + { + "given": "Zhanwei", + "family": "Du" + } + ], + "title": "Serial intervals and incubation periods of the monkeypox virus clades", + "journal": "Journal of Travel Medicine", + "year": 2022, + "pmid": 36130210, + "doi": "10.1093/jtm/taac105" + }, + "metadata": { + "units": "days", + "sample_size": 27, + "region": "USA", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Systematic review" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus Clade IIb", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "median": 8.26, + "median_ci_limits": [7.55, 8.97], + "median_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Shuqi", + "family": "Wang" + }, + { + "given": "Fengdi", + "family": "Zhang" + }, + { + "given": "Zhilu", + "family": "Yuan" + }, + { + "given": "Mingda", + "family": "Xu" + }, + { + "given": "Zhen", + "family": "Wang" + }, + { + "given": "Chao", + "family": "Gao" + }, + { + "given": "Renzhong", + "family": "Guo" + }, + { + "given": "Zhanwei", + "family": "Du" + } + ], + "title": "Serial intervals and incubation periods of the monkeypox virus clades", + "journal": "Journal of Travel Medicine", + "year": 2022, + "pmid": 36130210, + "doi": "10.1093/jtm/taac105" + }, + "metadata": { + "units": "days", + "sample_size": 114, + "region": "mixed", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Systematic review" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 8.13, + "mean_ci_limits": [4.9, 19.5], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Fengying", + "family": "Wei" + }, + { + "given": "Zhihang", + "family": "Peng" + }, + { + "given": "Zhen", + "family": "Jin" + }, + { + "given": "Jinjie", + "family": "Wang" + }, + { + "given": "Ximing", + "family": "Xu" + }, + { + "given": "Xinyan", + "family": "Zhang" + }, + { + "given": "Jun", + "family": "Xu" + }, + { + "given": "Zixiong", + "family": "Ren" + }, + { + "given": "Yao", + "family": "Bai" + }, + { + "given": "Xiaoli", + "family": "Wang" + }, + { + "given": "Bulai", + "family": "Lu" + }, + { + "given": "Zhaojun", + "family": "Wang" + }, + { + "given": "Jianguo", + "family": "Xu" + }, + { + "given": "Senzhong", + "family": "Huang" + } + ], + "title": "Study and prediction of the 2022 global monkeypox epidemic", + "journal": "Journal of Biosafety and Biosecurity", + "year": 2022, + "pmid": 36573222, + "doi": "10.1016/j.jobb.2022.12.001" + }, + "metadata": { + "units": "days", + "sample_size": null, + "region": "USA", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 8.08, + "mean_ci_limits": [4.8, 21], + "mean_ci": 95 + }, + "citation": { + "author": [ + { + "given": "Fengying", + "family": "Wei" + }, + { + "given": "Zhihang", + "family": "Peng" + }, + { + "given": "Zhen", + "family": "Jin" + }, + { + "given": "Jinjie", + "family": "Wang" + }, + { + "given": "Ximing", + "family": "Xu" + }, + { + "given": "Xinyan", + "family": "Zhang" + }, + { + "given": "Jun", + "family": "Xu" + }, + { + "given": "Zixiong", + "family": "Ren" + }, + { + "given": "Yao", + "family": "Bai" + }, + { + "given": "Xiaoli", + "family": "Wang" + }, + { + "given": "Bulai", + "family": "Lu" + }, + { + "given": "Zhaojun", + "family": "Wang" + }, + { + "given": "Jianguo", + "family": "Xu" + }, + { + "given": "Senzhong", + "family": "Huang" + } + ], + "title": "Study and prediction of the 2022 global monkeypox epidemic", + "journal": "Journal of Biosafety and Biosecurity", + "year": 2022, + "pmid": 36573222, + "doi": "10.1016/j.jobb.2022.12.001" + }, + "metadata": { + "units": "days", + "sample_size": null, + "region": "Europe", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution" +}, +{ + "disease": "Mpox", + "pathogen": "Mpox Virus", + "epi_name": "incubation period", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 8.23, + "mean_ci_limits": [4.9, 21.4], + "mean_ci": 95, + "quantile_values": [20], + "quantile_names": ["95"] + }, + "citation": { + "author": [ + { + "given": "Fengying", + "family": "Wei" + }, + { + "given": "Zhihang", + "family": "Peng" + }, + { + "given": "Zhen", + "family": "Jin" + }, + { + "given": "Jinjie", + "family": "Wang" + }, + { + "given": "Ximing", + "family": "Xu" + }, + { + "given": "Xinyan", + "family": "Zhang" + }, + { + "given": "Jun", + "family": "Xu" + }, + { + "given": "Zixiong", + "family": "Ren" + }, + { + "given": "Yao", + "family": "Bai" + }, + { + "given": "Xiaoli", + "family": "Wang" + }, + { + "given": "Bulai", + "family": "Lu" + }, + { + "given": "Zhaojun", + "family": "Wang" + }, + { + "given": "Jianguo", + "family": "Xu" + }, + { + "given": "Senzhong", + "family": "Huang" + } + ], + "title": "Study and prediction of the 2022 global monkeypox epidemic", + "journal": "Journal of Biosafety and Biosecurity", + "year": 2022, + "pmid": 36573222, + "doi": "10.1016/j.jobb.2022.12.001" + }, + "metadata": { + "units": "days", + "sample_size": null, + "region": "Global", + "transmission_mode": "natural_unknown", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "SEIR model from 10.1016/j.mbs.2008.06.005 where the IP is assumed to follow a gamma distribution" +}, +{ + "disease": "Chikungunya", + "pathogen": "Chikungunya Virus", + "epi_name": "generation time", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 14, + "sd": 6.2 + }, + "citation": { + "author": [ + { + "given": "Henrik", + "family": "Salje" + }, + { + "given": "Simon", + "family": "Cauchemez" + }, + { + "given": "Maria Theresa", + "family": "Alera" + }, + { + "given": "Isabel", + "family": "Rodriguez-Barraquer" + }, + { + "given": "Butsaya", + "family": "Thaisomboonsuk" + }, + { + "given": "Anon", + "family": "Srikiatkhachorn" + }, + { + "given": "Catherine B.", + "family": "Lago" + }, + { + "given": "Daisy", + "family": "Villa" + }, + { + "given": "Chonticha", + "family": "Klungthong" + }, + { + "given": "Ilya A.", + "family": "Tac-An" + }, + { + "given": "Stefan", + "family": "Fernandez" + }, + { + "given": "John Mark", + "family": "Velasco" + }, + { + "given": "Vito G.", + "family": "Roque Jr" + }, + { + "given": "Ananda", + "family": "Nisalak" + }, + { + "given": "Louis R.", + "family": "Macareo" + }, + { + "given": "Jens W.", + "family": "Levy" + }, + { + "given": "Derek", + "family": "Cummings" + }, + { + "given": "In-Kyu", + "family": "Yoon" + } + ], + "title": "Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission", + "journal": "The Journal of Infectious Diseases", + "year": 2015, + "pmid": 26410592, + "doi": "10.1093/infdis/jiv470" + }, + "metadata": { + "units": "days", + "sample_size": null, + "region": "Philippines", + "transmission_mode": "vector_borne", + "vector": "mosquito", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Database entry per communication K. Charniga, Z. Cucunubá & Laura Gomez Bermeo." +}, +{ + "disease": "Chikungunya", + "pathogen": "Chikungunya Virus", + "epi_name": "generation time", + "probability_distribution": { + "prob_distribution": "gamma", + "parameters": { } + }, + "summary_statistics": { + "mean": 12.4, + "mean_ci_limits": [11.7, 13.3], + "mean_ci": 95, + "quantile_values": [5.6, 22.1], + "quantile_names": ["2.5", "97.5"] + }, + "citation": { + "author": [ + { + "given": "Giorgio", + "family": "Guzzetta" + }, + { + "given": "Francesco", + "family": "Vairo" + }, + { + "given": "Alessia", + "family": "Mammone" + }, + { + "given": "Simone", + "family": "Lanini" + }, + { + "given": "Piero", + "family": "Poletti" + }, + { + "given": "Mattia", + "family": "Manica" + }, + { + "given": "Roberto", + "family": "Rosa" + }, + { + "given": "Beniamino", + "family": "Caputo" + }, + { + "given": "Angelo", + "family": "Solimini" + }, + { + "given": "Alessandra", + "family": "della Torre" + }, + { + "given": "Paola", + "family": "Scognamiglio" + }, + { + "given": "Alimuddin", + "family": "Zumla" + }, + { + "given": "Giuseppe", + "family": "Ippolito" + }, + { + "given": "Stefano", + "family": "Merler" + } + ], + "title": "Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis", + "journal": "BMC Medicine", + "year": 2020, + "pmid": 32762750, + "doi": "10.1186/s12916-020-01674-y" + }, + "metadata": { + "units": "days", + "sample_size": 412, + "region": "Italy", + "transmission_mode": "vector_borne", + "vector": "Aedes albopictus", + "extrinsic": false, + "inference_method": "bayesian" + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": false, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "No additional notes." +}, +{ + "disease": "Chikungunya", + "pathogen": "Chikungunya Virus", + "epi_name": "case fatality risk", + "probability_distribution": { + "prob_distribution": null, + "parameters": { } + }, + "summary_statistics": { + "mean": 1.3 + }, + "citation": { + "author": [ + { + "given": "William M", + "family": "de Souza" + }, + { + "given": "Shirlene T. S.", + "family": "de Lima" + }, + { + "given": "Leda M Simões", + "family": "Mello" + }, + { + "given": "Darlan S.", + "family": "Candido" + }, + { + "given": "Lewis", + "family": "Buss" + }, + { + "given": "Charles", + "family": "Whittaker" + }, + { + "given": "Ingra M", + "family": "Claro" + }, + { + "given": "Nilani", + "family": "Chandradeva" + }, + { + "given": "Fabiana", + "family": "Granja" + }, + { + "given": "Ronaldo", + "family": "de Jesus" + }, + { + "given": "Poliana S.", + "family": "Lemos" + }, + { + "given": "Daniel A.", + "family": "Toledo-Teixeira" + }, + { + "given": "Priscilla P.", + "family": "Barbosa" + }, + { + "given": "Antonio Carlos L.", + "family": "Firmino" + }, + { + "given": "Mariene R.", + "family": "Amorim" + }, + { + "given": "Larissa M. F.", + "family": "Duarte" + }, + { + "given": "Ivan B.", + "family": "Pessoa Jr" + }, + { + "given": "Julia", + "family": "Forato" + }, + { + "given": "Irihane L.", + "family": "Vasconcelos" + }, + { + "given": "Ana Carolina B. M.", + "family": "Maximo" + }, + { + "given": "Emerson L. L.", + "family": "Araújo" + }, + { + "given": "Liana Perdigão", + "family": "Mello" + }, + { + "given": "Ester C.", + "family": "Sabino" + }, + { + "given": "José Luiz", + "family": "Proença-Módena" + }, + { + "given": "Nuno R.", + "family": "Faria" + }, + { + "given": "Scott C.", + "family": "Weaver" + } + ], + "title": "Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study", + "journal": "The Lancet Microbe", + "year": 2023, + "pmid": 37031687, + "doi": "10.1016/S2666-5247(23)00033-2" + }, + "metadata": { + "units": "deaths per 1000 cases", + "sample_size": 253545, + "region": "Brazil", + "transmission_mode": "vector_borne", + "vector": "Aedes aegypti and Aedes albopictus", + "extrinsic": false, + "inference_method": null + }, + "method_assessment": { + "truncation": null, + "discretised": false, + "censored": true, + "right_truncated": false, + "phase_bias_adjusted": false + }, + "notes": "Case fatality risk is given in deaths per 1,000 cases. It was calculated as a cumulative case fatality ratio. CFR is a population-wide estimate. Odds of chikungunya-related death were not significantly different between males and females. Odds of chikungunya-related death were significantly higher for 55-74 years old, and >75 years old compared to <18." +} +] From f772f9af08cad016058b2ef02d727f3e871c0c5b Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:56:54 +0000 Subject: [PATCH 13/48] update documentation --- man/dot-cite_author.Rd | 21 +++++++++++++++++++++ man/dot-is_pkg_installed.Rd | 22 ++++++++++++++++++++++ man/dot-read_db.Rd | 17 +++++++++++++++++ man/epiparameterDB-package.Rd | 29 +++++++++++++++++++++++++++++ man/epiparameterDB.Rd | 22 ++++++++++++++++++++++ man/packagetemplate-package.Rd | 28 ---------------------------- 6 files changed, 111 insertions(+), 28 deletions(-) create mode 100644 man/dot-cite_author.Rd create mode 100644 man/dot-is_pkg_installed.Rd create mode 100644 man/dot-read_db.Rd create mode 100644 man/epiparameterDB-package.Rd create mode 100644 man/epiparameterDB.Rd delete mode 100644 man/packagetemplate-package.Rd diff --git a/man/dot-cite_author.Rd b/man/dot-cite_author.Rd new file mode 100644 index 0000000..92ac34d --- /dev/null +++ b/man/dot-cite_author.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{.cite_author} +\alias{.cite_author} +\title{Format author names for short citation from epidemiological parameter +database} +\usage{ +.cite_author(x) +} +\arguments{ +\item{x}{A single \code{list} entry from the list of epidemiological parameter +database.} +} +\value{ +A \code{character} string with the short citation. +} +\description{ +Format author names for short citation from epidemiological parameter +database +} +\keyword{internal} diff --git a/man/dot-is_pkg_installed.Rd b/man/dot-is_pkg_installed.Rd new file mode 100644 index 0000000..eba7403 --- /dev/null +++ b/man/dot-is_pkg_installed.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read.R +\name{.is_pkg_installed} +\alias{.is_pkg_installed} +\title{Check whether a package is installed} +\usage{ +.is_pkg_installed(package) +} +\arguments{ +\item{package}{string naming the package/name space to load.} +} +\value{ +Invisibly returns a boolean \code{logical}. +} +\description{ +Check whether a package is installed +} +\details{ +This functions allows testing for when a suggested package +dependency is not installed to check if conditional code can be run. +} +\keyword{internal} diff --git a/man/dot-read_db.Rd b/man/dot-read_db.Rd new file mode 100644 index 0000000..cd3696e --- /dev/null +++ b/man/dot-read_db.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read.R +\name{.read_db} +\alias{.read_db} +\title{Reads in parameter library from JSON} +\usage{ +.read_db() +} +\value{ +\code{list}. +} +\description{ +Read epidemiological parameter database from JSON using +\code{\link[jsonlite:read_json]{jsonlite::read_json()}} and returns the list with a \verb{} +class attribute to validate it has been read using this function. +} +\keyword{internal} diff --git a/man/epiparameterDB-package.Rd b/man/epiparameterDB-package.Rd new file mode 100644 index 0000000..2853abd --- /dev/null +++ b/man/epiparameterDB-package.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/package.R +\docType{package} +\name{epiparameterDB-package} +\alias{epiparameterDB-package} +\title{epiparameterDB: Database of epidemiological parameters} +\description{ +Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) \doi{10.5281/zenodo.6619350}. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/epiverse-trace/epiparameterDB/} + \item \url{https://epiverse-trace.github.io/epiparameterDB/} + \item Report bugs at \url{https://github.com/epiverse-trace/epiparameterDB/issues} +} + +} +\author{ +\strong{Maintainer}: Joshua W. Lambert \email{joshua.lambert@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5218-3046}{ORCID}) [copyright holder] + +Authors: +\itemize{ + \item Adam Kucharski \email{adam.kucharski@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-8814-9421}{ORCID}) + \item Carmen Tamayo \email{carmen.tamayo-cuartero@lshtm.ac.uk} (\href{https://orcid.org/0000-0003-4184-2864}{ORCID}) +} + +} +\keyword{internal} diff --git a/man/epiparameterDB.Rd b/man/epiparameterDB.Rd new file mode 100644 index 0000000..abb35f9 --- /dev/null +++ b/man/epiparameterDB.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{epiparameterDB} +\alias{epiparameterDB} +\title{A list of epidemiological parameters.} +\format{ +\subsection{\code{epiparameterDB}}{ + +A \code{list} of epidemiological parameters read from \code{extdata/parameters.json} +with 125 database entries. The object +is tagged with the class attribute \verb{} to validate the +parameter library has been loaded using the \code{{epiparameterDB}} package. +} +} +\usage{ +epiparameterDB +} +\description{ +A list of epidemiological parameters. +} +\keyword{datasets} diff --git a/man/packagetemplate-package.Rd b/man/packagetemplate-package.Rd deleted file mode 100644 index 8499b1b..0000000 --- a/man/packagetemplate-package.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/package.R -\docType{package} -\name{packagetemplate-package} -\alias{packagetemplate} -\alias{packagetemplate-package} -\title{packagetemplate: Your Package Title in Titlecase} -\description{ -Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) \doi{10.5281/zenodo.6619350}. -} -\author{ -\strong{Maintainer}: Hugo Gruson \email{hugo@data.org} (\href{https://orcid.org/0000-0002-4094-1476}{ORCID}) - -Authors: -\itemize{ - \item James M. Azam \email{james.azam@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5782-7330}{ORCID}) - \item Pratik Gupte \email{pratik.gupte@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5294-7819}{ORCID}) - \item Joshua W. Lambert \email{joshua.lambert@lshtm.ac.uk} (\href{https://orcid.org/0000-0001-5218-3046}{ORCID}) - \item Karim Mané \email{karim.mane@lshtm.ac.uk} (\href{https://orcid.org/0000-0002-9892-2999}{ORCID}) -} - -Other contributors: -\itemize{ - \item Jaime A. Pavlich-Mariscal \email{jpavlich@javeriana.edu.co} (\href{https://orcid.org/0000-0002-3892-6680}{ORCID}) [contributor] -} - -} -\keyword{internal} From dc76fc382413e3635bd601dcceda5b31075e9079 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:57:25 +0000 Subject: [PATCH 14/48] added unit tests for internal functions --- tests/testthat.R | 4 ++-- tests/testthat/test-read.R | 23 +++++++++++++++++++++++ tests/testthat/test-utils.R | 19 +++++++++++++++++++ 3 files changed, 44 insertions(+), 2 deletions(-) create mode 100644 tests/testthat/test-read.R create mode 100644 tests/testthat/test-utils.R diff --git a/tests/testthat.R b/tests/testthat.R index df57fd9..cc0453c 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -7,6 +7,6 @@ # * https://testthat.r-lib.org/articles/special-files.html library(testthat) -library(packagetemplate) +library(epiparameterDB) -test_check("packagetemplate", stop_on_warning = FALSE) +test_check("epiparameterDB", stop_on_warning = FALSE) diff --git a/tests/testthat/test-read.R b/tests/testthat/test-read.R new file mode 100644 index 0000000..12bb17f --- /dev/null +++ b/tests/testthat/test-read.R @@ -0,0 +1,23 @@ +test_that(".read_db works as expected when jsonlite is installed", { + db <- .read_db() + expect_s3_class(db, class = "epiparameterDB") + expect_type(db, type = "list") + expect_length(db, 125) +}) + + +test_that(".read_db fails correctly when jsonlite is not installed", { + with_mocked_bindings( + .is_pkg_installed = function(package) FALSE, + code = expect_error( + .read_db(), + regexp = + "Cannot use this internal function without \\{jsonlite\\} installed" # nolint file.path + ) + ) +}) + +test_that(".is_pkg_installed works as expected", { + expect_true(.is_pkg_installed(package = "distributional")) + expect_false(.is_pkg_installed(package = "jsonlit")) +}) diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R new file mode 100644 index 0000000..8f24889 --- /dev/null +++ b/tests/testthat/test-utils.R @@ -0,0 +1,19 @@ +{ + db <- .read_db() +} + +test_that(".cite_author works as expected for 1 author", { + expect_identical(.cite_author(db[[27]]), "Pavlin") +}) + +test_that(".cite_author works as expected for 2 authors", { + expect_identical(.cite_author(db[[15]]), "Nishiura & Inaba") +}) + +test_that(".cite_author works as expected for > 2 authors", { + expect_identical(.cite_author(db[[1]]), "Lessler et al.") +}) + +test_that(".cite_author works as expected for org author", { + expect_identical(.cite_author(db[[64]]), "The Ebola Outbreak Epidemiology Team et al.") +}) From f7c80c982a3c834a6988d635dc258c5823147246 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:57:43 +0000 Subject: [PATCH 15/48] write design-principles vignette for {epiparameterDB} --- vignettes/design-principles.Rmd | 38 ++++++++++++++++++++------------- 1 file changed, 23 insertions(+), 15 deletions(-) diff --git a/vignettes/design-principles.Rmd b/vignettes/design-principles.Rmd index 1bdf189..b10e64f 100644 --- a/vignettes/design-principles.Rmd +++ b/vignettes/design-principles.Rmd @@ -1,8 +1,8 @@ --- -title: "Design Principles for {packagetemplate}" +title: "Design Principles for {epiparameterDB}" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Design Principles for {packagetemplate}} + %\VignetteIndexEntry{Design Principles for {epiparameterDB}} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- @@ -14,35 +14,43 @@ knitr::opts_chunk$set( ) ``` -This vignette outlines the design decisions that have been taken during the development of the `{packagetemplate}` R package, and provides some of the reasoning, and possible pros and cons of each decision. +This vignette outlines the design decisions that have been taken during the development of the `{epiparameterDB}` R package, and provides some of the reasoning, and possible pros and cons of each decision. This document is primarily intended to be read by those interested in understanding the code within the package and for potential package contributors. - - ## Scope -< Outline the aims of the package, potentially mention some of the key exported functions, and maybe how it links with other R packages. It is also possible to mention certain aspects that fall outside of the package's scope. > - -## Naming conventions +`{epiparameterDB}` provides a database of epidemiological parameters available in R. It is the data component of the `{epiparameter}` R package, and is in a separate R package to appropriately license the data (stored in this package) and the code for working with epidemiological parameters (stored in `{epiparameter}`). -< Description of the scheme and/or conventions used for naming functions and arguments. This can be the use of a prefix on all exported functions, a name mould ("all function are named verb_object"), or any other naming convention that is used throughout the package. > +This R package only exports data, it does not export any R functions. It contains a few internal functions that are used for data processing and vignettes. ## Input/Output/Interoperability -< Describe the data structures (i.e. vectors, `` or classes) that are given as input to the key functions and what data structures the functions return. The design decisions around these I/O choices could also mention how it enhances interoperability with other R packages or pipelines (e.g. with `%>%`). > +The epidemiological parameter database is exported by the package as `epiparameterDB::epiparameterDB`. The `epiparameterDB` data object is a list for flexible hierarchical parameter data. +The raw epidemiological parameter data is stored within this package as a `.json` file to enable structured and nested data objects and the file is read into R using `jsonlite::read_json()` in the `.read_db()` internal function. + +The `epiparameterDB` data object is then used within the `{epiparameter}` package and converted to a list of `` objects, with a `` class attribute to enable custom methods for multiple `` objects. This conversion and class specification all takes place in `{epiparameter}` to prevent duplicating code across packages and to keep `{epiparameterDB}` to remain a minimal and data-focused as possible. ## Design decisions -< A list of bullet points each explaining a design decision and its reasoning. > +* The package exports the raw JSON list not a `` formatted object due to the dependencies (e.g. `{distributional}` and `{checkmate}`) and `{epiparameter}` functions (e.g. `create_prob_distribution()`). + +- `.cite_author()` is a simpler version of the internal `.citet()` function in `{epiparameter}`. In `{epiparameterDB}` the parameter database is validated by the `json-validate.yaml` workflow so the format is consistent and the individual elements for the short citation in the `database.Rmd` vignette can be extracted and only the author formatting needs to be packaged into a function. + +- the `` class attribute attached to the epidemiological parameter list is to ensure the `parameters.json` file has been read using `.read_db()` and suggests the file has not be read or invalidated using other functions. It has no role in for object-oriented programming (e.g. class methods). ## Dependencies -< A list of dependencies used by the package with some explanation as to why they are required. Not all dependencies need to be explained and it is best to explain the key dependencies. It can be used to give context to why certain dependencies are used (e.g. "This package is expected to be used in tidyverse pipelines and as such, we consider these tidyverse packages good dependencies that will already be installed on a user's computer."). This section can also mention dependencies that are planned to be removed or added in future development. Suggested dependencies do not need to be explained unless they are unusual and may surprise developers with their inclusion. > +The `{epiparameterDB}` package has no imported (i.e. hard) dependencies. It is a data package and does not require any imported functionality. + +There are a handful of suggested (i.e. soft) dependencies. These enable the data to be read from file and to render the vignettes. + +* [`{jsonlite}`](https://CRAN.R-project.org/package=jsonlite): used by `.read_db()` to load the `parameters.json` parameter library into memory. +* [`{DT}`](https://CRAN.R-project.org/package=DT): used by the `database.Rmd` to render a [`DataTables`](https://datatables.net/) on the vignette. + +There are some additional suggested dependencies for vignette rendering and testing the package: `{knitr}`, `{rmarkdown}`, `{spelling}`, `{testthat}`. ## Development journey -< If the package has undergone any large refactoring this section can be used to explain the changes. > +The data exported in this package was original included in the `{epiparameter}` R package. Due to CRAN regulations, it was not possible to dual license `{epiparameter}` with MIT and CC0 for the code and data respectively. Therefore, `{epiparameterDB}` is the data storage and distribution component of the `{epiparameter}` project. From 15ba1b73eb08fdba5125e1049019dbcbf6b6a31c Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:57:52 +0000 Subject: [PATCH 16/48] add database.Rmd vignette --- vignettes/database.Rmd | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 vignettes/database.Rmd diff --git a/vignettes/database.Rmd b/vignettes/database.Rmd new file mode 100644 index 0000000..b3bcd19 --- /dev/null +++ b/vignettes/database.Rmd @@ -0,0 +1,39 @@ +--- +title: "Current database" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Current database} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r echo = FALSE} +library("DT") +library("epiparameterDB") + +db <- epiparameterDB:::.read_db() +tbl <- lapply(db, function(x) { + data.frame( + disease = x$disease, + pathogen = x$pathogen, + epi_name = x$epi_name, + citation_info = paste0( + epiparameterDB:::.cite_author(x), # nolint undesirable_operator_linter + "(", x$citation$year, ")", + ", DOI: ", + "", + x$citation$doi, "" + ) + ) +}) +tb <- do.call(rbind, tbl) +## sort by disease then pathogen +tb <- tb[order(tb$disease, tb$pathogen), ] +datatable( + tb, + rownames = FALSE, + colnames = c("Disease", "Pathogen", "Distribution", "Reference"), + escape = FALSE, + options = list(pageLength = 50) +) +``` From c241ae630a08f3d84060d2ab7a22f5a0841bfcc6 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:58:10 +0000 Subject: [PATCH 17/48] add data-raw to .Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index bfe7068..23265c8 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ ^docs$ ^pkgdown$ ^tools$ +^data-raw$ From 7632bd6820cceb7ccbff7383b3badc0f17060f3f Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:58:24 +0000 Subject: [PATCH 18/48] add .Rproj --- epiparameterDB.Rproj | 19 +++++++++++++++++++ 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z#(A6GY0EZ-h16JZxg`OZw%j;tzqcCFk%snzYTIGyN@J+Ax5bP1H8XHrV-wf%2#B1Z7V*eQHX(de@sL4)=|bxqQf{daN^@#x(r z`Q$+ueBSE*iJKCleOupI{WS|a291coLPng%si z!{VbTZtS_Gzi%>Y{j+QX6@NSiGSd9eh+eYs$zCkWLprkQZPVM3?|t;>{D7i*X5scF zCG-`94(qqqs_yxV_q?W>6B+Rz9XMluK3* zJ3$EPlsi`pFEja}`|5wC6Xb&W%Lm27D$qZ^kDv-0vk25{MR8Y;CCkGU|9WeN2eRI^ zZbtpTcc9|XnQ~4I2{1iiSCfVcTU}j^?)nU5(5T#%pPjr3Mf`U`=t7`pj@E_^0b#pN m2+{uk?SJ_U+ze|vr|t;rxnz=j4si$o6rZU+EtfNW{eJ-L*ShTh literal 0 HcmV?d00001 From f80eb3859eb436e076fff0afcc8a45eaa132ab32 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:58:45 +0000 Subject: [PATCH 20/48] add validate-json GHA workflow --- .github/workflows/validate-json.yaml | 47 ++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 .github/workflows/validate-json.yaml diff --git a/.github/workflows/validate-json.yaml b/.github/workflows/validate-json.yaml new file mode 100644 index 0000000..4c7766a --- /dev/null +++ b/.github/workflows/validate-json.yaml @@ -0,0 +1,47 @@ +name: Validate JSONs + +on: + push: + branches: [main, master] + paths: + - 'R/sysdata.rda' + - 'inst/extdata/**' + - 'data-raw/parameters.R' + - '.github/workflows/validate-json.yaml' + merge_group: + pull_request: + paths: + - 'R/sysdata.rda' + - 'inst/extdata/**' + - 'data-raw/parameters.R' + - '.github/workflows/validate-json.yaml' + +jobs: + validate-json: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + packages: + any::jsonvalidate + + - name: Validate JSON + run: | + jsonvalidate::json_validate( + json = file.path("inst", "extdata", "parameters.json"), + schema = file.path("inst", "extdata", "data_dictionary.json"), + engine = "ajv", + verbose = TRUE, + greedy = TRUE, + strict = FALSE, + error = TRUE + ) + shell: Rscript {0} From 58ff04321c5cdf18c6f59ffe181ca947fc84ad6b Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 12:58:54 +0000 Subject: [PATCH 21/48] update WORDLIST --- inst/WORDLIST | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index ad08587..65c8e9f 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,21 +1,9 @@ CMD Codecov Epiverse +Lassa Lifecycle -Mariscal ORCID -Pavlich -RECON -Titlecase -codecov -com +SARS doi -gh -github -io -lifecycle -packagename -svg -tidyverse -yaml zenodo From 85c6e3cdfc9d6630d7fdc950c2034b30d8ae3a4a Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 28 Oct 2024 13:01:20 +0000 Subject: [PATCH 22/48] Automatic readme update --- README.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 7a36d69..8bb7f31 100644 --- a/README.md +++ b/README.md @@ -103,20 +103,21 @@ languages, but also differs from them in the following aspects: ``` r citation("epiparameterDB") -#> #> To cite package 'epiparameterDB' in publications use: #> -#> Lambert J, Kucharski A, Tamayo C (????). _epiparameterDB: Database of -#> epidemiological parameters_. -#> https://github.com/epiverse-trace/epiparameterDB/, -#> https://epiverse-trace.github.io/epiparameterDB/. +#> Lambert J, Kucharski A, Tamayo C (2024). _epiparameterDB: Database of +#> epidemiological parameters_. R package version 0.0.0.9000, +#> https://epiverse-trace.github.io/epiparameterDB/, +#> . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {epiparameterDB: Database of epidemiological parameters}, #> author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo}, -#> note = {https://github.com/epiverse-trace/epiparameterDB/, +#> year = {2024}, +#> note = {R package version 0.0.0.9000, #> https://epiverse-trace.github.io/epiparameterDB/}, +#> url = {https://github.com/epiverse-trace/epiparameterDB/}, #> } ``` From 4a233eb0d65131964ce3287b22a160ea3bb0ea38 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 13:12:31 +0000 Subject: [PATCH 23/48] add articles to _pkgdown.yml --- _pkgdown.yml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index 387754d..8c645d4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -10,3 +10,15 @@ reference: desc: Data stored in the package contents: - epiparameterDB + +articles: + +- title: Parameter library + navbar: Epiparameter Data + contents: + - database + +- title: Developer Documentation + navbar: Developer Documentation + contents: + - design-principles From d240917ef8048563f53d49e4031c147e30da8c2f Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 13:15:10 +0000 Subject: [PATCH 24/48] use exported data directly in database.Rmd --- vignettes/database.Rmd | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/vignettes/database.Rmd b/vignettes/database.Rmd index b3bcd19..8ace812 100644 --- a/vignettes/database.Rmd +++ b/vignettes/database.Rmd @@ -11,8 +11,7 @@ vignette: > library("DT") library("epiparameterDB") -db <- epiparameterDB:::.read_db() -tbl <- lapply(db, function(x) { +tbl <- lapply(epiparameterDB::epiparameterDB, function(x) { data.frame( disease = x$disease, pathogen = x$pathogen, From b27de62ffc85e56b5c6304759b6cd61df258d773 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 13:16:57 +0000 Subject: [PATCH 25/48] fix typo in .read_db --- R/read.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/read.R b/R/read.R index 8681f48..39c73ec 100644 --- a/R/read.R +++ b/R/read.R @@ -20,7 +20,7 @@ path = system.file( "extdata", "parameters.json", - package = "epiparameter", + package = "epiparameterDB", mustWork = TRUE ) ) From 5fdf287053bb9ec3eb55da3336c26b5816f06ea6 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 13:17:21 +0000 Subject: [PATCH 26/48] use R recommended package to test .is_pkg_installed --- tests/testthat/test-read.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-read.R b/tests/testthat/test-read.R index 12bb17f..8ae5bab 100644 --- a/tests/testthat/test-read.R +++ b/tests/testthat/test-read.R @@ -18,6 +18,6 @@ test_that(".read_db fails correctly when jsonlite is not installed", { }) test_that(".is_pkg_installed works as expected", { - expect_true(.is_pkg_installed(package = "distributional")) + expect_true(.is_pkg_installed(package = "methods")) expect_false(.is_pkg_installed(package = "jsonlit")) }) From cc6b2ad8fc1885925ebabf499fd8bdaffc49027d Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 13:21:59 +0000 Subject: [PATCH 27/48] remove old use_data call from data-raw/parameters.R --- data-raw/parameters.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/data-raw/parameters.R b/data-raw/parameters.R index 20f51e4..90aaa6c 100644 --- a/data-raw/parameters.R +++ b/data-raw/parameters.R @@ -1,5 +1,3 @@ -usethis::use_data(parameters, overwrite = TRUE) - ## code to prepare `parameters` dataset goes here epiparameterDB <- epiparameterDB:::.read_db() From 27eff09e177b7dc94f328725f009cf8660fbe0c4 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 15:34:57 +0000 Subject: [PATCH 28/48] add pkg logo --- man/figures/logo.svg | 4756 ++++++++++++++++++++++++++++-------------- 1 file changed, 3179 insertions(+), 1577 deletions(-) diff --git a/man/figures/logo.svg b/man/figures/logo.svg index b1a2f55..211029d 100644 --- a/man/figures/logo.svg +++ b/man/figures/logo.svg @@ -1,8 +1,61 @@ - + - - From 3e1556a42c48205612b5f1aabbf8891cec6094b8 Mon Sep 17 00:00:00 2001 From: Joshua 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a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..8c6f45f --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,165 @@ +# -------------------------------------------- +# CITATION file created with {cffr} R package +# See also: https://docs.ropensci.org/cffr/ +# -------------------------------------------- + +cff-version: 1.2.0 +message: 'To cite package "epiparameterDB" in publications use:' +type: software +license: CC0-1.0 +title: 'epiparameterDB: Database of epidemiological parameters' +version: 0.0.0.9000 +identifiers: +- type: url + value: https://epiverse-trace.github.io/epiparameterDB/ +abstract: 'Your package description. It must end with a period (".") and include relevant + bibliographical references if applicable, using the following format: Author et + al. (2023) .' +authors: +- family-names: Lambert + given-names: Joshua W. + email: joshua.lambert@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-5218-3046 +- family-names: Kucharski + given-names: Adam + email: adam.kucharski@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-8814-9421 +- family-names: Tamayo + given-names: Carmen + email: carmen.tamayo-cuartero@lshtm.ac.uk + orcid: https://orcid.org/0000-0003-4184-2864 +repository-code: https://github.com/epiverse-trace/epiparameterDB +url: https://github.com/epiverse-trace/epiparameterDB/ +contact: +- family-names: Lambert + given-names: Joshua W. + email: joshua.lambert@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-5218-3046 +references: +- type: software + title: 'R: A Language and Environment for Statistical Computing' + notes: Depends + url: https://www.R-project.org/ + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' + version: '>= 4.0.0' +- type: software + title: DT + abstract: 'DT: A Wrapper of the JavaScript Library ''DataTables''' + notes: Suggests + url: https://github.com/rstudio/DT + repository: https://CRAN.R-project.org/package=DT + authors: + - family-names: Xie + given-names: Yihui + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Tan + given-names: Xianying + year: '2024' + doi: 10.32614/CRAN.package.DT +- type: software + title: jsonlite + abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R' + notes: Suggests + url: https://jeroen.r-universe.dev/jsonlite + repository: https://CRAN.R-project.org/package=jsonlite + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroenooms@gmail.com + orcid: https://orcid.org/0000-0002-4035-0289 + year: '2024' + doi: 10.32614/CRAN.package.jsonlite +- type: software + title: knitr + abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R' + notes: Suggests + url: https://yihui.org/knitr/ + repository: https://CRAN.R-project.org/package=knitr + authors: + - family-names: Xie + given-names: Yihui + email: xie@yihui.name + orcid: https://orcid.org/0000-0003-0645-5666 + year: '2024' + doi: 10.32614/CRAN.package.knitr +- type: software + title: rmarkdown + abstract: 'rmarkdown: Dynamic Documents for R' + notes: Suggests + url: https://pkgs.rstudio.com/rmarkdown/ + repository: https://CRAN.R-project.org/package=rmarkdown + authors: + - family-names: Allaire + given-names: JJ + email: jj@posit.co + - family-names: Xie + given-names: Yihui + email: xie@yihui.name + orcid: https://orcid.org/0000-0003-0645-5666 + - family-names: Dervieux + given-names: Christophe + email: cderv@posit.co + orcid: https://orcid.org/0000-0003-4474-2498 + - family-names: McPherson + given-names: Jonathan + email: jonathan@posit.co + - family-names: Luraschi + given-names: Javier + - family-names: Ushey + given-names: Kevin + email: kevin@posit.co + - family-names: Atkins + given-names: Aron + email: aron@posit.co + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Chang + given-names: Winston + email: winston@posit.co + - family-names: Iannone + given-names: Richard + email: rich@posit.co + orcid: https://orcid.org/0000-0003-3925-190X + year: '2024' + doi: 10.32614/CRAN.package.rmarkdown +- type: software + title: spelling + abstract: 'spelling: Tools for Spell Checking in R' + notes: Suggests + url: https://ropensci.r-universe.dev/spelling + repository: https://CRAN.R-project.org/package=spelling + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroenooms@gmail.com + orcid: https://orcid.org/0000-0002-4035-0289 + - family-names: Hester + given-names: Jim + email: james.hester@rstudio.com + year: '2024' + doi: 10.32614/CRAN.package.spelling +- type: software + title: testthat + abstract: 'testthat: Unit Testing for R' + notes: Suggests + url: https://testthat.r-lib.org + repository: https://CRAN.R-project.org/package=testthat + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2024' + doi: 10.32614/CRAN.package.testthat + version: '>= 3.0.0' + From e5e719f9809382decc57fa9a8b3a524db12ad928 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 25 Oct 2024 15:00:20 +0000 Subject: [PATCH 32/48] Bump untitaker/hyperlink from 0.1.32 to 0.1.35 Bumps [untitaker/hyperlink](https://github.com/untitaker/hyperlink) from 0.1.32 to 0.1.35. - [Release notes](https://github.com/untitaker/hyperlink/releases) - [Commits](https://github.com/untitaker/hyperlink/compare/0.1.32...0.1.35) --- updated-dependencies: - dependency-name: untitaker/hyperlink dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index bd7259c..08f7a23 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -72,7 +72,7 @@ jobs: shell: Rscript {0} - name: Check website links - uses: untitaker/hyperlink@0.1.32 + uses: untitaker/hyperlink@0.1.35 with: args: docs/ From 81b714021cf52ce75880d154068fd908415bac20 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 16:06:14 +0000 Subject: [PATCH 33/48] bump to version 0.1.0 --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c1a15dd..eaca1fd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: epiparameterDB Title: Database of epidemiological parameters -Version: 0.0.0.9000 +Version: 0.1.0 Authors@R: c( person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = c("cre", "aut", "cph"), comment = c(ORCID = "0000-0001-5218-3046")), diff --git a/NEWS.md b/NEWS.md index 8c2a2e2..6d39969 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# epiparameterDB (development version) +# epiparameterDB 0.1.0 This is the first minor release of the `{epiparameterDB}` R package. It contains the epidemiological parameter database originally part of the `{epiparameter}` R package. From d070acfffbe806861d4a8eaa3a4bf9ea5a04961f Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 16:27:20 +0000 Subject: [PATCH 34/48] remove LICENSE file --- DESCRIPTION | 2 +- LICENSE | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) delete mode 100644 LICENSE diff --git a/DESCRIPTION b/DESCRIPTION index eaca1fd..3f766dd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,7 +12,7 @@ Authors@R: c( Description: Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) . -License: CC0 + file LICENSE +License: CC0 URL: https://github.com/epiverse-trace/epiparameterDB/, https://epiverse-trace.github.io/epiparameterDB/ BugReports: https://github.com/epiverse-trace/epiparameterDB/issues diff --git a/LICENSE b/LICENSE deleted file mode 100644 index ae90a21..0000000 --- a/LICENSE +++ /dev/null @@ -1,2 +0,0 @@ -YEAR: 2024 -COPYRIGHT HOLDER: epiparameterDB authors From 402b52448a56dc431de78b6c16ad165a1022f59b Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Mon, 28 Oct 2024 16:40:45 +0000 Subject: [PATCH 35/48] bump untitaker/hyperlink in pkgdown workflow --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 08f7a23..e6a2977 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -72,7 +72,7 @@ jobs: shell: Rscript {0} - name: Check website links - uses: untitaker/hyperlink@0.1.35 + uses: untitaker/hyperlink@0.1.40 with: args: docs/ From 761d8566ebcc211a3605141479e6271f2320ac88 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Wed, 20 Nov 2024 15:16:43 +0000 Subject: [PATCH 36/48] bump action versions in pkgdown workflow --- .github/workflows/pkgdown.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index e6a2977..5b2272f 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -72,13 +72,13 @@ jobs: shell: Rscript {0} - name: Check website links - uses: untitaker/hyperlink@0.1.40 + uses: untitaker/hyperlink@0.1.43 with: args: docs/ - name: Deploy to GitHub pages 🚀 if: github.event_name != 'merge_group' && github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.6.8 + uses: JamesIves/github-pages-deploy-action@v4.6.9 with: # We clean on releases because we want to remove old vignettes, # figures, etc. that have been deleted from the `main` branch. From 6695bd973aafafc125e7f548dce57fe2005dbdba Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Wed, 20 Nov 2024 15:32:01 +0000 Subject: [PATCH 37/48] run `pkgdown::build_favicons(overwrite = TRUE)` with {pkgdown} v2.1.1 --- pkgdown/favicon/favicon.svg | 1534 +++++++++++++++++------------------ 1 file changed, 767 insertions(+), 767 deletions(-) diff --git a/pkgdown/favicon/favicon.svg b/pkgdown/favicon/favicon.svg index 9f52ee6..5dad12f 100644 --- a/pkgdown/favicon/favicon.svg +++ b/pkgdown/favicon/favicon.svg @@ -1,5 +1,5 @@ - - \ No newline at end of file From fe9065402204bcab975ec2589abd5f469910f7ae Mon Sep 17 00:00:00 2001 From: joshwlambert <46606402+joshwlambert@users.noreply.github.com> Date: Wed, 20 Nov 2024 16:33:49 +0000 Subject: [PATCH 38/48] Update `CITATION.cff` --- CITATION.cff | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 8c6f45f..f2cd7ad 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,7 @@ message: 'To cite package "epiparameterDB" in publications use:' type: software license: CC0-1.0 title: 'epiparameterDB: Database of epidemiological parameters' -version: 0.0.0.9000 +version: 0.1.0 identifiers: - type: url value: https://epiverse-trace.github.io/epiparameterDB/ @@ -35,6 +35,12 @@ contact: given-names: Joshua W. email: joshua.lambert@lshtm.ac.uk orcid: https://orcid.org/0000-0001-5218-3046 +keywords: +- data-package +- epidemiology +- epiverse +- r +- r-package references: - type: software title: 'R: A Language and Environment for Statistical Computing' From d207f344dc4fd983ffdb69011e7f4076d5d87115 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:06:33 +0000 Subject: [PATCH 39/48] add package Description to DESCRIPTION file --- DESCRIPTION | 6 +++--- man/epiparameterDB-package.Rd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3f766dd..2c60162 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,9 +9,9 @@ Authors@R: c( person("Carmen", "Tamayo", , "carmen.tamayo-cuartero@lshtm.ac.uk", role = "aut", comment = c(ORCID = "0000-0003-4184-2864")) ) -Description: Your package description. It must end with a period (".") and - include relevant bibliographical references if applicable, using the - following format: Author et al. (2023) . +Description: A data package containing a database of epidemiological + parameters. It stores the data for the {epiparameter} R package. + Epidemiological parameter estimates are extracted from the literature. License: CC0 URL: https://github.com/epiverse-trace/epiparameterDB/, https://epiverse-trace.github.io/epiparameterDB/ diff --git a/man/epiparameterDB-package.Rd b/man/epiparameterDB-package.Rd index 2853abd..f890e0a 100644 --- a/man/epiparameterDB-package.Rd +++ b/man/epiparameterDB-package.Rd @@ -5,7 +5,7 @@ \alias{epiparameterDB-package} \title{epiparameterDB: Database of epidemiological parameters} \description{ -Your package description. It must end with a period (".") and include relevant bibliographical references if applicable, using the following format: Author et al. (2023) \doi{10.5281/zenodo.6619350}. +A data package containing a database of epidemiological parameters. It stores the data for the {epiparameter} R package. Epidemiological parameter estimates are extracted from the literature. } \seealso{ Useful links: From 6099017930b77b1c11fb4bd86331eef1fcda2b38 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:11:05 +0000 Subject: [PATCH 40/48] update WORDLIST --- inst/WORDLIST | 1 + 1 file changed, 1 insertion(+) diff --git a/inst/WORDLIST b/inst/WORDLIST index 65c8e9f..f9d2981 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,5 +1,6 @@ CMD Codecov +epiparameter Epiverse Lassa Lifecycle From 70c00a3301ca76a9c551917ca27627c51dbe6454 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:16:42 +0000 Subject: [PATCH 41/48] use single quotes instead of curly bracket for package name in DESCRIPTION --- DESCRIPTION | 2 +- man/epiparameterDB-package.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2c60162..aa1ab12 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,7 @@ Authors@R: c( comment = c(ORCID = "0000-0003-4184-2864")) ) Description: A data package containing a database of epidemiological - parameters. It stores the data for the {epiparameter} R package. + parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature. License: CC0 URL: https://github.com/epiverse-trace/epiparameterDB/, diff --git a/man/epiparameterDB-package.Rd b/man/epiparameterDB-package.Rd index f890e0a..b3b6ff7 100644 --- a/man/epiparameterDB-package.Rd +++ b/man/epiparameterDB-package.Rd @@ -5,7 +5,7 @@ \alias{epiparameterDB-package} \title{epiparameterDB: Database of epidemiological parameters} \description{ -A data package containing a database of epidemiological parameters. It stores the data for the {epiparameter} R package. Epidemiological parameter estimates are extracted from the literature. +A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature. } \seealso{ Useful links: From 57051b1c6ea8253ff8b02efe5e765b3e7b5f2fc2 Mon Sep 17 00:00:00 2001 From: joshwlambert <46606402+joshwlambert@users.noreply.github.com> Date: Thu, 21 Nov 2024 14:24:43 +0000 Subject: [PATCH 42/48] Update `CITATION.cff` --- CITATION.cff | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index f2cd7ad..28f4cdd 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -12,9 +12,9 @@ version: 0.1.0 identifiers: - type: url value: https://epiverse-trace.github.io/epiparameterDB/ -abstract: 'Your package description. It must end with a period (".") and include relevant - bibliographical references if applicable, using the following format: Author et - al. (2023) .' +abstract: A data package containing a database of epidemiological parameters. It stores + the data for the 'epiparameter' R package. Epidemiological parameter estimates are + extracted from the literature. authors: - family-names: Lambert given-names: Joshua W. From 6fdb9219b9aa162d9ffd3c7f822d27672b1e8efa Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:24:43 +0000 Subject: [PATCH 43/48] add cran-comments --- .Rbuildignore | 1 + cran-comments.md | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index 23265c8..02d388c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -14,3 +14,4 @@ ^pkgdown$ ^tools$ ^data-raw$ +^cran-comments\.md$ diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..858617d --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. From c7050936409ecfaf73a82cb1e465db26a35dbdaa Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:25:55 +0000 Subject: [PATCH 44/48] add CRAN install instructions to README --- README.Rmd | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.Rmd b/README.Rmd index 2b6113b..88e2951 100644 --- a/README.Rmd +++ b/README.Rmd @@ -36,6 +36,12 @@ using this package. `epiparameter::epiparameter_db()` function formats the epide ## Installation +You can install `{epiparameterDB}` from CRAN with: + +``` r +install.packages("epiparameterDB") +``` + You can install the development version of `{epiparameterDB}` from [GitHub](https://github.com/) with: From f596a3f1158a42efc3f91d073ff314fd68af554b Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:26:41 +0000 Subject: [PATCH 45/48] remove extra whitespace from DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index aa1ab12..bedfb8b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,7 @@ Authors@R: c( comment = c(ORCID = "0000-0003-4184-2864")) ) Description: A data package containing a database of epidemiological - parameters. It stores the data for the 'epiparameter' R package. + parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature. License: CC0 URL: https://github.com/epiverse-trace/epiparameterDB/, From cc4492ef7221d80bad4acb1c6299395df73adc29 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 14:34:01 +0000 Subject: [PATCH 46/48] change Title in DESCRIPTION to title case --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bedfb8b..b9ca1f2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: epiparameterDB -Title: Database of epidemiological parameters +Title: Database of Epidemiological Parameters Version: 0.1.0 Authors@R: c( person("Joshua W.", "Lambert", , "joshua.lambert@lshtm.ac.uk", role = c("cre", "aut", "cph"), From e83f68411aabd44789471c2ce169447f05f4a0b1 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 21 Nov 2024 16:18:52 +0000 Subject: [PATCH 47/48] fix MIT license badge URL flagged by urlchecker::url_check() --- README.Rmd | 4 ++-- man/epiparameterDB-package.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index 88e2951..0d86466 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,7 +21,7 @@ knitr::opts_chunk$set( # `{epiparameterDB}` -[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/) +[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit) [![R-CMD-check](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epiverse-trace/epiparameterDB/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameterDB?branch=main) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) @@ -83,7 +83,7 @@ Please note that the `{epiparameterDB}` project is released with a [Contributor This project is related to other existing projects in R or other languages, but also differs from them in the following aspects: -- `{epireview}`: An R package containing epidemiological parameters for a range of priority pathogens (e.g. Ebola, Lassa SARS). These can be read into R as tabular data. To fully utilise data stored in `{epireview}` we recommend converting the epidemiological parameter of choice into an `` object using `epiparameter::as_epiparameter()`, see [`data_from_epireview` vignette](https://epiverse-trace.github.io/epiparameter/articles/data_from_epireview.html). +- `{epireview}`: An R package containing epidemiological parameters for a range of priority pathogens (e.g. Ebola, Lassa and SARS). These can be read into R as tabular data. To fully utilise data stored in `{epireview}` we recommend converting the epidemiological parameter of choice into an `` object using `epiparameter::as_epiparameter()`, see [`data_from_epireview` vignette](https://epiverse-trace.github.io/epiparameter/articles/data_from_epireview.html). ## Citing this package diff --git a/man/epiparameterDB-package.Rd b/man/epiparameterDB-package.Rd index b3b6ff7..401f09e 100644 --- a/man/epiparameterDB-package.Rd +++ b/man/epiparameterDB-package.Rd @@ -3,7 +3,7 @@ \docType{package} \name{epiparameterDB-package} \alias{epiparameterDB-package} -\title{epiparameterDB: Database of epidemiological parameters} +\title{epiparameterDB: Database of Epidemiological Parameters} \description{ A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature. } From 54b3fb732a554347a62d498e242a7c16500a805b Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 21 Nov 2024 16:21:38 +0000 Subject: [PATCH 48/48] Automatic readme update --- README.md | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 8bb7f31..97774af 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ [![License: -MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/) +MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit) [![R-CMD-check](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/epiparameterDB/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epiverse-trace/epiparameterDB/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/epiparameterDB?branch=main) @@ -38,6 +38,12 @@ Medicine](https://www.lshtm.ac.uk/) as part of ## Installation +You can install `{epiparameterDB}` from CRAN with: + +``` r +install.packages("epiparameterDB") +``` + You can install the development version of `{epiparameterDB}` from [GitHub](https://github.com/) with: @@ -92,8 +98,8 @@ This project is related to other existing projects in R or other languages, but also differs from them in the following aspects: - `{epireview}`: An R package containing epidemiological parameters for - a range of priority pathogens (e.g. Ebola, Lassa SARS). These can be - read into R as tabular data. To fully utilise data stored in + a range of priority pathogens (e.g. Ebola, Lassa and SARS). These can + be read into R as tabular data. To fully utilise data stored in `{epireview}` we recommend converting the epidemiological parameter of choice into an `` object using `epiparameter::as_epiparameter()`, see [`data_from_epireview` @@ -106,17 +112,17 @@ citation("epiparameterDB") #> To cite package 'epiparameterDB' in publications use: #> #> Lambert J, Kucharski A, Tamayo C (2024). _epiparameterDB: Database of -#> epidemiological parameters_. R package version 0.0.0.9000, +#> Epidemiological Parameters_. R package version 0.1.0, #> https://epiverse-trace.github.io/epiparameterDB/, #> . #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, -#> title = {epiparameterDB: Database of epidemiological parameters}, +#> title = {epiparameterDB: Database of Epidemiological Parameters}, #> author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo}, #> year = {2024}, -#> note = {R package version 0.0.0.9000, +#> note = {R package version 0.1.0, #> https://epiverse-trace.github.io/epiparameterDB/}, #> url = {https://github.com/epiverse-trace/epiparameterDB/}, #> }