Full package review for v0.1.0 release

.Rbuildignore

@@ -13,3 +13,5 @@
 ^docs$
 ^pkgdown$
 ^tools$
+^data-raw$
+^cran-comments\.md$

.github/workflows/pkgdown.yaml

@@ -72,13 +72,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Check website links
-        uses: untitaker/[email protected].32
+        uses: untitaker/[email protected].43
         with:
           args: docs/
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
-        uses: JamesIves/[email protected].8
+        uses: JamesIves/[email protected].9
         with:
           # We clean on releases because we want to remove old vignettes,
           # figures, etc. that have been deleted from the `main` branch.

.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}

CITATION.cff

@@ -0,0 +1,171 @@
+# --------------------------------------------
+# 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: 0.1.0
+identifiers:
+- type: url
+  value: https://epiverse-trace.github.io/epiparameterDB/
+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.
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-5218-3046
+- family-names: Kucharski
+  given-names: Adam
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-8814-9421
+- family-names: Tamayo
+  given-names: Carmen
+  email: [email protected]
+  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: [email protected]
+  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'
+  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: [email protected]
+  - 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: [email protected]
+    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: [email protected]
+    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: [email protected]
+  - family-names: Xie
+    given-names: Yihui
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: Dervieux
+    given-names: Christophe
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4474-2498
+  - family-names: McPherson
+    given-names: Jonathan
+    email: [email protected]
+  - family-names: Luraschi
+    given-names: Javier
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Atkins
+    given-names: Aron
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Cheng
+    given-names: Joe
+    email: [email protected]
+  - family-names: Chang
+    given-names: Winston
+    email: [email protected]
+  - family-names: Iannone
+    given-names: Richard
+    email: [email protected]
+    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: [email protected]
+    orcid: https://orcid.org/0000-0002-4035-0289
+  - family-names: Hester
+    given-names: Jim
+    email: [email protected]
+  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: [email protected]
+  year: '2024'
+  doi: 10.32614/CRAN.package.testthat
+  version: '>= 3.0.0'
+

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: 0.1.0
 Authors@R: c(
-    person("James M.", "Azam", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0001-5782-7330")),
-    person("Hugo", "Gruson", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0002-4094-1476")),
-    person("Pratik", "Gupte", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0001-5294-7819")),
-    person("Joshua W.", "Lambert", , "[email protected]", role = "aut",
+    person("Joshua W.", "Lambert", , "[email protected]", role = c("cre", "aut", "cph"),
            comment = c(ORCID = "0000-0001-5218-3046")),
-    person("Karim", "Mané", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0002-9892-2999")),
-    person("Jaime A.", "Pavlich-Mariscal", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0002-3892-6680")),
-    person("Chris", "Hartgerink", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0003-1050-6809"))
+    person("Adam", "Kucharski", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-8814-9421")),
+    person("Carmen", "Tamayo", , "[email protected]", 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) <doi:10.5281/zenodo.6619350>.
-License: MIT + file LICENSE
+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/
+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

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").
+
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+
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+
+1. __Copyright and Related Rights.__ A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following:
+
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+
+    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.
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+4. __Limitations and Disclaimers.__
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+
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NEWS.md

@@ -1,5 +1,16 @@
-# 0.1.0
+# epiparameterDB 0.1.0
 
-* 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

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 `<epiparamterDB>` to validate the
+#' parameter library has been loaded using the `{epiparameterDB}` package.
+#'
+"epiparameterDB"