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^.*\.Rproj$ | ||
^\.Rproj\.user$ |
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*.qmd linguist-language=RMarkdown |
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# To get started with Dependabot version updates, you'll need to specify which | ||
# package ecosystems to update and where the package manifests are located. | ||
# Please see the documentation for all configuration options: | ||
# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates | ||
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version: 2 | ||
updates: | ||
- package-ecosystem: "github-actions" # See documentation for possible values | ||
directory: "/" # Location of package manifests | ||
schedule: | ||
interval: "weekly" |
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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples | ||
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
on: | ||
workflow_dispatch: | ||
schedule: | ||
- cron: '0 0 1 * *' # Run at 00:00 on the 1st of every month | ||
push: | ||
branches: [main] | ||
pull_request: | ||
merge_group: | ||
|
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name: deploy | ||
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jobs: | ||
deploy: | ||
runs-on: ubuntu-latest | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
LANG: "en_US.UTF-8" | ||
LC_ALL: "en_US.UTF-8" | ||
steps: | ||
- uses: actions/checkout@v4 | ||
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- uses: quarto-dev/quarto-actions/setup@v2 | ||
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- uses: r-lib/actions/setup-r@v2 | ||
with: | ||
use-public-rspm: true | ||
extra-repositories: 'https://stan-dev.r-universe.dev' | ||
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- name: Install dependencies | ||
uses: r-lib/actions/setup-r-dependencies@v2 | ||
with: | ||
extra-packages: | ||
any::gh, | ||
any::knitr, | ||
any::rmarkdown, | ||
local::., | ||
|
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- name: Install cmdstan | ||
uses: epinowcast/actions/install-cmdstan@v1 | ||
with: | ||
cmdstan-version: 'latest' | ||
num-cores: 2 | ||
|
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- name: Render site | ||
run: quarto render | ||
|
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- name: Upload website | ||
uses: actions/upload-artifact@v4 | ||
if: github.event_name == 'pull_request' | ||
with: | ||
name: site | ||
retention-days: 5 | ||
path: _site | ||
|
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- name: Deploy to GitHub pages 🚀 | ||
if: github.ref_name == 'main' | ||
uses: JamesIves/github-pages-deploy-action@v4.6.8 | ||
with: | ||
branch: gh-pages | ||
folder: _site | ||
single-commit: true | ||
clean: true |
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name: render-readme | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.head_ref }} | ||
cancel-in-progress: true | ||
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on: | ||
workflow_dispatch: | ||
push: | ||
branches: | ||
- main | ||
|
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jobs: | ||
render-readme: | ||
runs-on: macos-latest | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
steps: | ||
- name: Checkout repos | ||
uses: actions/checkout@v4 | ||
|
||
- name: Setup R | ||
uses: r-lib/actions/setup-r@v2 | ||
with: | ||
use-public-rspm: true | ||
extra-repositories: 'https://stan-dev.r-universe.dev' | ||
|
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- name: Setup pandoc | ||
uses: r-lib/actions/setup-pandoc@v2 | ||
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- name: Install dependencies | ||
uses: r-lib/actions/setup-r-dependencies@v2 | ||
with: | ||
extra-packages: any::rmarkdown, any::allcontributors | ||
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- name: Update contributors | ||
if: github.ref == 'refs/heads/main' | ||
run: allcontributors::add_contributors(format = "text", check_urls = FALSE) | ||
shell: Rscript {0} | ||
|
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- name: Compile the readme | ||
run: | | ||
rmarkdown::render("README.Rmd") | ||
shell: Rscript {0} | ||
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- name: Upload README.md as an artifact | ||
uses: actions/upload-artifact@v4 | ||
with: | ||
name: readme | ||
path: README.md | ||
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- name: Create Pull Request | ||
if: github.ref == 'refs/heads/main' | ||
uses: peter-evans/create-pull-request@v7 | ||
with: | ||
commit-message: "Automatic README update" | ||
title: "Update README" | ||
body: "This is an automated pull request to update the README." | ||
branch: "update-readme-${{ github.run_number }}" | ||
labels: "documentation" | ||
add-paths: | | ||
README.Rmd | ||
README.md | ||
token: ${{ secrets.GITHUB_TOKEN }} |
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.Rproj.user | ||
.Rhistory | ||
.RData | ||
.Ruserdata | ||
_site | ||
.DS_Store | ||
*_files/ | ||
/.quarto/ | ||
inst/stan/simple-nowcast | ||
inst/stan/* | ||
!inst/stan/functions | ||
!inst/stan/*.stan | ||
*.html | ||
*.rmarkdown | ||
.vscode/ | ||
Empty file.
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Package: nfidd | ||
Title: Material to support course on nowcasting and forecasting of infectious | ||
disease dynamics | ||
Version: 0.1.0.9000 | ||
Authors@R: c( | ||
person( | ||
given = "NFIDD course contributors", | ||
family = "", | ||
role = c("cre", "aut"), | ||
email = "epiforecasts@gmail.com" | ||
) | ||
) | ||
Description: Resources to support a short course on nowcasting and forecasting | ||
of infectious disease dynamics. | ||
License: MIT + file LICENSE | ||
URL: https://github.com/nfidd/nfidd | ||
BugReports: https://github.com/nfidd/nfidd/issues | ||
Depends: | ||
R (>= 4.2.0) | ||
Imports: | ||
dplyr, | ||
tidyr | ||
Suggests: | ||
bayesplot, | ||
cmdstanr, | ||
ggplot2, | ||
lubridate, | ||
posterior, | ||
purrr, | ||
rmarkdown, | ||
scoringutils, | ||
tidybayes, | ||
qra | ||
Remotes: | ||
epiforecasts/scoringutils@b370557, | ||
epiforecasts/qra@v0.1.0 | ||
Additional_repositories: | ||
https://stan-dev.r-universe.dev | ||
Encoding: UTF-8 | ||
Language: en-GB | ||
RoxygenNote: 7.3.2 | ||
LazyData: true |
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MIT License | ||
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Copyright (c) 2024 NFIDD contributors | ||
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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. |
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# Generated by roxygen2: do not edit by hand | ||
|
||
export(add_delays) | ||
export(censored_delay_pmf) | ||
export(convolve_with_delay) | ||
export(geometric_diff_ar) | ||
export(geometric_random_walk) | ||
export(make_daily_infections) | ||
export(make_gen_time_pmf) | ||
export(make_ip_pmf) | ||
export(nfidd_cmdstan_model) | ||
export(nfidd_load_stan_functions) | ||
export(nfidd_stan_function_files) | ||
export(nfidd_stan_functions) | ||
export(nfidd_stan_models) | ||
export(nfidd_stan_path) | ||
export(renewal) | ||
export(simulate_onsets) | ||
importFrom(dplyr,count) | ||
importFrom(dplyr,full_join) | ||
importFrom(dplyr,if_else) | ||
importFrom(dplyr,join_by) | ||
importFrom(dplyr,left_join) | ||
importFrom(dplyr,mutate) | ||
importFrom(dplyr,n) | ||
importFrom(dplyr,select) | ||
importFrom(dplyr,tibble) | ||
importFrom(dplyr,transmute) | ||
importFrom(stats,rbinom) | ||
importFrom(stats,rgamma) | ||
importFrom(stats,rlnorm) | ||
importFrom(stats,rpois) | ||
importFrom(tidyr,expand) | ||
importFrom(tidyr,replace_na) |
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# nfidd 0.1.0.9000 | ||
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In development version of the package and teaching material for teaching in Bangkok in November 2024. | ||
|
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# nfidd 0.1.0 | ||
|
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Initial release of the `nfidd` package and teaching material for teaching in June 2024 in Stockholm. |
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#' Simulate symptom onset and hospitalization times from infection times | ||
#' | ||
#' @param infection_times A data frame containing a column of infection times | ||
#' | ||
#' @return A data frame with columns for infection time, onset time, and | ||
#' hospitalization time (with 70% of hospitalizations set to NA) | ||
#' | ||
#' @importFrom dplyr mutate n if_else | ||
#' @importFrom stats rgamma rlnorm rbinom | ||
#' | ||
#' @export | ||
#' | ||
#' @examples | ||
#' add_delays(infection_times) | ||
add_delays <- function(infection_times) { | ||
# Add random delays from appropriate probability distributions | ||
df <- infection_times |> | ||
mutate( | ||
# Gamma distribution for onset times | ||
onset_time = infection_time + rgamma(n(), shape = 5, rate = 1), | ||
# Lognormal distribution for hospitalisation times | ||
hosp_time = onset_time + rlnorm(n(), meanlog = 1.75, sdlog = 0.5) | ||
) | ||
|
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# Set random 70% of hospitalization dates to NA (30% hospitalized) | ||
df <- df |> | ||
mutate( | ||
hosp_time = if_else( | ||
# use the binomial distribution for random binary outcomes | ||
rbinom(n = n(), size = 1, prob = 0.3) == 1, | ||
hosp_time, | ||
NA_real_ | ||
) | ||
) | ||
|
||
return(df) | ||
} |
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#' Discretise a Continuous Delay Distribution | ||
#' | ||
#' This function discretises a continuous delay distribution into a probability | ||
#' mass function (PMF) over discrete days. | ||
#' | ||
#' @param rgen A function that generates random delays, e.g., `rgamma`, | ||
#' `rlnorm`. | ||
#' @param max The maximum delay. | ||
#' @param n The number of replicates to simulate. Defaults to `1e+6`. | ||
#' @param ... Additional parameters of the delay distribution. | ||
#' | ||
#' @return A vector of probabilities corresponding to discrete indices from | ||
#' `0` to `max`, representing the discretised delay distribution. | ||
#' | ||
#' @export | ||
#' | ||
#' @examples | ||
#' censored_delay_pmf(rgen = rgamma, max = 14, shape = 5, rate = 1) | ||
censored_delay_pmf <- function(rgen, max, n = 1e+6, ...) { | ||
## first, simulate exact time of first event (given by day), uniformly | ||
## between 0 and 1 | ||
first <- runif(n, min = 0, max = 1) | ||
## now, simulate the exact time of the second event | ||
second <- first + rgen(n, ...) | ||
## round down to get the delay in days | ||
delay <- floor(second) | ||
## get vector of counts | ||
counts <- table(factor(delay, levels = seq(0, max))) | ||
## normalise to get pmf | ||
pmf <- counts / sum(counts) | ||
## return | ||
return(pmf) | ||
} |
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#' Convolve a Time Series with a Delay Distribution | ||
#' | ||
#' This function convolves a time series with a delay distribution given as a | ||
#' probability mass function (PMF). | ||
#' | ||
#' @param ts A vector of the time series to convolve. | ||
#' @param delay_pmf The probability mass function of the delay, given as a | ||
#' vector of probabilities, corresponding to discrete indices 0, 1, 2 of the | ||
#' discretised delay distribution. | ||
#' | ||
#' @return A vector of the convolved time series. | ||
#' | ||
#' @export | ||
#' | ||
#' @examples | ||
#' convolve_with_delay(ts = c(10, 14, 10, 10), delay_pmf = c(0.1, 0.6, 0.3)) | ||
convolve_with_delay <- function(ts, delay_pmf) { | ||
max_delay <- length(delay_pmf) - 1 ## subtract one because zero-indexed | ||
convolved <- vapply(seq_along(ts), \(i) { | ||
## get vector of infections over the possible window of the delay period | ||
first_index <- max(1, i - max_delay) | ||
ts_segment <- ts[seq(first_index, i)] | ||
## take reverse of pmf and cut if needed | ||
pmf <- rev(delay_pmf)[seq_len(i - first_index + 1)] | ||
## convolve with delay distribution | ||
ret <- sum(ts_segment * pmf) | ||
return(ret) | ||
}, numeric(1)) | ||
return(convolved) | ||
} |
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