Dev webrd (#32)

* test epidemics

* changes to vignette

* testing epidemics

* testing site

* improved vignette

* improved vignette

* improved vignette

* improved vignette with contributions

* improved vignette with contributions

* improved vignette with refernces

* improved vignette with references

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* improved vignette with use cases

* use cases

* use cases

* update preloaded package datasets. mydata and serodata contain a copy of the same dataset for the time being.

* add additional changes to add multiple datasets to the package.

* doc: add datasets documentation files.

* use cases

* adding veev panama

* adding chik 2015

* adding chik 2015

* removing unnecesary data

* correcting chik data for nicaragua

* correcting chagas data for Colombia

* correcting chagas data for Colombia

* doc: add mydata and serodata documentation and .R files.

* doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012.

* doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012.

---------

Co-authored-by: Zulma Cucunubá <[email protected]>
Co-authored-by: Zulma M Cucunubá <[email protected]>

.github/CONTRIBUTING.md

@@ -0,0 +1,40 @@
+# Contributing to serofoi
+
+This outlines how to propose a change to serofoi.
+
+## Making changes
+
+If you want to make a change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). See [bug report template](../.github/ISSUE_TEMPLATE/bug_report.md). If you have a feature request see [feature request](../.github/ISSUE_TEMPLATE/feature_request.md).
+
+### Pull request process
+
+See [pull request template](../.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("epiverse-trace/serofoi", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the serofoi 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.

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -54,3 +54,4 @@ tests/testthat/Rplots.pdf
 t,
 tests/testthat/extdata/plots/actual/*.png
 tests/testthat/extdata/dataframes/actual/*.csv
+docs

DESCRIPTION

@@ -3,15 +3,33 @@ Type: Package
 Title: Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies
 Version: 0.1.0
 Authors@R: 
-  c(
-    person("Zulma M. Cucunubá", role = "aut"),
-    person("Ben Lambert", role = "aut"),
-    person("Pierre Nouvellet", role = "aut"),
-    person("N. T. Domínguez", role = c("aut", "cre"), email = "[email protected]")
-  )
+    c(
+        person(
+            given = "Zulma M.",
+            family = "Cucunubá",
+            role = c("aut", "cre"),
+            email = "[email protected]",
+            comment = c(ORCID = "https://orcid.org/0000-0002-8165-3198")
+        ),
+        person(
+            given = "Nicolás",
+            family = "Torres",
+            role = c("aut")
+        ),
+        person(
+            given = "Ben",
+            family = "Lambert",
+            role = c("aut")
+        ),
+        person(
+            given = "Pierre",
+            family = "Nouvellet",
+            role = c("aut")
+        )
+    )
 Contributor: Miguel Gámez, Geraldine Gómez, Jaime A. Pavlich-Mariscal
 Maintainer: The package maintainer <[email protected]>
-Description: R package to estimate time-varying Force-of-Infection of a given pathogen from population based sero-prevalence studies on a bayesian framework.
+Description: R package to estimate time-varying Force-of-Infection of a given pathogen from population based sero-prevalence studies using a bayesian framework.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -43,5 +61,4 @@ Suggests:
     knitr,
     rmarkdown
 VignetteBuilder: knitr
-Additional_repositories:
-    https://mc-stan.org/r-packages/
+URL: https://trace-lac.github.io/serofoi/

R/chagas2012.R

@@ -0,0 +1,15 @@
+#' Seroprevalence data on serofoi
+#'
+#' Data from a serological surveys
+#'
+#' @docType data
+#'
+#' @usage chagas2012
+#'
+#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' chagas2012
+"chagas2012"

data/data_test.R → R/chik2015.R

@@ -4,12 +4,12 @@
 #'
 #' @docType data
 #'
-#' @usage data_test
+#' @usage chik2015
 #'
 #' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
 #'
 #' @keywords datasets
 #'
 #' @examples
-#' data_test
-"serofoi"
+#' chik2015
+"chik2015"

R/modelling.R

@@ -1,7 +1,6 @@
 # TODO For some reason, the examples cannot access the mydata variable
-#' Run model
+#' Run the specified stan model for the force-of-infection
 #'
-#' Runs the specified stan model for the force-of-infection
 #' @param model_data A data frame containing the data from a seroprevalence survey.
 #' This data frame must contain the following columns:
 #' \tabular{ll}{
@@ -71,7 +70,7 @@ run_model <- function(model_data,
 #' Save or load model
 #'
 #' This function determines whether the corresponding .RDS file of the selected model exists or not.
-#' In case the .RDS file exists, it is read and returned; otherwise, the object model is created through the 
+#' In case the .RDS file exists, it is read and returned; otherwise, the object model is created through the
 #' \link[rstan]{stan_model} function, saved as an .RDS file and returned as the output of the function.
 #' @param model_name Name of the selected model. Current version provides three options:
 #' \describe{

R/mydata.R

@@ -0,0 +1,15 @@
+#' Seroprevalence data on serofoi
+#'
+#' Data from a serological surveys
+#'
+#' @docType data
+#'
+#' @usage mydata
+#'
+#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' mydata
+"mydata"

R/veev2012.R

@@ -0,0 +1,15 @@
+#' Seroprevalence data on serofoi
+#'
+#' Data from a serological surveys
+#'
+#' @docType data
+#'
+#' @usage veev2012
+#'
+#' @format An object of class \code{"cross"}; see \code{\link[qtl]{read.cross}}.
+#'
+#' @keywords datasets
+#'
+#' @examples
+#' veev2012
+"veev2012"