Merge branch 'main' into clean_simulation_vignette

.Rbuildignore

@@ -23,3 +23,5 @@ allpopsamples_hlye.csv$
 ^CRAN-SUBMISSION$
 ^README\.qmd$
 ^codecov\.yml$
+^\.lintr$
+^man/df_to_array\.Rd$

.gitattributes

@@ -0,0 +1 @@
+NEWS.md merge=union

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,21 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+---
+
+Please briefly describe your problem and what output you expect. 
+If you have a question, please don't use this form. 
+Instead, ask on 
+<https://github.com/UCD-SERG/serocalculator/discussions/categories/q-a>.
+
+Please include a minimal reproducible example (AKA a reprex). 
+If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, 
+start by reading <https://www.tidyverse.org/help/#reprex>.
+
+For more advice on how to write a great issue, see <https://code-review.tidyverse.org/issues/>.
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+Thank you for taking the time to submit a pull request!
+
+To maximize the chances of acceptance:
+
+- [ ] The title of your PR should briefly describe the change.
+- [ ] The body of your PR should contain `Fixes #issue-number` (if relevant).
+- [ ] Commit/merge messages to be included in NEWS.md should begin with `-`.
+- [ ] Code should follow the tidyverse [style guide](https://style.tidyverse.org).
+- [ ] Documentation should use roxygen2, with Markdown syntax.
+- [ ] Contributions should include unit tests (using `testthat`).
+
+For more information see [Contributing](/.github/CONTRIBUTING.md).

.github/workflows/R-CMD-check.yaml

@@ -5,7 +5,7 @@ on:
     branches: [main, master]
   pull_request:
 
-name: R-CMD-check
+name: R-CMD-check.yaml
 
 jobs:
   R-CMD-check:

.github/workflows/check-readme.yaml

@@ -0,0 +1,66 @@
+# 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]
+
+name: check-readme
+
+jobs:
+  check-readme:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: "release" }
+          #- { os: ubuntu-latest, r: "devel" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "latest"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          upgrade: "TRUE"
+          extra-packages: |
+            local::.
+            any::gghalves
+            any::ggplot2
+            any::quarto
+            any::ggridges
+            any::ggbeeswarm
+            any::PairedData
+            any::metaviz
+            any::metaplus
+
+      - name: Render README
+        run: |
+          options(
+            crayon.enabled = TRUE,
+            # warnPartialMatchArgs = TRUE,
+            # warnPartialMatchAttr = TRUE,
+            # warnPartialMatchDollar = TRUE,
+            warn = 2L
+          )
+          quarto::quarto_render("README.qmd")
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -9,7 +9,7 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
 
 jobs:
   pkgdown:
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +41,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -4,9 +4,8 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"

DESCRIPTION

@@ -1,19 +1,27 @@
-Package: serocalculator
 Type: Package
+Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.2.0.9005
+Version: 1.2.0.9012
 Authors@R: c(
-  person(given = "Peter", family = "Teunis", email = "[email protected]", role = c("aut", "cph"), comment = "Author of the method and original code."),
-  person(given = "Kristina", family = "Lai", email = "[email protected]", role = c("aut", "cre")), 
-  person(given = "Chris", family = "Orwa", role = "aut"), 
-  person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut")),
-  person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut")))
-Description: Translates antibody levels measured in cross-sectional population 
-  samples into estimates of the frequency with which seroconversions (infections) 
-  occur in the sampled populations. Replaces the previous `seroincidence` package.
-Depends: R (>= 4.1.0)
+    person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"),
+           comment = "Author of the method and original code."),
+    person("Kristina", "Lai", , "[email protected]", role = c("aut", "cre")),
+    person("Chris", "Orwa", role = "aut"),
+    person("Kristen", "Aiemjoy", , "[email protected]", role = "aut"),
+    person("Douglas Ezra", "Morrison", , "[email protected]", role = "aut")
+  )
+Description: Translates antibody levels measured in cross-sectional
+    population samples into estimates of the frequency with which
+    seroconversions (infections) occur in the sampled populations.
+    Replaces the previous `seroincidence` package.
 License: GPL-3
+URL: https://github.com/UCD-SERG/serocalculator,
+    https://ucd-serg.github.io/serocalculator/
+BugReports: https://github.com/UCD-SERG/serocalculator/issues
+Depends: 
+    R (>= 4.1.0)
 Imports: 
+    cli,
     doParallel,
     dplyr (>= 1.1.1),
     foreach,
@@ -29,28 +37,33 @@ Imports:
     stats,
     tibble,
     tidyr,
-    utils,
     tidyselect,
-    cli
+    utils
 Suggests:
-    parallel,
+    bookdown,
+    devtag (>= 0.0.0.9000),
+    DT,
+    fs,
+    ggbeeswarm,
     knitr,
+    pak,
+    parallel,
+    readr,
     rmarkdown,
-    tidyverse,
-    fs,
+    spelling,
+    ssdtools (>= 1.0.6.9016),
     testthat (>= 3.0.0),
-    readr,
-    bookdown,
-    ggbeeswarm,
-    DT,
-    spelling
-LazyData: true
-Encoding: UTF-8
-URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/
-RoxygenNote: 7.3.2
-NeedsCompilation: no
+    tidyverse
 LinkingTo: 
     Rcpp
-Language: en-US
-Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
+Config/Needs/build: moodymudskipper/devtag
+Encoding: UTF-8
+Language: en-US
+LazyData: true
+NeedsCompilation: no
+Remotes: 
+    bcgov/ssdtools,
+    moodymudskipper/devtag
+Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace", "devtag::dev_roclet"))
+RoxygenNote: 7.3.2

NAMESPACE

@@ -6,23 +6,10 @@ S3method(autoplot,pop_data)
 S3method(autoplot,seroincidence)
 S3method(autoplot,seroincidence.by)
 S3method(autoplot,summary.seroincidence.by)
-S3method(get_age,pop_data)
-S3method(get_age_var,pop_data)
-S3method(get_biomarker_levels,pop_data)
-S3method(get_biomarker_names,pop_data)
-S3method(get_biomarker_names_var,pop_data)
-S3method(get_id,pop_data)
-S3method(get_id_var,pop_data)
-S3method(get_value,pop_data)
-S3method(get_value_var,pop_data)
 S3method(print,seroincidence)
 S3method(print,seroincidence.by)
 S3method(print,summary.pop_data)
 S3method(print,summary.seroincidence.by)
-S3method(set_age,pop_data)
-S3method(set_biomarker_var,pop_data)
-S3method(set_id,pop_data)
-S3method(set_value,pop_data)
 S3method(strata,seroincidence.by)
 S3method(summary,pop_data)
 S3method(summary,seroincidence)

NEWS.md

@@ -4,11 +4,39 @@
 
 * Updated `simulate_xsectionalData.Rmd()` (linting, removing deprecated functions).
 
+* Added default value for `antigen_isos` argument in `log_likelihood()` (#286)
+
+* Updated enteric fever example article with upgraded code and visualizations (#290)
+
+* Added template for reporting Issues 
+(from `usethis::use_tidy_issue_template()`) (#270)
+
+* Added template for pull requests 
+(from <https://github.com/bcgov/ssdtools>) (#265)
+
 ## Developer-facing changes
 
+* initialized [`lintr`](https://lintr.r-lib.org/) with `lintr::use_lint()` (#278)
+
+* created unit test for `df_to_array()` (#276)
+
+* fixed `dplyr::select()` deprecation warning in `df_to_array()` (#276)
+
+* Added `devtag` to package (using `devtag::use_devtag()`) (#292)
+* Added `@dev` tag to `?df_to_array()` (#292)
+
+* Generalized `get_()` and `set_()` methods to be general-purpose
+(no S3 class-specific methods needed yet) (#274).
+
+* Updated GitHub Action files and reformatted `DESCRIPTION` (#268)
+* Added `.gitattributes` file (<https://git-scm.com/docs/gitattributes>)
+copied from <https://github.com/tidyverse/ggplot2>
+
 * Added additional automated checks through 
 [GitHub actions](https://docs.github.com/en/actions), 
 including:
+  - check that `README.qmd` still compiles 
+  (advice from [preventive-r-package-care](https://indrajeetpatil.github.io/preventive-r-package-care)) (#259)
   - check `NEWS.md` for updated change log (#257)
   - lint changed files (#256)
 

R/as_curve_params.R

@@ -1,8 +1,10 @@
 #' Load antibody decay curve parameter
 #'
 #' @param data a [data.frame()] or [tibble::tbl_df]
-#' @param antigen_isos [character()] vector of antigen isotypes to be used in analyses
-#' @returns a `curve_data` object (a [tibble::tbl_df] with extra attribute `antigen_isos`)
+#' @param antigen_isos a [character()] vector of antigen isotypes
+#' to be used in analyses
+#' @returns a `curve_data` object
+#' (a [tibble::tbl_df] with extra attribute `antigen_isos`)
 #' @export
 #' @examples
 #' library(magrittr)
@@ -14,8 +16,7 @@
 #' print(curve_data)
 as_curve_params <- function(data, antigen_isos = NULL) {
 
-  if(!is.data.frame(data))
-  {
+  if (!is.data.frame(data)) {
     cli::cli_abort(
       class = "not data.frame",
       message = c(
@@ -31,16 +32,18 @@ as_curve_params <- function(data, antigen_isos = NULL) {
     data %>%
     tibble::as_tibble()
 
+  # check if object has expected columns:
+
   # define curve columns
   curve_cols <- c("antigen_iso", "y0", "y1", "t1", "alpha", "r")
 
-  # check if object is curve (with columns)
-  if (!all(is.element(curve_cols, curve_data %>% names()))) {
-    # get columns from provided data
-    data_cols <- data %>% names()
+  # get columns from provided data
+  data_cols <- data %>% names()
+
+  # get any missing column(s)
+  missing_cols <- setdiff(x = curve_cols, y = data_cols)
 
-    # get any missing column(s)
-    missing_cols <- setdiff(x = curve_cols, y = data_cols)
+  if (length(missing_cols) > 0) {
 
     cli::cli_abort(
       class = "not curve_params",
@@ -67,5 +70,8 @@ as_curve_params <- function(data, antigen_isos = NULL) {
   # assign antigen attribute
   attr(curve_data, "antigen_isos") <- antigen_isos
 
+  curve_data <- curve_data %>%
+    set_biomarker_var(biomarker = "antigen_iso", standardize = FALSE)
+
   return(curve_data)
 }