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Merge pull request #464 from UCD-SERG/CRAN-fix-release-1.3.0
Cran fix release 1.3.0
2 parents bab8f09 + 20a81c8 commit 4fc3b75

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‎.gitignore‎

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**/.quarto/
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*.pdf
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junit.xml
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**/*.quarto_ipynb

‎DESCRIPTION‎

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Type: Package
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Package: serocalculator
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Title: Estimating Infection Rates from Serological Data
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Version: 1.3.0.9059
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Version: 1.3.0.9061
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Authors@R: c(
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person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
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comment = "Author of the method and original code."),
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LazyData: true
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NeedsCompilation: no
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Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace", "devtag::dev_roclet"))
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3

‎NAMESPACE‎

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export(est.incidence.by)
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export(est_seroincidence)
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export(est_seroincidence_by)
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export(expect_snapshot_data)
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export(f_dev)
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export(f_dev0)
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export(fdev)

‎NEWS.md‎

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## Internal changes
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* switched `expect_snapshot_data()` to an internal function due to CRAN errors (#464)
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* generalized `ab1()`
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* added codecov/test-results-action to test-coverage.yaml workflow
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* added test for censored data in f_dev() (#399)

‎R/check_strata.R‎

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#' sees_pop_data_pk_100 |>
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#' check_strata(strata = c("ag", "catch", "Count")) |>
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#' try()
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#' @dev
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#' @keywords internal
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check_strata <- function(pop_data,
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strata,
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biomarker_names_var =

‎R/expect_snapshot_data.R‎

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#' Snapshot testing for [data.frame]s
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#' @description
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#' copied from <https://github.com/bcgov/ssdtools>
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#' with permission (<https://github.com/bcgov/ssdtools/issues/379>)
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#'
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#' @param x a [data.frame] to snapshot
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#' @param name [character] snapshot name
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#' @param digits [integer] passed to [signif()] for numeric variables
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#'
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#' @returns [NULL] (from [testthat::expect_snapshot_file()])
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#' @export
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#' @keywords internal
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#' @examples
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#' \dontrun{
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#' expect_snapshot_data(iris, name = "iris")
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#' }
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expect_snapshot_data <- function(x, name, digits = 6) {
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fun <- function(x) signif(x, digits = digits)
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lapply_fun <- function(x) I(lapply(x, fun))
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x <- dplyr::mutate(x, dplyr::across(tidyselect::where(is.numeric), fun))
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x <- dplyr::mutate(x, dplyr::across(tidyselect::where(is.list), lapply_fun))
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path <- save_csv(x)
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testthat::expect_snapshot_file(
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path,
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paste0(name, ".csv"),
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compare = testthat::compare_file_text
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)
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}
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save_csv <- function(x) {
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path <- tempfile(fileext = ".csv")
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readr::write_csv(x, path)
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path
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}

‎R/sim_pop_data.R‎

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#' * `"long"` (one measurement per row) or
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#' * `"wide"` (one serum sample per row)
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#' @inheritDotParams simcs.tinf
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#' @inheritDotParams ldpar
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#' @inheritDotParams ab
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#' @inheritDotParams mk_baseline
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#' @inheritParams log_likelihood # verbose
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#' @return a [tibble::tbl_df] containing simulated cross-sectional serosurvey
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#' data, with columns:

‎README.Rmd‎

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Another great resource is **The Epidemiologist R Handbook**,
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which includes an introductory page on asking for help with R packages via GitHub:
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https://epirhandbook.com/en/getting-help.html
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https://epirhandbook.com/en/new_pages/help.html
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## Contributing to this project
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‎README.md‎

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Another great resource is **The Epidemiologist R Handbook**, which
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includes an introductory page on asking for help with R packages via
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GitHub: <https://epirhandbook.com/en/getting-help.html>
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GitHub: <https://epirhandbook.com/en/new_pages/help.html>
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## Contributing to this project
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‎_quarto.yml‎

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project:
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render: ['*.qmd']
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render:
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- "*.qmd" # Render all Quarto markdown files
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- "!data-raw/" # Exclude anything in the data-raw directory
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author: "UC Davis Seroepidemiology Research Group (UCD-SERG)"
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date: '`r Sys.Date()`'
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format:

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