From 306031824e60b4de90eb413fdc823a55180beee8 Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Wed, 22 Jan 2025 17:41:36 -0800 Subject: [PATCH 01/10] Update Description and News --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 36f204d3..0c4bd122 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: serocalculator Title: Estimating Infection Rates from Serological Data -Version: 1.2.0.9027 +Version: 1.3.0 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), diff --git a/NEWS.md b/NEWS.md index 3c065bed..2643c932 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# serocalculator (development version) +# serocalculator 1.3.0 ## New features From 0ca2bc49fcd1e1d532aca48f4d65e312e4a0562c Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Wed, 22 Jan 2025 20:15:01 -0800 Subject: [PATCH 02/10] Fix url based on results of `urlchecker::url_check()` [as recommended by r-pkgs.org] --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 2643c932..343849db 100644 --- a/NEWS.md +++ b/NEWS.md @@ -75,7 +75,7 @@ copied from [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) + (advice from [preventive-r-package-care](https://indrajeetpatil.github.io/preventive-r-package-care/#/preventive-care-for-r-packages)) (#259) - check `NEWS.md` for updated change log (#257) - lint changed files (#256) From 7e7078255089495dcfb2fb3d387bb1596d2eaeb4 Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Wed, 22 Jan 2025 20:20:48 -0800 Subject: [PATCH 03/10] Add \donttest for example taking >5 sec --- R/graph.decay.curves.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/graph.decay.curves.R b/R/graph.decay.curves.R index d0f61fc7..4b53c26b 100644 --- a/R/graph.decay.curves.R +++ b/R/graph.decay.curves.R @@ -31,6 +31,7 @@ #' * If the user directly specifies the `rows_to_graph` argument, #' then `n_curves` has no effect. #' @examples +#' \donttest{ #' library(dplyr) # loads the `%>%` operator and `dplyr::filter()` #' #' curve <- @@ -39,7 +40,7 @@ #' serocalculator:::plot_curve_params_one_ab() #' #' curve -#' +#' } plot_curve_params_one_ab <- function( object, verbose = FALSE, From 23996f7a54569339643cea43ed5f924caf467f6d Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Thu, 23 Jan 2025 13:24:24 -0800 Subject: [PATCH 04/10] Update CRAN comments and add \donttest for example taking longer than 5 sec --- cran-comments.md | 14 +++++++++----- man/plot_curve_params_one_ab.Rd | 3 ++- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 650d0918..10819181 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,11 +1,15 @@ -## Resubmission - -* Reduced run time of examples +## Resubmission +* Package had been archived from CRAN on 26-11-2024 following policy violation (Internet Access) +* In response, we removed urls with unstable servers and added internal datasets for examples and testing +* Includes additional developments consistent with a minor version increase. +* Full updates are described in NEWS.md. +* There are currently no downstream dependencies for this package ## R CMD check results -0 errors | 0 warnings | 1 note +0 errors | 0 warnings | 2 notes -* This is a new release. +* There are some words flagged as misspellings in DESCRIPTION, however these are spelled correctly. +* Package was previously archived on CRAN diff --git a/man/plot_curve_params_one_ab.Rd b/man/plot_curve_params_one_ab.Rd index 3393a245..e62a3fa2 100644 --- a/man/plot_curve_params_one_ab.Rd +++ b/man/plot_curve_params_one_ab.Rd @@ -113,6 +113,7 @@ then \code{n_curves} has no effect. } } \examples{ +\donttest{ library(dplyr) # loads the `\%>\%` operator and `dplyr::filter()` curve <- @@ -121,5 +122,5 @@ curve <- serocalculator:::plot_curve_params_one_ab() curve - +} } From 9883788ab589a54f21c3c56f91706fa0cd4aae7d Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Fri, 24 Jan 2025 10:00:22 -0800 Subject: [PATCH 05/10] Update devtag and sim.cs based on notes --- DESCRIPTION | 4 ---- R/sim.cs.R | 1 - man/sim.cs.Rd | 6 +----- 3 files changed, 1 insertion(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0c4bd122..f7c9519a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,6 @@ Imports: stringr Suggests: bookdown, - devtag (>= 0.0.0.9000), DT, fs, ggbeeswarm, @@ -70,8 +69,5 @@ 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 diff --git a/R/sim.cs.R b/R/sim.cs.R index fd1afc3e..b354e936 100644 --- a/R/sim.cs.R +++ b/R/sim.cs.R @@ -23,7 +23,6 @@ #' * `"long"` (one measurement per row) or #' * `"wide"` (one serum sample per row) #' @param ... additional arguments passed to `simcs.tinf()` -#' @inheritDotParams simcs.tinf #' @inheritParams log_likelihood # verbose #' @return a [tibble::tbl_df] containing simulated cross-sectional serosurvey data, with columns: #' * `age`: age (in days) diff --git a/man/sim.cs.Rd b/man/sim.cs.Rd index 2d07314f..233028a1 100644 --- a/man/sim.cs.Rd +++ b/man/sim.cs.Rd @@ -70,11 +70,7 @@ combinations \item{verbose}{logical: if TRUE, print verbose log information to console} -\item{...}{ - Arguments passed on to \code{\link[=simcs.tinf]{simcs.tinf}} - \describe{ - \item{\code{}}{} - }} +\item{...}{additional arguments passed to \code{simcs.tinf()}} } \value{ a \link[tibble:tbl_df-class]{tibble::tbl_df} containing simulated cross-sectional serosurvey data, with columns: From 6977bb19cf638d9a8dee1b5195c851c8bb577f7a Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Fri, 24 Jan 2025 12:11:14 -0800 Subject: [PATCH 06/10] Update cran comments --- cran-comments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 10819181..f4aa9e39 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -8,7 +8,7 @@ ## R CMD check results -0 errors | 0 warnings | 2 notes +0 errors | 0 warnings | 1 note * There are some words flagged as misspellings in DESCRIPTION, however these are spelled correctly. From 5fcd894598445401335aa66a892f13874f730eeb Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Fri, 24 Jan 2025 14:08:31 -0800 Subject: [PATCH 07/10] remove any::metaplus --- .github/workflows/check-readme.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/check-readme.yaml b/.github/workflows/check-readme.yaml index 73b59b43..f6f8b58a 100644 --- a/.github/workflows/check-readme.yaml +++ b/.github/workflows/check-readme.yaml @@ -51,7 +51,6 @@ jobs: any::ggbeeswarm any::PairedData any::metaviz - any::metaplus - name: Render README run: | From 07e792eda2378cca604b76ee05ef2924c0207e1b Mon Sep 17 00:00:00 2001 From: kristinawlai Date: Sat, 25 Jan 2025 13:35:53 -0800 Subject: [PATCH 08/10] Successful CRAN submission --- CRAN-SUBMISSION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 52429240..2162dbec 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.0.0 -Date: 2024-03-12 23:48:24 UTC -SHA: 9feb9f5f1965fd7b48031b941d6570bde33f538b +Version: 1.3.0 +Date: 2025-01-25 00:47:14 UTC +SHA: 5fcd894598445401335aa66a892f13874f730eeb From ee5a7ea7faa03809d9463b5ab2631614153c411b Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Sun, 26 Jan 2025 16:31:37 -0800 Subject: [PATCH 09/10] Increment version number to 1.3.0.9000 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f7c9519a..f4ca3de9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: serocalculator Title: Estimating Infection Rates from Serological Data -Version: 1.3.0 +Version: 1.3.0.9000 Authors@R: c( person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), diff --git a/NEWS.md b/NEWS.md index 343849db..09857752 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# serocalculator (development version) + # serocalculator 1.3.0 ## New features From 84f7187c2b65eb8c4b5804c96da3930756a05137 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Sun, 26 Jan 2025 16:32:11 -0800 Subject: [PATCH 10/10] removing `CRAN-SUBMISSION` --- CRAN-SUBMISSION | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION deleted file mode 100644 index 2162dbec..00000000 --- a/CRAN-SUBMISSION +++ /dev/null @@ -1,3 +0,0 @@ -Version: 1.3.0 -Date: 2025-01-25 00:47:14 UTC -SHA: 5fcd894598445401335aa66a892f13874f730eeb