340/cran release/update version

.github/workflows/check-readme.yaml

@@ -51,7 +51,6 @@ jobs:
             any::ggbeeswarm
             any::PairedData
             any::metaviz
-            any::metaplus
 
       - name: Render README
         run: |

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.2.0.9027
+Version: 1.3.0.9000
 Authors@R: c(
     person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"),
            comment = "Author of the method and original code."),
@@ -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

NEWS.md

@@ -1,5 +1,7 @@
 # serocalculator (development version)
 
+# serocalculator 1.3.0
+
 ## New features
 
 * Removed function 'get_additional_data()' (#332)
@@ -75,7 +77,7 @@ copied from <https://github.com/tidyverse/ggplot2>
 [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)
 

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,

R/sim.cs.R

@@ -4,18 +4,18 @@
 #' Makes a cross-sectional data set (age, y(t) set)
 #'  and adds noise, if desired.
 
 #' @param lambda a [numeric()] scalar indicating the incidence rate (in events per person-years)
 #' @param n.smpl number of samples to simulate
 #' @param age.rng age range of sampled individuals, in years
 #' @param age.fx specify the curve parameters to use by age (does nothing at present?)
 #' @param antigen_isos Character vector with one or more antibody names. Values must match `curve_params`.
 #' @param n.mc how many MCMC samples to use:
 #' * when `n.mc` is in `1:4000` a fixed posterior sample is used
 #' * when `n.mc` = `0`, a random sample is chosen
 #' @param renew.params whether to generate a new parameter set for each infection
 #' * `renew.params = TRUE` generates a new parameter set for each infection
 #' * `renew.params = FALSE` keeps the one selected at birth, but updates baseline y0
 #' @param add.noise a [logical()] indicating whether to add biological and measurement noise
 #' @inheritParams log_likelihood
 
 #' @param noise_limits biologic noise distribution parameters
@@ -23,9 +23,8 @@
 #' * `"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)
 #' * one column for each element in the `antigen_iso` input argument
 #' @export
@@ -69,10 +68,10 @@
 #'   format = "long"
 #' )
 #'
 sim.cs <- function(
     lambda = 0.1,
     n.smpl = 100,
     age.rng = c(0, 20),
     age.fx = NA,
     antigen_isos,
     n.mc = 0,

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
 
-* 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