Cran fix release 1.3.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.3.0.9059
+Version: 1.3.0.9060
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),
@@ -76,4 +76,5 @@ Language: en-US
 LazyData: true
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE, roclets = c("collate", "rd", "namespace", "devtag::dev_roclet"))
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
+Config/Needs/build: moodymudskipper/devtag

NAMESPACE

@@ -27,6 +27,7 @@ export(est.incidence)
 export(est.incidence.by)
 export(est_seroincidence)
 export(est_seroincidence_by)
+export(expect_snapshot_data)
 export(f_dev)
 export(f_dev0)
 export(fdev)

NEWS.md

@@ -61,6 +61,7 @@ would get merged by `ggplot2::aes(group = iter)` (#382)
 
 ## Internal changes
 
+* switched `expect_snapshot_data()` to an internal function due to CRAN errors (#464)
 * generalized `ab1()`
 * added codecov/test-results-action to test-coverage.yaml workflow
 * added test for censored data in f_dev() (#399)

R/check_strata.R

@@ -10,7 +10,7 @@
 #' sees_pop_data_pk_100 |>
 #'   check_strata(strata = c("ag", "catch", "Count")) |>
 #'   try()
-#' @dev
+
 check_strata <- function(pop_data,
                          strata,
                          biomarker_names_var =

R/expect_snapshot_data.R

@@ -0,0 +1,35 @@
+#' Snapshot testing for [data.frame]s
+#' @description
+#' copied from <https://github.com/bcgov/ssdtools>
+#' with permission (<https://github.com/bcgov/ssdtools/issues/379>)
+#'
+#' @param x a [data.frame] to snapshot
+#' @param name [character] snapshot name
+#' @param digits [integer] passed to [signif()] for numeric variables
+#'
+#' @returns [NULL] (from [testthat::expect_snapshot_file()])
+#' @export
+#' @keywords internal
+#' @examples
+#' \dontrun{
+#' expect_snapshot_data(iris, name = "iris")
+#' }
+expect_snapshot_data <- function(x, name, digits = 6) {
+  fun <- function(x) signif(x, digits = digits)
+  lapply_fun <- function(x) I(lapply(x, fun))
+  x <- dplyr::mutate(x, dplyr::across(tidyselect::where(is.numeric), fun))
+  x <- dplyr::mutate(x, dplyr::across(tidyselect::where(is.list), lapply_fun))
+  path <- save_csv(x)
+  testthat::expect_snapshot_file(
+    path,
+    paste0(name, ".csv"),
+    compare = testthat::compare_file_text
+  )
+}
+
+
+save_csv <- function(x) {
+  path <- tempfile(fileext = ".csv")
+  readr::write_csv(x, path)
+  path
+}

inst/WORDLIST

@@ -123,3 +123,5 @@ varepsilon
 vec
 vee
 yaml
+mitre
+colour

pkgdown/_pkgdown.yml

@@ -22,6 +22,7 @@ reference:
   - load_noise_params
   - check_pop_data
   - strata
+  - check_strata
 - title: Extract information from data, seroresponse models, and noise parameters
   contents:
   - get_biomarker_levels

tests/testthat/test-ab.R

@@ -1,32 +1,32 @@
 test_that("`ab()` works consistently", {
 
-   par1 <- matrix(
-       c(
-         1.11418923843475, 1, 0.12415057798022207, 0.24829344792968783,
-         0.01998946878312856, 0.0012360802436587237, 1.297194045996013,
-         1.3976510415108334, 1, 0.2159993563893431, 0.4318070551383313,
-         0.0015146395107173347, 0.0003580062906750277, 1.5695811573082081
-       ),
-       nrow = 7L,
-       ncol = 2L,
-       dimnames = list(
-         params = c("y0", "b0", "mu0", "mu1", "c1", "alpha", "shape_r"),
-         antigen_iso = c("HlyE_IgA", "HlyE_IgG")
-       )
-       )
-   t <- 0:1444
-   blims <- matrix(
-      rep(c(0, 0.5), each = 2L),
-      nrow = 2L,
-      ncol = 2L,
-      dimnames = list(c("HlyE_IgA", "HlyE_IgG"), c("min", "max"))
-      )
-   preds <- ab(t = t, par = par1, blims = blims)
+  par1 <- matrix(
+    c(
+      1.11418923843475, 1, 0.12415057798022207, 0.24829344792968783,
+      0.01998946878312856, 0.0012360802436587237, 1.297194045996013,
+      1.3976510415108334, 1, 0.2159993563893431, 0.4318070551383313,
+      0.0015146395107173347, 0.0003580062906750277, 1.5695811573082081
+    ),
+    nrow = 7L,
+    ncol = 2L,
+    dimnames = list(
+      params = c("y0", "b0", "mu0", "mu1", "c1", "alpha", "shape_r"),
+      antigen_iso = c("HlyE_IgA", "HlyE_IgG")
+    )
+  )
+  t <- 0:1444
+  blims <- matrix(
+    rep(c(0, 0.5), each = 2L),
+    nrow = 2L,
+    ncol = 2L,
+    dimnames = list(c("HlyE_IgA", "HlyE_IgG"), c("min", "max"))
+  )
+  preds <- ab(t = t, par = par1, blims = blims)
 
-   colnames(preds) <- colnames(par1)
+  colnames(preds) <- colnames(par1)
 
-   preds2 <- preds |> as_tibble()
+  preds2 <- preds |> as_tibble()
 
-   ssdtools:::expect_snapshot_data(preds2, name = "ab-preds")
+  expect_snapshot_data(preds2, name = "ab-preds")
 
 })

tests/testthat/test-analyze_sims.R

@@ -7,7 +7,7 @@ test_that(
 
     test_sim_results |>
       analyze_sims() |>
-      ssdtools:::expect_snapshot_data(name = "sim_results")
+      expect_snapshot_data(name = "sim_results")
 
   }
 )

tests/testthat/test-as_sr_params.R

@@ -30,7 +30,7 @@ test_that("`as_sr_params()` produces expected results", {
 
   expect_snapshot_value(x = test_data, style = "serialize")
 
-  test_data |>  ssdtools:::expect_snapshot_data(name = "curve-data")
+  test_data |>  expect_snapshot_data(name = "curve-data")
 
 
 })

tests/testthat/test-sim_pop_data.R

@@ -38,5 +38,5 @@ test_that("`sim_pop_data()` produces consistent results", {
     format = "long"
   )
 
-  ssdtools:::expect_snapshot_data(csdata, "sim_pop_data")
+  expect_snapshot_data(csdata, name = "sim_pop_data")
 })

tests/testthat/test-sim_pop_data_multi.R

@@ -11,7 +11,6 @@ test_that("`sim_pop_data_multi()` works consistently", {
 
   # Simulated incidence rate per person-year
   lambdas <- c(.05, .1, .15, .2, .3)
-  # lambdas <- c(.05)
   # Range covered in simulations
   lifespan <- c(0, 10)
 
@@ -39,5 +38,5 @@ test_that("`sim_pop_data_multi()` works consistently", {
   )
 
   pop_data_multi |>
-    ssdtools:::expect_snapshot_data(name = "pop_data_multi")
+    expect_snapshot_data(name = "pop_data_multi")
 })

tests/testthat/test-strata.R

@@ -2,7 +2,7 @@ test_that("results are consistent", {
 
   sees_typhoid_ests_strat |>
     strata() |>
-    ssdtools:::expect_snapshot_data(name = "strata-ests")
+    expect_snapshot_data(name = "strata-ests")
 
 
 })