Merge pull request #344 from njtierney/prep-release-1-1-0-i343

Prep release 1.1.0
njtierney · Mar 4, 2024 · d06760b · d06760b
2 parents 1b5e2c7 + d62680f
commit d06760b
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Showing 40 changed files with 455 additions and 346 deletions.
diff --git a/R/add-cols.R b/R/add-cols.R
@@ -21,8 +21,8 @@
 add_shadow <- function(data, ...){
 
   test_if_dots_missing(
-    missing(...),
-    "{.fun add_shadow} requires variables to be selected"
+    dots_empty = missing(...),
+    msg = "{.fun add_shadow} requires variables to be selected"
     )
   shadow_df <- dplyr::select(data, ...) %>% as_shadow()
 

diff --git a/R/cast-shadows.R b/R/cast-shadows.R
@@ -36,8 +36,8 @@
 cast_shadow <- function(data, ...){
 
   test_if_dots_missing(
-    ...,
-    "{.fun cast_shadow} requires variables to be selected after the data"
+    dots_empty = missing(...),
+    msg = "{.fun cast_shadow} requires variables to be selected after the data"
     )
 
     shadow_vars <- tibble::as_tibble(as_shadow(dplyr::select(data, ...)))
@@ -108,8 +108,8 @@ cast_shadow_shift <- function(data, ...){
 cast_shadow_shift_label <- function(data, ...){
 
   test_if_dots_missing(
-    ...,
-    "{.fun cast_shadow_shift_label} requires variables to be selected after the data"
+    dots_empty = missing(...),
+    msg = "{.fun cast_shadow_shift_label} requires variables to be selected after the data"
     )
 
   shadow_vars <- dplyr::select(data, ...) %>% cast_shadow(...)

diff --git a/R/mcar-test.R b/R/mcar-test.R
@@ -20,10 +20,10 @@
 #'   *Journal of the American Statistical Association* 83 (404):
 #'   1198--1202. \doi{10.1080/01621459.1988.10478722}.
 #'
-#' @note Code is adapted from LittleMCAR() in the now-orphaned {BaylorEdPsych}
+#' @note Code is adapted from LittleMCAR() in the now-orphaned `BaylorEdPsych`
 #'   package: \url{https://rdrr.io/cran/BaylorEdPsych/man/LittleMCAR.html}. Some of
 #'   code is adapted from Eric Stemmler: \url{https://web.archive.org/web/20201120030409/https://stats-bayes.com/post/2020/08/14/r-function-for-little-s-test-for-data-missing-completely-at-random/}
-#'   using Maximum likelihood estimation from {norm}.
+#'   using Maximum likelihood estimation from `norm`.
 #'
 #' @author Andrew Heiss, \email{[email protected]}
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -54,14 +54,16 @@ group_by_fun <- function(data, .fun, ...) {
 #' }
 #' @keywords internal
 #' @noRd
-test_if_null <- function(x) {
+test_if_null <- function(x,
+                         call = rlang::caller_env()) {
   # test for null
   if (is.null(x)) {
     cli::cli_abort(
-      c(
+      message = c(
         "Input must not be NULL",
         "Input is {.cls {class(x)}}"
-      )
+      ),
+      call = call
     )
   }
 }
@@ -128,27 +130,32 @@ test_if_dots_missing <- function(dots_empty,
 #'
 #' @keywords internal
 #' @noRd
-test_if_dataframe <- function(x) {
+test_if_dataframe <- function(x,
+                              arg = rlang::caller_arg(x),
+                              call = rlang::caller_env()) {
   # test for dataframe
   if (!inherits(x, "data.frame")) {
     cli::cli_abort(
-      c(
+      message = c(
         "Input must inherit from {.cls data.frame}",
         "We see class: {.cls {class(x)}}"
-      )
+      ),
+      call = call
     )
   }
 }
 
-test_if_any_shade <- function(x) {
+test_if_any_shade <- function(x,
+                              call = rlang::caller_env()) {
   # test for dataframe
   test_if_dataframe(x)
   if (!any_shade(x)) {
-    cli::format_error(
-      c(
+    cli::cli_abort(
+      message = c(
         "Input must contain a shade column.",
         "See {.code ?shade}, {.code ?shade}, and {.code ?bind_shadow}"
-      )
+      ),
+      call = call
     )
   }
 }
@@ -251,36 +258,42 @@ vecIsFALSE <- Vectorize(isFALSE)
 
 are_any_false <- function(x, ...) any(vecIsFALSE(x), ...)
 
-check_btn_0_1 <- function(prop) {
+check_btn_0_1 <- function(prop,
+                          call = rlang::caller_env()) {
   if (prop < 0 || prop > 1) {
     cli::cli_abort(
-      c(
+      message = c(
         "{.var prop} must be between 0 and 1",
         "{.var prop} is {prop}"
-      )
+      ),
+      call = call
     )
   }
 }
 
-check_is_integer <- function(x) {
+check_is_integer <- function(x,
+                             call = rlang::caller_env()) {
   if (x < 0) {
     cli::cli_abort(
-      c(
+      message = c(
         "{.var x} must be greater than 0",
         "{.var x} is {.val {x}}"
-      )
+      ),
+      call = call
     )
   }
   vctrs::vec_cast(x, integer())
 }
 
-check_is_scalar <- function(x) {
+check_is_scalar <- function(x,
+                            call = rlang::caller_env()) {
   if (length(x) != 1) {
     cli::cli_abort(
-      c(
+      message = c(
         "{.var x} must be length 1",
         "{.var x} is {x}, and {.var x} has length: {length(x)}"
-      )
+      ),
+      call = call
     )
   }
 }
diff --git a/README.md b/README.md
@@ -310,7 +310,7 @@ which both return output ordered by the number of missing values.
 miss_var_summary(airquality)
 #> # A tibble: 6 × 3
 #>   variable n_miss pct_miss
-#>   <chr>     <int>    <dbl>
+#>   <chr>     <int>    <num>
 #> 1 Ozone        37    24.2 
 #> 2 Solar.R       7     4.58
 #> 3 Wind          0     0   
@@ -354,7 +354,7 @@ airquality %>%
 #> # A tibble: 25 × 4
 #> # Groups:   Month [5]
 #>    Month variable n_miss pct_miss
-#>    <int> <chr>     <int>    <dbl>
+#>    <int> <chr>     <int>    <num>
 #>  1     5 Ozone         5     16.1
 #>  2     5 Solar.R       4     12.9
 #>  3     5 Wind          0      0  

diff --git a/cran-comments.md b/cran-comments.md
@@ -9,37 +9,21 @@ There were no ERRORs or WARNINGs, and one NOTE:
 
 ```
 Found the following (possibly) invalid URLs:
-  URL: https://web.archive.org/web/20201120030409/https://stats-bayes.com/post/2020/08/14/r-function-for-little-s-test-for-data-missing-completely-at-random/
-    From: man/mcar_test.Rd
-    Status: Error
-    Message: Failed to connect to web.archive.org port 443 after 21108 ms: Timed out
   URL: https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily
     From: inst/doc/special-missing-values.html
     Status: Error
     Message: Empty reply from server
-  URL: https://www.researchgate.net/publication/2758672_Missing_Data_in_Interactive_High-Dimensional_Data_Visualization
-    From: man/as_shadow.Rd
-          inst/doc/getting-started-w-naniar.html
-          inst/doc/special-missing-values.html
-          README.md
-    Status: 403
-    Message: Forbidden
-
-Found the following (possibly) invalid DOIs:
-  DOI: 10.18637/jss.v105.i07
-    From: DESCRIPTION
-          inst/CITATION
-    Status: 404
-    Message: Not Found
 ```
 
-The DOI in the CITATION is for a new JSS publication that will be registered after publication on CRAN.
+Navigating to the website works on my machine, but I note that the NCEI website states in a banner:
+
+> Please note: Due to a system outage, many NCEI systems are currently unavailable. We are working to resolve these issues as soon as possible. We apologize for any inconvenience.
 
-The other links all work locally for me on my machine, and checking with `wget` locally they also work. I'm not sure how to best proceed with these?
+Which makes me think that perhaps this is an issue related to that?
 
 ## Reverse dependencies
 
-We checked 3 reverse dependencies (2 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 6 reverse dependencies (5 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages

diff --git a/man/mcar_test.Rd b/man/mcar_test.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,25 +1,26 @@
 # Platform
 
-|field    |value                                                                                       |
-|:--------|:-------------------------------------------------------------------------------------------|
-|version  |R version 4.2.1 (2022-06-23)                                                                |
-|os       |macOS Monterey 12.3.1                                                                       |
-|system   |aarch64, darwin20                                                                           |
-|ui       |RStudio                                                                                     |
-|language |(EN)                                                                                        |
-|collate  |en_US.UTF-8                                                                                 |
-|ctype    |en_US.UTF-8                                                                                 |
-|tz       |Australia/Hobart                                                                            |
-|date     |2023-02-01                                                                                  |
-|rstudio  |2022.12.0+353 Elsbeth Geranium (desktop)                                                    |
-|pandoc   |2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) |
+|field    |value                               |
+|:--------|:-----------------------------------|
+|version  |R version 4.3.3 (2024-02-29)        |
+|os       |macOS Sonoma 14.3.1                 |
+|system   |aarch64, darwin20                   |
+|ui       |RStudio                             |
+|language |(EN)                                |
+|collate  |en_US.UTF-8                         |
+|ctype    |en_US.UTF-8                         |
+|tz       |Australia/Melbourne                 |
+|date     |2024-03-04                          |
+|rstudio  |2023.12.1+402 Ocean Storm (desktop) |
+|pandoc   |NA                                  |
 
 # Dependencies
 
 |package |old   |new   |Δ  |
 |:-------|:-----|:-----|:--|
-|naniar  |0.6.1 |0.9.0 |*  |
-|forcats |NA    |1.0.0 |*  |
+|naniar  |1.0.0 |1.1.0 |*  |
+|ggplot2 |NA    |3.5.0 |*  |
+|viridis |NA    |0.6.5 |*  |
 
 # Revdeps
 
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 3 reverse dependencies (2 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 6 reverse dependencies (5 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages

diff --git a/tests/testthat/_snaps/add-shadow.md b/tests/testthat/_snaps/add-shadow.md
@@ -2,8 +2,8 @@
 
     Code
       add_shadow(dat)
-    Warning <lifecycle_warning_deprecated>
-      The `value` argument of `names<-` must have the same length as `x` as of tibble 3.0.0.
-    Error <vctrs_error_incompatible_size>
-      Can't recycle `..1` (size 5) to match `..2` (size 0).
+    Condition
+      Error in `add_shadow()`:
+      ! argument must be specified
+      {.fun add_shadow} requires variables to be selected
 
diff --git a/tests/testthat/_snaps/add-shadow.new.md b/tests/testthat/_snaps/add-shadow.new.md
diff --git a/tests/testthat/_snaps/as-shadow.md b/tests/testthat/_snaps/as-shadow.md
@@ -3,7 +3,7 @@
     Code
       as_shadow(0)
     Condition
-      Error in `test_if_dataframe()`:
+      Error in `as_shadow()`:
       ! Input must inherit from <data.frame>
       We see class: <numeric>
 
@@ -12,7 +12,7 @@
     Code
       as_shadow("a")
     Condition
-      Error in `test_if_dataframe()`:
+      Error in `as_shadow()`:
       ! Input must inherit from <data.frame>
       We see class: <character>
 
@@ -21,7 +21,7 @@
     Code
       as_shadow(matrix(airquality))
     Condition
-      Error in `test_if_dataframe()`:
+      Error in `as_shadow()`:
       ! Input must inherit from <data.frame>
       We see class: <matrix/array>
 
@@ -30,7 +30,7 @@
     Code
       as_shadow(NULL)
     Condition
-      Error in `test_if_null()`:
+      Error in `as_shadow()`:
       ! Input must not be NULL
       Input is <NULL>
 
diff --git a/tests/testthat/_snaps/cast-shadow-shift-label.md b/tests/testthat/_snaps/cast-shadow-shift-label.md
@@ -2,8 +2,8 @@
 
     Code
       cast_shadow_shift(airquality)
-    Warning <lifecycle_warning_deprecated>
-      The `value` argument of `names<-` must have the same length as `x` as of tibble 3.0.0.
-    Error <vctrs_error_incompatible_size>
-      Can't recycle `..1` (size 153) to match `..2` (size 0).
+    Condition
+      Error in `cast_shadow()`:
+      ! argument must be specified
+      {.fun cast_shadow} requires variables to be selected after the data
 
diff --git a/tests/testthat/_snaps/cast-shadow-shift.md b/tests/testthat/_snaps/cast-shadow-shift.md
@@ -2,8 +2,8 @@
 
     Code
       cast_shadow_shift(airquality)
-    Warning <lifecycle_warning_deprecated>
-      The `value` argument of `names<-` must have the same length as `x` as of tibble 3.0.0.
-    Error <vctrs_error_incompatible_size>
-      Can't recycle `..1` (size 153) to match `..2` (size 0).
+    Condition
+      Error in `cast_shadow()`:
+      ! argument must be specified
+      {.fun cast_shadow} requires variables to be selected after the data