Minor fixes for release (#273)

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.1
-Date: 2024-01-25 08:55:36 UTC
-SHA: 634055424dfbbb642ab2a7b79b7fb1aa5e4268d6
+Version: 1.0.4
+Date: 2024-02-28 21:56:01 UTC
+SHA: 19c35ea247d31386d052a43cd34827a010b15bdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: saros
 Title: Semi-Automatic Reporting of Ordinary Surveys
-Version: 1.0.1.9003
+Version: 1.0.4
 Authors@R: c(
     person(given = "Stephan", 
            family = "Daus", 

NEWS.md

@@ -1,15 +1,18 @@
 <!-- NEWS.md is maintained by https://cynkra.github.io/fledge, do not edit -->
 
-# saros 1.0.1.9003
+# saros 1.0.3
 
 - Added more arguments for plot text sizes, with more useful defaults for Word and HTML layouts.
-
-
-# saros 1.0.1.9002
-
-# saros 1.0.1.9001
-
-* Minor fix in sanitize_labels
+- `attach_qualtrics_labels` is now more flexible.
+- Minor fix in `sanitize_labels`.
+- Internal change to accommodate ggplot2 3.5.0.
+- Improved performance for argument validation checks.
+- `setup_access_restrictions` now accepts NULL password input.
+- `setup_access_restrictions` now can warn instead of error if `rel_parent_path` does not exist.
+- `sort_by` now correctly sorts with `descend=TRUE` for ".upper", etc.
+- Fixed `list_available_element_types`
+- Set one long-running test for `draft_report` to only run on maintainer's local computer.
+- `sanitize_labels` now has option to translate ASCII HTML-escaped characters to unicode.
 
 # saros 1.0.1
 

R/cat_prop_plot_html.R

@@ -228,7 +228,9 @@ prep_cat_prop_plot_html <-
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' embed_cat_prop_plot(data = ex_survey, dep = b_1:b_3)
+#' }
 embed_cat_prop_plot <-
   function(data,
            ...,

R/qualtrics.R

@@ -51,6 +51,7 @@ attach_qualtrics_labels <- function(data, questions, reverse_stata_replacement=F
 #' @param data data.frame or tibble
 #' @param sep String, separates main question from subquestion
 #' @param multi_sep_replacement String. If multiple sep are found, replace the first ones with this.
+#' @param replace_ascii_with_utf Flag. If TRUE, downloads a list from W3 used to convert html characters as ASCII to UTF8.
 #' @param questions Data frame with questions obtained from `qualtRics::survey_questions()`
 #'
 #' @return Identical data.frame as input, with only variable labels changed.
@@ -61,9 +62,11 @@ attach_qualtrics_labels <- function(data, questions, reverse_stata_replacement=F
 sanitize_labels <- function(data,
                             sep = " - ",
                             multi_sep_replacement = ": ",
+                            replace_ascii_with_utf = FALSE,
                             questions = NULL) {
 
   # scrape lookup table of accented char html codes, from the 2nd table on this page
+  if(isTRUE(replace_ascii_with_utf)) {
   ref_url <- 'http://www.w3schools.com/charsets/ref_html_8859.asp'
   cols <- c("Character", "Entity Name")
   char_table <- rvest::read_html(ref_url)
@@ -72,6 +75,7 @@ sanitize_labels <- function(data,
   char_table <- lapply(char_table, function(x) x[, cols])
   char_table <- do.call(rbind, char_table)
   char_table <- char_table[!duplicated(char_table[[cols[2]]]) & char_table[[cols[2]]] != "", ]
+  }
 
   # here's a test string loaded with different html accents
   # test_str <- '&Agrave; &Aacute; &Acirc; &Atilde; &Auml; &Aring; &AElig; &Ccedil; &Egrave; &Eacute; &Ecirc; &Euml; &Igrave; &Iacute; &Icirc; &Iuml; &ETH; &Ntilde; &Ograve; &Oacute; &Ocirc; &Otilde; &Ouml; &times; &Oslash; &Ugrave; &Uacute; &Ucirc; &Uuml; &Yacute; &THORN; &szlig; &agrave; &aacute; &acirc; &atilde; &auml; &aring; &aelig; &ccedil; &egrave; &eacute; &ecirc; &euml; &igrave; &iacute; &icirc; &iuml; &eth; &ntilde; &ograve; &oacute; &ocirc; &otilde; &ouml; &divide; &oslash; &ugrave; &uacute; &ucirc; &uuml; &yacute; &thorn; &yuml;'
@@ -83,11 +87,7 @@ sanitize_labels <- function(data,
     label <- attr(data[[var]], "label")
 
     if(is_string(label)) {
-      for(i in seq_len(nrow(char_table))) {
-        label <- stringi::stri_replace_all_fixed(str = label,
-                                                 pattern = char_table[i, cols[2], drop=TRUE],
-                                                 replacement = char_table[i, cols[1], drop=TRUE])
-      }
+
 
       # Replace references with those provided in questions, if any
       if(!is.null(questions) &&
@@ -108,6 +108,14 @@ sanitize_labels <- function(data,
         }
       }
 
+      if(isTRUE(replace_ascii_with_utf)) {
+        for(i in seq_len(nrow(char_table))) {
+          label <- stringi::stri_replace_all_fixed(str = label,
+                                                   pattern = char_table[i, cols[2], drop=TRUE],
+                                                   replacement = char_table[i, cols[1], drop=TRUE])
+        }
+      }
+
       label <- stringi::stri_replace_all_regex(label, pattern = "- Selected Choice ", replacement = "- ")
       label <- stringi::stri_replace_all_regex(label, pattern = "<.+?>|\\[.*\\]| - tekst", replacement = "")
       label <- stringi::stri_replace_all_regex(label, pattern = "\\$\\{[[:alnum:]]+[^[:alnum:]]([[:alnum:]]+)\\}", replacement = "$1")

README.Rmd

@@ -52,13 +52,6 @@ pak::pak("sda030/saros")
 ```
 
 
-## Initialize a social science project
-
-```{r example}
-### CURRENTLY NOT WORKING. MOVE TO ANOTHER PACKAGE?
-#> saros::initialize(folder = getwd())
-```
-
 ## Draft a report
 ```{r example2}
 # Define temporary folder for storing the elements
@@ -99,8 +92,6 @@ output_index_qmd <-
                hide_label_if_prop_below = .05, 
                hide_test_if_n_below = 10,
                mesos_first = TRUE,
-               colour_palette_nominal = nifutheme::nifu_cols(),
-               colour_palette_ordinal = nifutheme::nifu_cols("reds"),
                digits = 0,
                data_label_decimal_symbol = ",",
              path = tempdir())

README.md

@@ -62,13 +62,6 @@ install.packages("pak")
 pak::pak("sda030/saros")
 ```
 
-## Initialize a social science project
-
-``` r
-### CURRENTLY NOT WORKING. MOVE TO ANOTHER PACKAGE?
-#> saros::initialize(folder = getwd())
-```
-
 ## Draft a report
 
 ``` r
@@ -82,7 +75,7 @@ output_index_qmd <-
              )
 #> Refining chapter_overview...Not using the following variables in `data`: `x2_human`, `a_7`, `a_8`, and
 #> `resp_status`.                             Generating for chapter Introduction: 1_Introduction                                                    Generating for chapter Ambivalence: 2_Ambivalence                                                  Generating for chapter Big mysteries: 3_Big_mysterie                                                     Generating for chapter Confidence: 4_Confidence                                                Generating for chapter Doubt: 5_Doubt                                      
-#> 77.14 4.67 105.45 NA NA
+#> 200.06 28.83 275.59 NA NA
 quarto::quarto_render(output_index_qmd, as_job = FALSE)
 #> pandoc 
 #>   to: html
@@ -133,27 +126,15 @@ output_index_qmd <-
                hide_label_if_prop_below = .05, 
                hide_test_if_n_below = 10,
                mesos_first = TRUE,
-               colour_palette_nominal = nifutheme::nifu_cols(),
-               colour_palette_ordinal = nifutheme::nifu_cols("reds"),
                digits = 0,
                data_label_decimal_symbol = ",",
              path = tempdir())
 #> Refining chapter_overview...Not using the following variables in `data`: `a_7`,
 #> `a_8`, and `resp_status`. Generating for chapter Introduction: 1_Introduction
 #> Generating for chapter Ambivalence: 2_Ambivalence Generating for chapter Big
 #> mysteries: 3_Big_mysterie Generating for chapter Confidence: 4_Confidence
-#> Warning: Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
-#> Fewer colours in user-provided colour palette than needed.
 #> Generating for chapter Doubt: 5_Doubt
-#> 85.45 6.3 108.1 NA NA
+#> 216.97 32.25 296.64 NA NA
 ```
 
 ``` r
@@ -185,7 +166,7 @@ system.time( # 519 sec
 #>   
 #> Output created: main_index.html
 #>    user  system elapsed 
-#>    0.05    0.00    2.99
+#>    0.00    0.00    6.02
 if(interactive()) {
   browseURL(fs::path(tempdir(), "Uni of C", "Uni of C_main_index.html"))
 }

cran-comments.md

@@ -1,18 +1,8 @@
-## Resubmission to new release
-
 ## R CMD check results
 
 0 errors | 0 warnings | 2 notes
 
-## Responses to manual review:
-  * Note that there are not yet any references to describe the methods used in the package, nor are there any new statistical methods applied.
-  * Description field in DESCRIPTION now has only single spaces.
-  * list_available_element_types and render_full_reports now have return values.
-  * Unexported functions now have no examples.
-  * All \dontrun-tags are removed, except one which is supposed to result in error and \donttest for embed_cat_freq_plot which takes > 5 sec.
-  * Removed default save locations and getwd() in arguments.
-  * No function writes by default to working directory/package folder. 
-  * The NOTE: Found the following files/directories: ''NULL'' is due to a bug in running the examples. (I can prove this is not particular to my package).
-  * Additonally, customizable has been rewritten to customized, in the description field.
-  * Following {goodpractice}-package I have also replaced sapply with vapply to ensure robustness.
-  * All cran checks have been rerun again.
+## Note
+
+- Set one long-running test only locally, saving many minutes.
+- Early update due to changes in ggplot2.

inst/WORDLIST

@@ -47,6 +47,7 @@ htpasswd
 https
 ifany
 indep
+maintainer's
 mesos
 missingess
 mschart
@@ -73,5 +74,6 @@ tabset
 tibble
 tibbles
 tidyselect
+unicode
 vec
 yaml

saros.Rproj

@@ -17,6 +17,7 @@ StripTrailingWhitespace: Yes
 LineEndingConversion: Posix
 
 BuildType: Package
+PackageUseDevtools: Yes
 PackageInstallArgs: --with-keep.source
 PackageRoxygenize: rd,collate,namespace,vignette
 

tests/testthat/test-draft_report.R

@@ -19,6 +19,8 @@ testthat::test_that("draft_report", {
 
 
   ##############################
+
+  if(Sys.getenv("USERNAME") == "py128") { # Run expensive >10 min test only for maintainer
   tmpdir <- file.path(tempdir(), "test-draft_report2")
   data <- saros::ex_survey |>
     dplyr::filter(f_uni %in% c("Uni of A", "Uni of B"))
@@ -35,4 +37,5 @@ testthat::test_that("draft_report", {
     object = length(output_files),
     expected = nrow(saros::ex_survey_ch_overview[1:3, ]) * dplyr::n_distinct(data$f_uni))
 
+  }
 })

tests/testthat/test-gen_qmd_index.R

@@ -4,7 +4,7 @@ testthat::test_that("gen_qmd_index works as expected", {
   # Test 1: Basic test with title, authors, and chapter files
   index_filepath <- tempfile(fileext = ".qmd")
   chapter_filepaths <- c(tempfile(fileext = ".qmd"), tempfile(fileext = ".qmd"))
-  result <- gen_qmd_index(
+  result <- saros:::gen_qmd_index(
     authors = c("Author 1", "Author 2"),
     index_filepath = index_filepath,
     chapter_filepaths = chapter_filepaths
@@ -15,7 +15,7 @@ testthat::test_that("gen_qmd_index works as expected", {
 
   # Test 2: Test with only title and chapter files
   index_filepath <- tempfile(fileext = ".qmd")
-  result <- gen_qmd_index(
+  result <- saros:::gen_qmd_index(
     index_filepath = index_filepath,
     chapter_filepaths = chapter_filepaths
   )
@@ -24,7 +24,7 @@ testthat::test_that("gen_qmd_index works as expected", {
 
   # Test 3: Test with only authors and chapter files
   index_filepath <- tempfile(fileext = ".qmd")
-  result <- gen_qmd_index(
+  result <- saros:::gen_qmd_index(
     authors = c("Author 1", "Author 2"),
     index_filepath = index_filepath,
     chapter_filepaths = chapter_filepaths
@@ -34,7 +34,7 @@ testthat::test_that("gen_qmd_index works as expected", {
 
   # Test 4: Test with only chapter files
   index_filepath <- tempfile(fileext = ".qmd")
-  result <- gen_qmd_index(
+  result <- saros:::gen_qmd_index(
     index_filepath = index_filepath,
     chapter_filepaths = chapter_filepaths
   )
@@ -44,7 +44,7 @@ testthat::test_that("gen_qmd_index works as expected", {
 
   # Test 5: Test with empty chapter filepaths
   index_filepath <- tempfile(fileext = ".qmd")
-  result <- gen_qmd_index(
+  result <- saros:::gen_qmd_index(
     authors = c("Author 1", "Author 2"),
     index_filepath = index_filepath,
     chapter_filepaths = NULL

tests/testthat/test-rename_by_labels.R

@@ -1,4 +1,4 @@
-test_that("rename_by_labels", {
+testthat::test_that("rename_by_labels", {
   suppressMessages(library(dplyr))
   library(labelled)
   testthat::expect_warning(object = {

tests/testthat/test-summarize_data.R

@@ -1,4 +1,5 @@
 testthat::test_that("summarize_data", {
+  #Takes on average 5 sec to run all.
 
   testthat::expect_equal(
     saros:::summarize_data(

tests/testthat/test-ungroup_data.R

@@ -1,4 +1,4 @@
-test_that("ungroup_data", {
+testthat::test_that("ungroup_data", {
   x <- saros::ex_survey %>%
     dplyr::group_by(.data$f_uni)
   testthat::expect_false(inherits(saros:::ungroup_data(x), "grouped_df"))

tests/testthat/test-utils.R

@@ -1,9 +1,7 @@
 testthat::test_that("col_to_binaries", {
-  suppressMessages(library(dplyr))
   test <-
-    ex_survey %>%
-    col_to_binaries(col = b_3, label_separator = "  -  ") %>%
-    pull(`b_3___A bit`)
+    col_to_binaries(ex_survey, col = b_3, label_separator = "  -  ") |>
+    dplyr::pull(`b_3___A bit`)
   testthat::expect_true(object = all(as.vector(test) %in% 0:1))
   testthat::expect_equal(attr(test, "label"),
                          expected = "How much do you like living in - Budapest  -  A bit")