Dev

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,28 +1,32 @@
 Type: Package
 Package: saros.contents
-Title: Semi-Automatic Reporting of Ordinary Surveys
-Version: 0.1
+Title: Contents for the Semi-Automatic Reporting of Ordinary Surveys (Saros)
+Version: 0.1.0
 Authors@R: c(
     person(given = "Stephan", 
            family = "Daus", 
            role = c("aut", "cre", "cph"),
            email = "[email protected]", 
            comment = c(ORCID = "0000-0003-0230-6997")),
+    person("Julia", "Silge", role = c("ctb"), comment = "Author of internal scale_x_reordered"),
+    person("David", "Robinson", role = c("ctb"), comment = "Author of internal scale_x_reordered"),
     person("Nordic Institute for The Studies of Innovation, Research and Education (NIFU)", 
            role = c("fnd")),
     person("Kristiania University College", 
            role = c("fnd"))
   )
 Maintainer: Stephan Daus <[email protected]>
-Description: Produces highly customized reports, primarily intended for survey
-    research. Building on 'Quarto' (<https://quarto.org>), it generates draft
-    chapters of all specified dependent/independent variables, which can be
-    further edited by hand, containing figures, tables and analyses (currently
-    only uni-/bivariate tests of equivalent means/proportions). The feature
-    'mesos'-reports offer tailor-made batch report production where e.g. an
-    institution can compare itself to all other participants. Publication tools
-    are also included, such as password generation for 'mesos'-report sections
-    on a 'Quarto' Website.
+Description: Offers a systematic way for conditional reporting of figures and tables for many
+    (and bivariate combinations of) variables, typically from survey data.
+    Contains interactive ggiraph-based 
+    (<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
+    data frame-based summary tables (bivariate significance tests, 
+    frequencies/proportions, unique open ended responses, etc) with
+    many arguments for customization, and extensions possible. Uses a global 
+    `options()` system for neatly reducing redundant code.
+    Also contains tools for immediate saving of objects and returning a hashed link to the object,
+    useful for creating download links to high resolution images upon rendering in Quarto.
+    See 'saros' (<https://CRAN.R-project.org/package=saros>) for the main umbrella package.
 Note: Free to use for non-Norwegian institutions, otherwise see LICENSE.
 License: MIT + file LICENSE
 URL: https://nifu-no.github.io/saros.contents/, https://github.com/NIFU-NO/saros.contents
@@ -31,7 +35,6 @@ Depends:
     R (>= 4.2.0)
 Imports: 
     cli,
-    saros.base,
     utils,
     vctrs,
     glue,
@@ -41,11 +44,11 @@ Imports:
     rlang,
     stringi,
     forcats,
-     ggplot2,
-     ggiraph,
-     mschart,
-     officer,
-     fs
+    ggplot2,
+    ggiraph,
+    mschart,
+    officer,
+    fs
 Suggests:
     covr,
     srvyr,
@@ -58,11 +61,11 @@ Suggests:
     withr,
     quarto,
     spelling
-SystemRequirements: Quarto command line tools (https://github.com/quarto-dev/quarto-cli) for the rendering wrapper functionality.
 Config/testthat/edition: 3
 Encoding: UTF-8
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Language: en-US
 Config/Needs/website: rmarkdown
 Config/testthat/parallel: true
+LazyData: true

NEWS.md

@@ -0,0 +1,3 @@
+# saros.contents 0.1.0
+
+* Initial CRAN submission.

R/colour.R

@@ -191,8 +191,8 @@ get_colour_set <-
 #' @return A colour set as character vector, where `NA` has the `colour_na`, and the rest are taken from colour_palette_nominal if available.
 #' @keywords internal
 #'
-# get_colour_palette(saros.base::ex_survey, col_pos=c("b_1", "b_2"))
-# get_colour_palette(saros.base::ex_survey, col_pos=c("b_1", "b_2"),
+# get_colour_palette(ex_survey, col_pos=c("b_1", "b_2"))
+# get_colour_palette(ex_survey, col_pos=c("b_1", "b_2"),
 #                   colour_palette_nominal = c("red", "blue", "orange"))
 get_colour_palette <-
   function(

R/crosstable.R

@@ -28,7 +28,7 @@ crosstable.data.frame <-
     }
 
     # indep_names <- colnames(data[, indep, drop = FALSE])
-    indep_labels <- saros.base::get_raw_labels(data = data, col_pos = indep)
+    indep_labels <- get_raw_labels(data = data, col_pos = indep)
     col_names <- colnames(data[ , dep, drop=FALSE])[!(colnames(data[ , dep, drop=FALSE]) %in% indep)]
 
 
@@ -147,7 +147,7 @@ crosstable.data.frame <-
                                              levels = fct_lvls,
                                              labels = fct_lvls,
                                              exclude = character())
-            summary_prop$.variable_label <- unname(saros.base::get_raw_labels(data = data, col_pos = .x))
+            summary_prop$.variable_label <- unname(get_raw_labels(data = data, col_pos = .x))
             # summary_prop$.mean_base <- as.integer(summary_prop$.category) * summary_prop$.count
             summary_prop$.count_se <- NA_real_
             summary_prop$.proportion_se <- NA_real_
@@ -168,7 +168,7 @@ crosstable.data.frame <-
             out$.variable_name <- .x
           } else {
             out <- data.frame(.variable_name = .x,
-                              .variable_label = unname(saros.base::get_raw_labels(data = data, col_pos = .x)),
+                              .variable_label = unname(get_raw_labels(data = data, col_pos = .x)),
                               .category = factor(NA),
                               .count = NA_integer_,
                               .count_se = NA_real_,
@@ -230,7 +230,7 @@ crosstable.tbl_svy <-
     showNA <- rlang::arg_match(showNA, values = eval(formals(makeme)$showNA), error_call = call)
 
     # indep_names <- colnames(data[, indep, drop = FALSE])
-    indep_labels <- saros.base::get_raw_labels(data = data$variables, col_pos = indep)
+    indep_labels <- get_raw_labels(data = data$variables, col_pos = indep)
     col_names <- colnames(data[, dep, drop = FALSE])[!(colnames(data[, dep, drop = FALSE]) %in% indep)]
 
     # indep_names <- colnames(srvyr::select(data, indep))
@@ -286,10 +286,10 @@ crosstable.tbl_svy <-
                                          .proportion = srvyr::survey_prop(proportion = TRUE))
         summary_prop <- srvyr::ungroup(summary_prop)
         summary_prop <- srvyr::as_tibble(summary_prop)
-        # print(saros.base::get_raw_labels(data = srvyr::as_tibble(data), col_pos = .x))
+        # print(get_raw_labels(data = srvyr::as_tibble(data), col_pos = .x))
         summary_prop <- dplyr::mutate(summary_prop,
                                       .category = factor(x = .data$.category, levels = fct_lvls, labels = fct_lvls),
-                                      .variable_label = saros.base::get_raw_labels(data = srvyr::as_tibble(data), col_pos = .x)
+                                      .variable_label = get_raw_labels(data = srvyr::as_tibble(data), col_pos = .x)
                                       # .mean_base = as.integer(.category) * .count
         )
 
@@ -302,7 +302,7 @@ crosstable.tbl_svy <-
 
       } else {
         out <- data.frame(.variable_name = .x,
-                          .variable_label = unname(saros.base::get_raw_labels(data = data, col_pos = .x)),
+                          .variable_label = unname(get_raw_labels(data = data, col_pos = .x)),
                           .category = factor(NA),
                           .count = NA_integer_,
                           .count_total = NA_integer_,

R/data.R

@@ -0,0 +1,58 @@
+# #' @inherit saros.base::ex_survey description source references title
+# #' @export
+# ex_survey <- saros.base::ex_survey
+
+#.not_used_fns <- function() {
+#  saros.base::read_default_draft_report_args
+#}
+
+#' ex_survey: Mockup dataset of a survey.
+#'
+#' A dataset containing fake respondents' answers to survey questions.
+#' The first two, x_sex and x_human, are intended to be independent variables,
+#' whereas the remaining are dependent. The underscore _ in variable names
+#' separates item groups (prefix) from items (suffix) (i.e. a_1-a_9 => a + 1-9),
+#'  whereas ' - ' separates the same for labels.
+#'  The latter corresponds with the default in SurveyXact.
+#'
+#' @format A data frame with 100 rows and 29 variables:
+#' \describe{
+#'   \item{x1_sex}{Gender}
+#'   \item{x2_human}{Is respondent human?}
+#'   \item{x3_nationality}{Where is the respondent born?}
+#'   \item{a_1}{Do you consent to the following? - Agreement #1}
+#'   \item{a_2}{Do you consent to the following? - Agreement #2}
+#'   \item{a_3}{Do you consent to the following? - Agreement #3}
+#'   \item{a_4}{Do you consent to the following? - Agreement #4}
+#'   \item{a_5}{Do you consent to the following? - Agreement #5}
+#'   \item{a_6}{Do you consent to the following? - Agreement #6}
+#'   \item{a_7}{Do you consent to the following? - Agreement #7}
+#'   \item{a_8}{Do you consent to the following? - Agreement #8}
+#'   \item{a_9}{Do you consent to the following? - Agreement #9}
+#'   \item{b_1}{How much do you like living in - Beijing}
+#'   \item{b_2}{How much do you like living in - Brussels}
+#'   \item{b_3}{How much do you like living in - Budapest}
+#'   \item{c_1}{How many years of experience do you have in - Company A}
+#'   \item{c_2}{How many years of experience do you have in - Company B}
+#'   \item{d_1}{Rate your degree of confidence doing the following - Driving}
+#'   \item{d_2}{Rate your degree of confidence doing the following - Drinking}
+#'   \item{d_3}{Rate your degree of confidence doing the following - Driving}
+#'   \item{d_4}{Rate your degree of confidence doing the following - Dancing}
+#'   \item{e_1}{How often do you do the following? - Eat}
+#'   \item{e_2}{How often do you do the following? - Eavesdrop}
+#'   \item{e_3}{How often do you do the following? - Exercise}
+#'   \item{e_4}{How often do you do the following? - Encourage someone whom you have only recently met and who struggles with simple tasks that they cannot achieve by themselves}
+#'   \item{p_1}{To what extent do you agree or disagree to the
+#'   following policies - Red Party}
+#'   \item{p_2}{To what extent do you agree or disagree to the
+#'   following policies - Green Party}
+#'   \item{p_3}{To what extent do you agree or disagree to the
+#'   following policies - Yellow Party}
+#'   \item{p_4}{To what extent do you agree or disagree to the
+#'   following policies - Blue Party}
+#'   \item{f_uni}{Which of the following universities would you
+#'   prefer to study at?}
+#'   \item{open_comments}{Do you have any comments to the survey?}
+#'   \item{resp_status}{Response status}
+#' }
+"ex_survey"