Merge pull request #118 from olivroy/fix

Adjustments to help bring package back to CRAN

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

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -19,8 +19,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,8 +41,8 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: docs

.github/workflows/render-readme.yaml

@@ -11,9 +11,9 @@ jobs:
     name: Render README
     runs-on: macOS-latest
     steps:
-      - uses: actions/checkout@v1
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-pandoc@v2
       - name: Install rmarkdown
         run: Rscript -e 'install.packages("rmarkdown")'
       - name: Render README

.github/workflows/test-coverage.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]
+
+name: test-coverage
+
+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
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - 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

@@ -52,17 +52,15 @@ Imports:
     tsibble (>= 0.8.2),
     vctrs
 Suggests: 
-    markdown,
-    covr,
     gapminder,
     gghighlight (>= 0.1.0),
     knitr (>= 1.23),
+    Matrix (>= 1.6-5),
     lme4,
     modelr,
-    readr (>= 1.3.1),
     rmarkdown (>= 1.14),
     spelling (>= 2.1),
-    testthat (>= 2.1.0),
+    testthat (>= 3.0.0),
     tsibbledata,
     vdiffr (>= 0.3.1)
 VignetteBuilder: 
@@ -71,5 +69,5 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3

R/b_summaries.R

@@ -98,9 +98,9 @@ b_range <- function(x, ... ){
 #' @name b_summaries
 #' @export
 b_range_diff <- function(x, ... ) {
-  diff(b_range(x, 
-               na.rm = TRUE,
-               ...))
+  the_range <- b_range(x, 
+                       ...)
+  diff(the_range)
 }
 
 #' @name b_summaries

R/brolgar-package.R

@@ -1,12 +1,9 @@
-#' brolgar
-#'
+#' @details
 #' `brolgar` stands for: **BR**owse over **L**ongitudinal data **G**raphically
-#'   and **A**nalytically in **R**.
+#' and **A**nalytically in **R**.
 #'
-#' @name brolgar
 #' @keywords internal
-#' @docType package
-NULL
+"_PACKAGE"
 
 #' @importFrom rlang .data quo quos enquo enquos quo_name sym ensym syms :=
 

R/keys_near.R

@@ -46,10 +46,10 @@ keys_near.tbl_ts <- function(.data,
       .vars = dplyr::vars( {{ var }} ),
       .funs = funs,
       ...) %>%
-    dplyr::select(key,
+    dplyr::select(dplyr::all_of(key),
                   {{ var }},
                   dplyr::any_of(names(funs))) %>%
-    tidyr::pivot_longer(cols = -c(key, {{ var }}),
+    tidyr::pivot_longer(cols = -c(dplyr::all_of(key), {{ var }}),
                         names_to = "stat",
                         values_to = "stat_value") %>% 
     dplyr::mutate(stat_diff = abs({{ var }} - stat_value)) %>%

README.Rmd

@@ -17,7 +17,10 @@ knitr::opts_chunk$set(
 # brolgar
 
 <!-- badges: start -->
-[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![R-CMD-check](https://github.com/njtierney/brolgar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/njtierney/brolgar/actions/workflows/R-CMD-check.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/brolgar)](https://CRAN.R-project.org/package=brolgar) [![Codecov test coverage](https://codecov.io/gh/njtierney/brolgar/branch/main/graph/badge.svg)](https://app.codecov.io/gh/njtierney/brolgar?branch=main)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[![R-CMD-check](https://github.com/njtierney/brolgar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/njtierney/brolgar/actions/workflows/R-CMD-check.yaml)
+[![CRAN status](https://www.r-pkg.org/badges/version/brolgar)](https://CRAN.R-project.org/package=brolgar)
+[![Codecov test coverage](https://codecov.io/gh/njtierney/brolgar/branch/main/graph/badge.svg)](https://app.codecov.io/gh/njtierney/brolgar?branch=main)
 
 <!-- badges: end -->
 

README.md

@@ -89,19 +89,20 @@ like this:
 wages
 #> # A tsibble: 6,402 x 9 [!]
 #> # Key:       id [888]
-#>       id ln_wages    xp   ged xp_since_ged black hispanic high_grade unemploy_…¹
-#>    <int>    <dbl> <dbl> <int>        <dbl> <int>    <int>      <int>       <dbl>
-#>  1    31     1.49 0.015     1        0.015     0        1          8        3.21
-#>  2    31     1.43 0.715     1        0.715     0        1          8        3.21
-#>  3    31     1.47 1.73      1        1.73      0        1          8        3.21
-#>  4    31     1.75 2.77      1        2.77      0        1          8        3.3 
-#>  5    31     1.93 3.93      1        3.93      0        1          8        2.89
-#>  6    31     1.71 4.95      1        4.95      0        1          8        2.49
-#>  7    31     2.09 5.96      1        5.96      0        1          8        2.6 
-#>  8    31     2.13 6.98      1        6.98      0        1          8        4.8 
-#>  9    36     1.98 0.315     1        0.315     0        0          9        4.89
-#> 10    36     1.80 0.983     1        0.983     0        0          9        7.4 
-#> # … with 6,392 more rows, and abbreviated variable name ¹​unemploy_rate
+#>       id ln_wages    xp   ged xp_since_ged black hispanic high_grade
+#>    <int>    <dbl> <dbl> <int>        <dbl> <int>    <int>      <int>
+#>  1    31     1.49 0.015     1        0.015     0        1          8
+#>  2    31     1.43 0.715     1        0.715     0        1          8
+#>  3    31     1.47 1.73      1        1.73      0        1          8
+#>  4    31     1.75 2.77      1        2.77      0        1          8
+#>  5    31     1.93 3.93      1        3.93      0        1          8
+#>  6    31     1.71 4.95      1        4.95      0        1          8
+#>  7    31     2.09 5.96      1        5.96      0        1          8
+#>  8    31     2.13 6.98      1        6.98      0        1          8
+#>  9    36     1.98 0.315     1        0.315     0        0          9
+#> 10    36     1.80 0.983     1        0.983     0        0          9
+#> # ℹ 6,392 more rows
+#> # ℹ 1 more variable: unemploy_rate <dbl>
 ```
 
 And under the hood, it was created with the following setup:
@@ -210,7 +211,7 @@ wages %>%
 #>  8   173 1.56   1.68  2.00  2.05  2.34
 #>  9   206 2.03   2.07  2.30  2.45  2.48
 #> 10   207 1.58   1.87  2.15  2.26  2.66
-#> # … with 878 more rows
+#> # ℹ 878 more rows
 ```
 
 This returns the id, and then the features.
@@ -235,7 +236,7 @@ wages %>%
 #>  8   173 FALSE    FALSE    FALSE  FALSE    
 #>  9   206 TRUE     FALSE    FALSE  TRUE     
 #> 10   207 FALSE    FALSE    FALSE  FALSE    
-#> # … with 878 more rows
+#> # ℹ 878 more rows
 ```
 
 You can read more about creating and using features in the [Finding
@@ -257,10 +258,6 @@ wages %>%
              group = id)) +
   geom_line() + 
   gghighlight(increase)
-#> Warning in left_join(., wages, by = "id"): Each row in `x` is expected to match at most 1 row in `y`.
-#> ℹ Row 1 of `x` matches multiple rows.
-#> ℹ If multiple matches are expected, set `multiple = "all"` to silence this
-#>   warning.
 #> Warning: Tried to calculate with group_by(), but the calculation failed.
 #> Falling back to ungrouped filter operation...
 #> label_key: id
@@ -311,7 +308,7 @@ wages %>%
 #>  8   173     6
 #>  9   206     3
 #> 10   207    11
-#> # … with 878 more rows
+#> # ℹ 878 more rows
 ```
 
 This returns a dataframe, with one row per key, and the number of
@@ -353,18 +350,15 @@ and [Identify Interesting
 Observations](https://brolgar.njtierney.com/articles/id-interesting-obs.html)
 vignettes. As a taster, here are some of the figures you can produce:
 
-    #> Warning in left_join(., wages, by = "id"): Each row in `x` is expected to match at most 1 row in `y`.
-    #> ℹ Row 1 of `x` matches multiple rows.
-    #> ℹ If multiple matches are expected, set `multiple = "all"` to silence this
-    #>   warning.
     #> Warning: Tried to calculate with group_by(), but the calculation failed.
     #> Falling back to ungrouped filter operation...
     #> label_key: id
     #> Too many data series, skip labeling
-    #> Warning in left_join(., wages, by = "id"): Each row in `x` is expected to match at most 1 row in `y`.
-    #> ℹ Row 1 of `x` matches multiple rows.
-    #> ℹ If multiple matches are expected, set `multiple = "all"` to silence this
-    #>   warning.
+    #> Warning in left_join(., wages, by = "id"): Detected an unexpected many-to-many relationship between `x` and `y`.
+    #> ℹ Row 1 of `x` matches multiple rows in `y`.
+    #> ℹ Row 1077 of `y` matches multiple rows in `x`.
+    #> ℹ If a many-to-many relationship is expected, set `relationship =
+    #>   "many-to-many"` to silence this warning.
 
 <img src="man/figures/README-show-wages-lg-1.png" width="75%" style="display: block; margin: auto;" />
 

inst/WORDLIST

@@ -11,6 +11,7 @@ Laa
 Lifecycle
 Modelling
 NLSY
+ORCID
 QLD
 Swihart
 Testthat