Merge pull request #346 from olivroy/site

Improve website rendering
njtierney · Mar 16, 2024 · 255cb25 · 255cb25
2 parents 4f8d7e5 + c6144a1
commit 255cb25
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +41,7 @@ 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

diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -47,7 +47,6 @@ Suggests:
     testthat (>= 3.0.0),
     rpart,
     rpart.plot,
-    covr,
     gridExtra,
     wakefield,
     vdiffr,
@@ -135,7 +134,7 @@ Collate:
     'utils.R'
     'where-na.R'
 URL: https://github.com/njtierney/naniar,
-    http://naniar.njtierney.com/
+    https://naniar.njtierney.com/
 BugReports: https://github.com/njtierney/naniar/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

diff --git a/R/geom-miss-point.R b/R/geom-miss-point.R
@@ -6,11 +6,11 @@
 #'   the same axis.
 #'
 #' @include legend-draw.R
-#' @name  geom_miss_point
-#' @title  geom_miss_point
-#' @note Warning message if na.rm = T is supplied.
+#' @name geom_miss_point
+#' @note Warning message if `na.rm = T` is supplied.
 #'
-#' @seealso [gg_miss_case()][gg_miss_case_cumsum()][gg_miss_fct()][gg_miss_span()][gg_miss_var()][gg_miss_var_cumsum()][gg_miss_which()]
+#' @seealso [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()]
+#'   [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 #'
 #' @param mapping Set of aesthetic mappings created by [ggplot2::aes()]
 #' or [ggplot2::aes_()]. If specified and `inherit.aes = TRUE`
@@ -79,17 +79,17 @@
 #'  facet_wrap(~Month)
 #'}
 #' @export
- geom_miss_point <- function(mapping = NULL,
-                             data = NULL,
-                             prop_below = 0.1,
-                             jitter = 0.05,
-                             stat = "miss_point",
-                             position = "identity",
-                             colour = ..missing..,
-                             na.rm = FALSE,
-                             show.legend = NA,
-                             inherit.aes = TRUE,
-                             ...) {
+geom_miss_point <- function(mapping = NULL,
+                            data = NULL,
+                            prop_below = 0.1,
+                            jitter = 0.05,
+                            stat = "miss_point",
+                            position = "identity",
+                            colour = ..missing..,
+                            na.rm = FALSE,
+                            show.legend = NA,
+                            inherit.aes = TRUE,
+                            ...) {
   layer(
     data = data,
     mapping = mapping,

diff --git a/R/gg-miss-case.R b/R/gg-miss-case.R
@@ -12,7 +12,7 @@
 #'
 #' @return a ggplot object depicting the number of missings in a given case.
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case_cumsum] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 #'
 #' @examples
 #'

diff --git a/R/gg-miss-fct.R b/R/gg-miss-fct.R
@@ -10,7 +10,7 @@
 #' @return ggplot object depicting the % missing of each factor level for
 #'   each variable.
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 #'
 #' @export
 #'

diff --git a/R/gg-miss-span.R b/R/gg-miss-span.R
@@ -10,7 +10,7 @@
 #' @param span_every integer describing the length of the span to be explored
 #' @param facet (optional) a single bare variable name, if you want to create a faceted plot.
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum] [gg_miss_fct()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 
 #' @return ggplot2 showing the number of missings in a span (window, or breaksize)
 #' @export

diff --git a/R/gg-miss-var-cumsum.R b/R/gg-miss-var-cumsum.R
@@ -8,7 +8,7 @@
 #'
 #' @return a ggplot object showing the cumulative sum of missings over the variables
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_which()]
 
 #' @export
 #'

diff --git a/R/gg-miss-var.R b/R/gg-miss-var.R
@@ -12,7 +12,7 @@
 #'
 #' @return a ggplot object depicting the number of missings in a given column
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 #'
 #' @export
 #'

diff --git a/R/gg-miss-which.R b/R/gg-miss-which.R
@@ -9,7 +9,7 @@
 #'
 #' @return a ggplot object of which variables contains missing values
 #'
-#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
+#' @seealso [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()]
 #'
 #' @export
 #'

diff --git a/R/naniar-package.R b/R/naniar-package.R
@@ -1,26 +1,17 @@
-#' naniar
-#'
+#' @description
 #' naniar is a package to make it easier to summarise and handle missing values
 #' in R. It strives to do this in a way that is as consistent with tidyverse
 #' principles as possible.  The work is fully discussed at Tierney & Cook (2023)
 #' <doi:10.18637/jss.v105.i07>.
 #'
 #' @name naniar
-#' @docType package
-#' @seealso [add_any_miss()] [add_label_missings()] [add_label_shadow()] [add_miss_cluster()] [add_n_miss()] [add_prop_miss()] [add_shadow()] [add_shadow_shift()] [as_shadow()] [bind_shadow()] [cast_shadow()] [cast_shadow_shift()] [cast_shadow_shift_label()] [draw_key_missing_point()] [gather_shadow()] [geom_miss_point()] [gg_miss_case()] [gg_miss_case_cumsum()] [gg_miss_fct()] [gg_miss_span()] [gg_miss_var()] [gg_miss_var_cumsum()] [gg_miss_which()] [label_miss_1d()] [label_miss_2d()] [label_missings()] [pct_miss_case()] [prop_miss_case()] [pct_miss_var()] [prop_miss_var()] [pct_complete_case()] [prop_complete_case()] [pct_complete_var()] [prop_complete_var()] [miss_prop_summary()] [miss_case_summary()] [miss_case_table()] [miss_summary()] [miss_var_prop()] [miss_var_run()] [miss_var_span()] [miss_var_summary()] [miss_var_table()] [n_complete()] [n_complete_row()] [n_miss()] [n_miss_row()] [pct_complete()] [pct_miss()] [prop_complete()] [prop_complete_row()] [prop_miss()] [prop_miss_row()] [replace_to_na()] [replace_with_na()] [replace_with_na_all()] [replace_with_na_at()] [replace_with_na_if()] [shadow_shift()] [stat_miss_point()] [vis_miss()] [where_na()]
 "_PACKAGE"
 
-#' @import ggplot2
-#' @import rlang
-NULL
-
-#' @importFrom stats median
-#' @importFrom visdat vis_miss
-#' @export
-visdat::vis_miss
-
 ## usethis namespace: start
 #' @importFrom lifecycle deprecated
+#' @import ggplot2
+#' @importFrom stats median
+#' @import rlang
 ## usethis namespace: end
 NULL
 

diff --git a/R/utils.R b/R/utils.R
@@ -10,6 +10,10 @@ rlang::is_na
 #' @export
 rlang::are_na
 
+#' @importFrom visdat vis_miss
+#' @export
+visdat::vis_miss
+
 #' Group By Helper
 #'
 #' This is a wrapper to facilitate the `grouped_df` S3 method.

diff --git a/README.Rmd b/README.Rmd
@@ -12,15 +12,15 @@ knitr::opts_chunk$set(
 )
 ```
 
-# naniar <a href="http://naniar.njtierney.com/"><img src="man/figures/logo.png" align="right" height="138" /></a>
+# naniar <a href="https://naniar.njtierney.com/"><img src="man/figures/logo.png" align="right" height="138" /></a>
 
 <!-- badges: start -->
-[![R build status](https://github.com/njtierney/naniar/workflows/R-CMD-check/badge.svg)](https://github.com/njtierney/naniar)
+[![R-CMD-check](https://github.com/njtierney/naniar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/njtierney/naniar/actions/workflows/R-CMD-check.yaml)
 [![Coverage Status](https://img.shields.io/codecov/c/github/njtierney/naniar/master.svg)](https://app.codecov.io/github/njtierney/naniar?branch=master)
 [![CRAN Status Badge](https://www.r-pkg.org/badges/version/naniar)](https://cran.r-project.org/package=naniar)
 [![CRAN Downloads Each Month](https://cranlogs.r-pkg.org/badges/naniar)](https://CRAN.R-project.org/package=naniar)
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-  <!-- badges: end -->
+<!-- badges: end -->
 
 `naniar` provides principled, tidy ways to summarise, visualise, and manipulate missing data with minimal deviations from the workflows in ggplot2 and tidy data. It does this by providing:
 
@@ -40,7 +40,7 @@ knitr::opts_chunk$set(
     - `gg_miss_case()`
     - `gg_miss_fct()`
 
-For more details on the workflow and theory underpinning naniar, read the vignette [Getting started with naniar](https://naniar.njtierney.com/articles/getting-started-w-naniar.html). 
+For more details on the workflow and theory underpinning naniar, read the vignette [Getting started with naniar](https://naniar.njtierney.com/articles/naniar.html). 
 
 For a short primer on the data visualisation available in naniar, read the vignette [Gallery of Missing Data Visualisations](https://naniar.njtierney.com/articles/naniar-visualisation.html).
 
@@ -217,7 +217,7 @@ airquality %>%
 
 ```
 
-You can read more about all of these functions in the vignette ["Getting Started with naniar"](https://naniar.njtierney.com/articles/getting-started-w-naniar.html).
+You can read more about all of these functions in the vignette ["Getting Started with naniar"](https://naniar.njtierney.com/articles/naniar.html).
 
 # Statistical tests of missingness
 

diff --git a/README.md b/README.md
@@ -1,12 +1,11 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# naniar <a href="http://naniar.njtierney.com/"><img src="man/figures/logo.png" align="right" height="138" /></a>
+# naniar <a href="https://naniar.njtierney.com/"><img src="man/figures/logo.png" align="right" height="138" /></a>
 
 <!-- badges: start -->
 
-[![R build
-status](https://github.com/njtierney/naniar/workflows/R-CMD-check/badge.svg)](https://github.com/njtierney/naniar)
+[![R-CMD-check](https://github.com/njtierney/naniar/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/njtierney/naniar/actions/workflows/R-CMD-check.yaml)
 [![Coverage
 Status](https://img.shields.io/codecov/c/github/njtierney/naniar/master.svg)](https://app.codecov.io/github/njtierney/naniar?branch=master)
 [![CRAN Status
@@ -40,7 +39,7 @@ ggplot2 and tidy data. It does this by providing:
 
 For more details on the workflow and theory underpinning naniar, read
 the vignette [Getting started with
-naniar](https://naniar.njtierney.com/articles/getting-started-w-naniar.html).
+naniar](https://naniar.njtierney.com/articles/naniar.html).
 
 For a short primer on the data visualisation available in naniar, read
 the vignette [Gallery of Missing Data
@@ -370,7 +369,7 @@ airquality %>%
 
 You can read more about all of these functions in the vignette [“Getting
 Started with
-naniar”](https://naniar.njtierney.com/articles/getting-started-w-naniar.html).
+naniar”](https://naniar.njtierney.com/articles/naniar.html).
 
 # Statistical tests of missingness