Upkeep (#254)

* remove date and author metadata from vignettes * bump to devel * update linter config * rename for effect size names * fix precommit workflow * use autoglobals tag * Update styler.yaml
IndrajeetPatil · Sep 22, 2023 · de77bdc · de77bdc
1 parent 86be583
commit de77bdc
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,6 +7,7 @@
 ^CRAN-RELEASE$
 ^CRAN-SUBMISSION$
 ^LICENSE\.md$
+^Makefile$
 ^Meta$
 ^NEWS$
 ^README-.*\.png$
@@ -48,4 +49,5 @@
 hextools
 publication/*
 references.bib
+shell
 tests\^spelling
diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
@@ -43,6 +43,7 @@ jobs:
             commented_code_linter = NULL,
             cyclocomp_linter(25L),
             extraction_operator_linter = NULL,
+            if_not_else_linter(exceptions = character(0L)),
             implicit_integer_linter = NULL,
             library_call_linter = NULL,
             line_length_linter(120L),

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -44,6 +44,7 @@ jobs:
             commented_code_linter = NULL,
             cyclocomp_linter(25L),
             extraction_operator_linter = NULL,
+            if_not_else_linter(exceptions = character(0L)),
             implicit_integer_linter = NULL,
             library_call_linter = NULL,
             line_length_linter(120L),
@@ -62,3 +63,5 @@ jobs:
             defaults = linters_with_tags(tags = NULL)
           ))
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/styler.yaml b/.github/workflows/styler.yaml
@@ -30,6 +30,7 @@ jobs:
             r-lib/pkgapi
             r-lib/styler
             r-lib/roxygen2
+            anthonynorth/roxyglobals
           needs: |
             styler
             roxygen2

diff --git a/.lintr b/.lintr
@@ -4,6 +4,7 @@ linters: linters_with_defaults(
     commented_code_linter = NULL,
     cyclocomp_linter(25L),
     extraction_operator_linter = NULL,
+    if_not_else_linter(exceptions = character(0L)),
     implicit_integer_linter = NULL,
     library_call_linter = NULL,
     line_length_linter(120L),

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "statsExpressions" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'statsExpressions: Tidy Dataframes and Expressions with Statistical Details'
-version: 1.5.2
+version: 1.5.2.9000
 doi: 10.21105/joss.03236
 abstract: 'Utilities for producing dataframes with rich details for the most common
   types of statistical approaches and tests: parametric, nonparametric, robust, and
@@ -110,7 +110,7 @@ references:
     given-names: Jeffrey N.
     email: [email protected]
   year: '2023'
-  version: '>= 0.9.12-4.4'
+  version: '>= 0.9.12-4.5'
 - type: software
   title: correlation
   abstract: 'correlation: Methods for Correlation Analysis'
@@ -149,7 +149,7 @@ references:
   abstract: 'datawizard: Easy Data Wrangling and Statistical Transformations'
   notes: Imports
   url: https://easystats.github.io/datawizard/
-  repository: https://easystats.r-universe.dev
+  repository: https://CRAN.R-project.org/package=datawizard
   authors:
   - family-names: Patil
     given-names: Indrajeet
@@ -176,7 +176,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2023'
-  version: '>= 0.8.0'
+  version: '>= 0.9.0'
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
@@ -234,7 +234,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4315-6788
   year: '2023'
-  version: '>= 0.8.5'
+  version: '>= 0.8.6'
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
@@ -255,7 +255,7 @@ references:
   abstract: 'insight: Easy Access to Model Information for Various Model Objects'
   notes: Imports
   url: https://easystats.github.io/insight/
-  repository: https://CRAN.R-project.org/package=insight
+  repository: https://easystats.r-universe.dev
   authors:
   - family-names: Lüdecke
     given-names: Daniel
@@ -290,7 +290,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9271-5075
   year: '2023'
-  version: '>= 0.19.4'
+  version: '>= 0.19.5'
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
@@ -369,7 +369,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9560-6336
   year: '2023'
-  version: '>= 0.10.4'
+  version: '>= 0.10.5'
 - type: software
   title: PMCMRplus
   abstract: 'PMCMRplus: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
@@ -589,12 +589,12 @@ references:
   title: metaBMA
   abstract: 'metaBMA: Bayesian Model Averaging for Random and Fixed Effects Meta-Analysis'
   notes: Suggests
-  url: https://github.com/danheck/metaBMA
+  url: https://danheck.github.io/metaBMA/
   repository: https://CRAN.R-project.org/package=metaBMA
   authors:
   - family-names: Heck
     given-names: Daniel W.
-    email: dheck@uni-marburg.de
+    email: daniel.heck@uni-marburg.de
     orcid: https://orcid.org/0000-0002-6302-9252
   year: '2023'
 - type: software

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,13 +26,13 @@ Depends:
     R (>= 4.1.0)
 Imports:
     afex (>= 1.3-0),
-    BayesFactor (>= 0.9.12-4.4),
+    BayesFactor (>= 0.9.12-4.5),
     correlation (>= 0.8.4),
-    datawizard (>= 0.8.0),
+    datawizard (>= 0.9.0),
     dplyr (>= 1.1.3),
-    effectsize (>= 0.8.5),
+    effectsize (>= 0.8.6),
     glue,
-    insight (>= 0.19.4),
+    insight (>= 0.19.5),
     magrittr,
     parameters (>= 0.21.1),
     performance (>= 0.10.5),
@@ -62,8 +62,11 @@ VignetteBuilder:
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace", "collate",
-    "pkgapi::api_roclet"))
+Roxygen: list(
+    markdown = TRUE,
+    roclets = c("collate", "namespace", "rd", "pkgapi::api_roclet", "roxyglobals::global_roclet")
+  )
 RoxygenNote: 7.2.3.9000
 Config/testthat/edition: 3
 Config/testthat/parallel: true
+Config/Needs/check: anthonynorth/roxyglobals
diff --git a/R/add_expression_col.R b/R/add_expression_col.R
@@ -47,6 +47,8 @@
 #' @inheritParams oneway_anova
 #' @inheritParams long_to_wide_converter
 #'
+#' @autoglobal
+#'
 #' @examples
 #' set.seed(123)
 #'

diff --git a/R/centrality_description.R b/R/centrality_description.R
@@ -24,6 +24,8 @@
 #' @inheritParams oneway_anova
 #' @param ... Currently ignored.
 #'
+#' @autoglobal
+#'
 #' @example man/examples/examples-centrality_description.R
 #' @export
 centrality_description <- function(data,

diff --git a/R/contingency_table.R b/R/contingency_table.R
@@ -47,6 +47,8 @@
 #' @inheritParams stats::chisq.test
 #' @inheritParams oneway_anova
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # for reproducibility
 #' set.seed(123)

diff --git a/R/corr_test.R b/R/corr_test.R
@@ -23,6 +23,8 @@
 #'   be plotted on the `y`-axis.
 #' @inheritParams oneway_anova
 #'
+#' @autoglobal
+#'
 #' @example man/examples/examples-corr_test.R
 #' @export
 corr_test <- function(data,

diff --git a/R/global_vars.R b/R/global_vars.R
diff --git a/R/globals.R b/R/globals.R
@@ -0,0 +1,35 @@
+# Generated by roxyglobals: do not edit by hand
+
+utils::globalVariables(c(
+  "method", # <add_expression_col>
+  "effectsize", # <add_expression_col>
+  "n.obs", # <add_expression_col>
+  "df", # <add_expression_col>
+  "n.obs", # <centrality_description>
+  "estimate", # <centrality_description>
+  ".counts", # <contingency_table>
+  ".f", # <contingency_table>
+  ".f.es", # <contingency_table>
+  ".", # <tidy_model_parameters>
+  "r.squared", # <tidy_model_parameters>
+  ".", # <tidy_model_effectsize>
+  ".rowid", # <long_to_wide_converter>
+  "nested_data", # <long_to_wide_converter>
+  ".ns", # <meta_analysis>
+  ".fn", # <meta_analysis>
+  ".f.args", # <meta_analysis>
+  ".rowid", # <oneway_anova>
+  "k.df", # <oneway_anova>
+  "k.df.error", # <oneway_anova>
+  ".f", # <oneway_anova>
+  ".rowid", # <pairwise_comparisons>
+  ".f", # <pairwise_comparisons>
+  "group1", # <pairwise_comparisons>
+  "group2", # <pairwise_comparisons>
+  ".ns", # <pairwise_comparisons>
+  ".fn", # <pairwise_comparisons>
+  "term", # <pairwise_comparisons>
+  "p.value", # <pairwise_comparisons>
+  "term", # <tidy_model_expressions>
+  NULL
+))
diff --git a/R/helpers_easystats.R b/R/helpers_easystats.R
@@ -3,6 +3,8 @@
 #'
 #' @inheritParams parameters::model_parameters
 #'
+#' @autoglobal
+#'
 #' @examples
 #' model <- lm(mpg ~ wt + cyl, data = mtcars)
 #' tidy_model_parameters(model)
@@ -12,7 +14,7 @@ tidy_model_parameters <- function(model, ...) {
     mutate(conf.method = . %@% "ci_method") %>%
     select(-matches("Difference")) %>%
     standardize_names(style = "broom") %>%
-    rename_all(~ gsub("cramers.", "", .x)) %>%
+    rename_all(~ gsub("cramers.|omega2.|eta2.", "", .x)) %>%
     rename_with(recode, bayes.factor = "bf10") %>%
     tidyr::fill(matches("^prior|^bf"), .direction = "updown") %>%
     mutate(across(matches("bf10"), ~ log(.x), .names = "log_e_{.col}"))
@@ -46,6 +48,8 @@ tidy_model_parameters <- function(model, ...) {
 #' @param data A data frame returned by `{effectsize}` functions.
 #' @param ... Currently ignored.
 #'
+#' @autoglobal
+#'
 #' @examples
 #' df <- effectsize::cohens_d(sleep$extra, sleep$group)
 #' tidy_model_effectsize(df)

diff --git a/R/long_to_wide_converter.R b/R/long_to_wide_converter.R
@@ -37,6 +37,8 @@
 #' @returns A data frame with `NA`s removed while respecting the
 #'   between-or-within-subjects nature of the dataset.
 #'
+#' @autoglobal
+#'
 #' @examples
 #' # for reproducibility
 #' library(statsExpressions)

diff --git a/R/meta_analysis.R b/R/meta_analysis.R
@@ -36,6 +36,8 @@
 #' needed package (`{metafor}`, `{metaplus}`, or `{metaBMA}`) for meta-analysis.
 #' If they are not available, you will be asked to install them.
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") && requireNamespace("metafor", quietly = TRUE)
 #' # setup
 #' set.seed(123)

diff --git a/R/one_sample_test.R b/R/one_sample_test.R
@@ -29,6 +29,8 @@
 #' ```{r child="man/rmd-fragments/return.Rmd"}
 #' ```
 #'
+#' @autoglobal
+#'
 #' @example man/examples/examples-one_sample_test.R
 #' @export
 one_sample_test <- function(data,

diff --git a/R/oneway_anova.R b/R/oneway_anova.R
@@ -41,6 +41,8 @@
 #' @param ... Additional arguments (currently ignored).
 #' @inheritParams stats::oneway.test
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # for reproducibility
 #' set.seed(123)

diff --git a/R/pairwise_comparisons.R b/R/pairwise_comparisons.R
@@ -32,6 +32,8 @@
 #' @references For more, see:
 #' <https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/pairwise.html>
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # for reproducibility
 #' set.seed(123)

diff --git a/R/switch_functions.R b/R/switch_functions.R
@@ -16,6 +16,8 @@
 #'
 #' You can specify just the initial letter.
 #'
+#' @autoglobal
+#'
 #' @examples
 #' stats_type_switch("p")
 #' stats_type_switch("bf")

diff --git a/R/tidy_model_expressions.R b/R/tidy_model_expressions.R
@@ -18,6 +18,8 @@
 #' This is an **experimental** function and may change in the future. Please do
 #' not use it yet in your workflow.
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # setup
 #' set.seed(123)

diff --git a/R/two_sample_test.R b/R/two_sample_test.R
@@ -24,9 +24,12 @@
 #' ```{r child="man/rmd-fragments/return.Rmd"}
 #' ```
 #'
+#' @autoglobal
+#'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' @example man/examples/examples-two_sample_test_within.R
 #' @example man/examples/examples-two_sample_test_between.R
+#'
 #' @export
 two_sample_test <- function(data,
                             x,

diff --git a/WIP/gallery.Rmd b/WIP/gallery.Rmd
@@ -1,7 +1,5 @@
 ---
 title: "Gallery of examples"
-author: "Indrajeet Patil"
-date: "`r Sys.Date()`"
 output:
   rmarkdown::html_vignette:
     fig_width: 6