Merge branch 'main' into joss-paper-draft

.Rbuildignore

@@ -10,6 +10,7 @@
 ^revdep$
 ^codecov\.yml$
 ^_pkgdown\.yml$
+^pkgdown$
 ^data-raw$
 ^\.httr-oauth$
 ^CRAN-RELEASE$
@@ -22,4 +23,4 @@ tests\^spelling
 ^\.pre-commit-config\.yaml$
 ^WIP/.
 \.code-workspace$
-^CRAN-SUBMISSION$
+^CRAN-SUBMISSION$

.github/workflows/check-random-test-order.yaml

@@ -0,0 +1,12 @@
+# Run tests in random order
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: check-random-test-order
+
+jobs:
+  check-random-test-order:
+    uses: easystats/workflows/.github/workflows/check-random-test-order.yaml@main

.lintr

@@ -1,6 +1,5 @@
 linters: linters_with_defaults(
     absolute_path_linter = NULL,
-    commented_code_linter = NULL,
     cyclocomp_linter = cyclocomp_linter(25),
     extraction_operator_linter = NULL,
     implicit_integer_linter = NULL,

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: report
 Title: Automated Reporting of Results and Statistical Models
-Version: 0.5.6
+Version: 0.5.7.10
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -37,7 +37,12 @@ Authors@R:
              family = "Siegel",
              role = "ctb",
              email = "[email protected]",
-             comment = c(ORCID = "0000-0002-6021-804X")))
+             comment = c(ORCID = "0000-0002-6021-804X")),
+     person(given = "Camden",
+            family = "Bock",
+            role = "ctb",
+            email = "[email protected]",
+            comment = c(ORCID = "0000-0002-3907-7748")))
 Maintainer: Rémi Thériault <[email protected]>
 Description: The aim of the 'report' package is to bridge the gap between
     R’s output and the formatted results contained in your manuscript.
@@ -52,10 +57,10 @@ Depends:
 Imports:
     bayestestR (>= 0.13.0),
     effectsize (> 0.8.2),
-    insight (>= 0.18.8),
-    parameters (>= 0.20.0),
-    performance (>= 0.9.2),
-    datawizard (>= 0.6.5),
+    insight (>= 0.19.1),
+    parameters (>= 0.20.2),
+    performance (>= 0.10.2),
+    datawizard (>= 0.7.0),
     stats,
     tools,
     utils
@@ -69,12 +74,14 @@ Suggests:
     rmarkdown,
     rstanarm,
     survival,
+    modelbased,
+    emmeans,
     testthat
 VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.2.3.9000
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3
 Config/Needs/website:
     rstudio/bslib,
@@ -86,6 +93,7 @@ Collate:
     'format_citation.R'
     'format_formula.R'
     'format_model.R'
+    'reexports.R'
     'report-package.R'
     'utils_combine_tables.R'
     'report.lm.R'
@@ -102,6 +110,7 @@ Collate:
     'report.compare_performance.R'
     'report.data.frame.R'
     'report.default.R'
+    'report.estimate_contrasts.R'
     'report.factor.R'
     'report.glm.R'
     'report.glmmTMB.R'
@@ -134,3 +143,4 @@ Collate:
     'utils_grouped_df.R'
     'zzz.R'
 Roxygen: list(markdown = TRUE)
+Remotes: easystats/insight

NAMESPACE

@@ -25,6 +25,9 @@ S3method(print,report_sample)
 S3method(print,report_statistics)
 S3method(print,report_table)
 S3method(print,report_text)
+S3method(print_html,report_sample)
+S3method(print_md,report_sample)
+S3method(report,Date)
 S3method(report,MixMod)
 S3method(report,anova)
 S3method(report,aov)
@@ -36,6 +39,7 @@ S3method(report,character)
 S3method(report,compare_performance)
 S3method(report,data.frame)
 S3method(report,default)
+S3method(report,estimate_contrasts)
 S3method(report,factor)
 S3method(report,glm)
 S3method(report,glmmTMB)
@@ -113,6 +117,7 @@ S3method(report_model,merMod)
 S3method(report_model,stanreg)
 S3method(report_model,survreg)
 S3method(report_model,zeroinfl)
+S3method(report_parameters,Date)
 S3method(report_parameters,MixMod)
 S3method(report_parameters,anova)
 S3method(report_parameters,aov)
@@ -161,6 +166,7 @@ S3method(report_random,glmmTMB)
 S3method(report_random,lme)
 S3method(report_random,merMod)
 S3method(report_random,stanreg)
+S3method(report_statistics,Date)
 S3method(report_statistics,MixMod)
 S3method(report_statistics,anova)
 S3method(report_statistics,aov)
@@ -184,6 +190,7 @@ S3method(report_statistics,stanreg)
 S3method(report_statistics,survreg)
 S3method(report_statistics,test_performance)
 S3method(report_statistics,zeroinfl)
+S3method(report_table,Date)
 S3method(report_table,MixMod)
 S3method(report_table,anova)
 S3method(report_table,aov)
@@ -195,6 +202,7 @@ S3method(report_table,character)
 S3method(report_table,compare_performance)
 S3method(report_table,data.frame)
 S3method(report_table,default)
+S3method(report_table,estimate_contrasts)
 S3method(report_table,factor)
 S3method(report_table,glm)
 S3method(report_table,glmmTMB)
@@ -212,6 +220,7 @@ S3method(report_table,stanreg)
 S3method(report_table,survreg)
 S3method(report_table,test_performance)
 S3method(report_table,zeroinfl)
+S3method(report_text,Date)
 S3method(report_text,MixMod)
 S3method(report_text,anova)
 S3method(report_text,aov)
@@ -223,6 +232,7 @@ S3method(report_text,character)
 S3method(report_text,compare_performance)
 S3method(report_text,data.frame)
 S3method(report_text,default)
+S3method(report_text,estimate_contrasts)
 S3method(report_text,factor)
 S3method(report_text,glm)
 S3method(report_text,glmmTMB)
@@ -273,6 +283,8 @@ export(format_citation)
 export(format_formula)
 export(format_model)
 export(is.report)
+export(print_html)
+export(print_md)
 export(report)
 export(report_date)
 export(report_effectsize)
@@ -292,3 +304,5 @@ export(report_system)
 export(report_table)
 export(report_text)
 importFrom(insight,display)
+importFrom(insight,print_html)
+importFrom(insight,print_md)

NEWS.md

@@ -1,3 +1,38 @@
+# report 0.5.8
+
+Minor changes 
+
+* `report` now supports variables of class `Date`, treating them like factors.
+
+* `report` now supports objects of class `estimate_contrasts`, from easystats'
+  `modelbased::estimate_contrasts`, outputting either the results in text form,
+  or as a table.
+
+* `report_sample`
+  * now reports the weighted number of observations when data
+  is both grouped an weighted.
+  * gains `ci`, `ci_method` and `ci_adjust` arguments, to compute
+  confidence intervals for proportions of factor levels. Currently, two different
+  methods (*Wald* and *Wilson*) are available.
+  * now works on grouped data frame, using the defined groups as
+  values for the `group_by` argument.
+  * can now summarize data based on more than one grouping variable
+  (i.e. `group_by` is allowed to be longer than 1).
+
+* The `print` method for `report_sample` gains a `layout` argument, to print
+  tables either in `"horizontal"` or `"vertical"` layout.
+
+Bug fixes
+
+* Fixed issue in `report_participants`, which did not print the `"gender"`
+  category for grouped output when that argument was written in lower-case.
+
+* Fixed printing issue for intercept-only models.
+
+# report 0.5.7
+
+Hotfix for CRAN reverse dependency compatibility.
+
 # report 0.5.6
 
 Breaking Changes

R/format_model.R

@@ -18,7 +18,7 @@ format_model <- function(x) {
 format_model.default <- function(x) {
   info <- insight::model_info(x)
 
-  if (insight::is_nullmodel(x)) {
+  if (suppressWarnings(insight::is_nullmodel(x))) {
     type <- "constant (intercept-only) "
   } else {
     type <- ""

R/reexports.R

@@ -0,0 +1,13 @@
+# ----------------------- insight -------------------------------------
+
+#' @importFrom insight print_html
+#' @export
+insight::print_html
+
+#' @importFrom insight print_md
+#' @export
+insight::print_md
+
+#' @importFrom insight display
+#' @export
+insight::display

R/report.aov.R

@@ -131,7 +131,8 @@ report_table.aov <- function(x, ...) {
 
   table <- datawizard::data_remove(
     table_full,
-    datawizard::data_find(table_full, select = "(_CI_low|_CI_high)$", regex = TRUE)
+    select = "(_CI_low|_CI_high)$",
+    regex = TRUE
   )
 
   as.report_table(

R/report.brmsfit.R

@@ -7,7 +7,7 @@
 #' @inheritParams report.lm
 #' @inherit report return seealso
 #'
-#' @examplesIf requireNamespace("brms", quietly = TRUE) && packageVersion("rstan") >= "2.26.0"
+#' @examplesIf require("brms", quietly = TRUE)
 #' \dontrun{
 #' # Bayesian models
 #' library(brms)
@@ -62,9 +62,11 @@ report_priors.brmsfit <- function(x, ...) {
   params <- params[params$Parameter != "(Intercept)", ]
 
   # Return empty if no priors info
-  if (!"Prior_Distribution" %in% names(params) ||
-    nrow(params) == 0 ||
-    all(is.na(params$Prior_Scale))) {
+  has_no_prior_information <- (!"Prior_Distribution" %in% names(params)) ||
+    nrow(params) == 0L ||
+    all(is.na(params$Prior_Scale))
+
+  if (has_no_prior_information) {
     return("")
   }
 
@@ -85,7 +87,7 @@ report_priors.brmsfit <- function(x, ...) {
 
   values <- paste0(params$Prior_Distribution, " (", values, ")")
 
-  if (length(unique(values)) == 1 && nrow(params) > 1) {
+  if (length(unique(values)) == 1L && nrow(params) > 1L) {
     text <- paste0("all set as ", values[1])
   } else {
     text <- paste0("set as ", values)

R/report.data.frame.R

@@ -379,12 +379,19 @@ report_table.grouped_df <- function(x,
     )
 
     current_table_full$Group <- group
-    # table_full <- rbind(table_full, current_table_full)
-    table_full <- merge(table_full, current_table_full, all = TRUE, sort = FALSE)
+    if (!length(table_full) == 0) {
+      table_full <- merge(table_full, current_table_full, all = TRUE, sort = FALSE)
+    } else {
+      table_full <- current_table_full
+    }
+
     current_table <- summary(current_table_full)
     current_table$Group <- group
-    # table <- rbind(table, current_table)
-    table <- merge(table, current_table, all = TRUE, sort = FALSE)
+    if (!length(table) == 0) {
+      table <- merge(table, current_table, all = TRUE, sort = FALSE)
+    } else {
+      table <- current_table
+    }
   }
 
   table <- datawizard::data_reorder(table, "Group")

R/report.estimate_contrasts.R

@@ -0,0 +1,52 @@
+#' Reporting `estimate_contrasts` objects
+#'
+#' Create reports for `estimate_contrasts` objects.
+#'
+#' @param x Object of class `estimate_contrasts`.
+#' @param table Provide the output of  `report_table()` to avoid its
+#'   re-computation.
+#' @inheritParams report
+#'
+#' @inherit report return seealso
+#'
+#' @examplesIf requireNamespace("modelbased", quietly = TRUE) && requireNamespace("emmeans", quietly = TRUE)
+#' library(modelbased)
+#' model <- lm(Sepal.Width ~ Species, data = iris)
+#' contr <- estimate_contrasts(model)
+#' report(contr)
+#' @return An object of class [report()].
+#' @export
+report.estimate_contrasts <- function(x, ...) {
+  table <- report_table(x, ...)
+  text <- report_text(x, table = table, ...)
+
+  as.report(text, table = table, ...)
+}
+
+# report_table ------------------------------------------------------------
+
+#' @rdname report.estimate_contrasts
+#' @export
+report_table.estimate_contrasts <- function(x, ...) {
+  as.report_table(x)
+}
+
+# report_text ------------------------------------------------------------
+
+#' @rdname report.estimate_contrasts
+#' @export
+report_text.estimate_contrasts <- function(x, table = NULL, ...) {
+  f_table <- insight::format_table(table)
+
+  text <- paste0("The difference between ", x$Level1, " and ", x$Level2, " is ",
+    ifelse(x$Difference < 0, " negative", "positive"), " and statistically ",
+    ifelse(x$p < 0.05, "significant", "non-significant"),
+    " (difference = ", f_table$Difference, ", 95% CI ", f_table$`95% CI`, ", ",
+    names(f_table)[6], " = ", f_table[[6]], ", ", insight::format_p(table$p), ")",
+    collapse = ". "
+  )
+
+  text <- paste("The marginal contrasts analysis suggests the following.", paste0(text, collapse = ""))
+
+  as.report_text(text)
+}