Merge branch 'main' into joss-paper-draft

.github/workflows/html-5-check.yaml

@@ -6,8 +6,8 @@ on:
   pull_request:
     branches: [main, master]
 
-name: HTML5 check
+name: html-5-check
 
 jobs:
-  HTML5-check:
+  html-5-check:
     uses: easystats/workflows/.github/workflows/html-5-check.yaml@main

.github/workflows/update-to-latest-easystats.yaml

@@ -0,0 +1,10 @@
+on:
+  schedule:
+    # Check for dependency updates once a month
+    - cron: "0 0 1 * *"
+
+name: update-to-latest-easystats
+
+jobs:
+  update-to-latest-easystats:
+    uses: easystats/workflows/.github/workflows/update-to-latest-easystats.yaml@main

DESCRIPTION

@@ -1,7 +1,7 @@
-Type: Package
 Package: report
+Type: Package
 Title: Automated Reporting of Results and Statistical Models
-Version: 0.5.7.10
+Version: 0.5.7.13
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -49,18 +49,18 @@ Description: The aim of the 'report' package is to bridge the gap between
     This package converts statistical models and data frames into textual
     reports suited for publication, ensuring standardization and quality
     in results reporting.
-License: GPL-3 | file LICENSE
+License: MIT + file LICENSE
 URL: https://easystats.github.io/report/
 BugReports: https://github.com/easystats/report/issues
 Depends:
     R (>= 3.6)
 Imports:
-    bayestestR (>= 0.13.0),
-    effectsize (> 0.8.2),
-    insight (>= 0.19.1),
-    parameters (>= 0.20.2),
-    performance (>= 0.10.2),
-    datawizard (>= 0.7.0),
+    bayestestR (>= 0.13.1),
+    effectsize (>= 0.8.6),
+    insight (>= 0.19.6),
+    parameters (>= 0.21.2),
+    performance (>= 0.10.8),
+    datawizard (>= 0.9.0),
     stats,
     tools,
     utils
@@ -81,7 +81,7 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.2.3
+RoxygenNote: 7.2.3.9000
 Config/testthat/edition: 3
 Config/Needs/website:
     rstudio/bslib,
@@ -125,6 +125,9 @@ Collate:
     'report_effectsize.R'
     'report_htest_chi2.R'
     'report_htest_cor.R'
+    'report_htest_fisher.R'
+    'report_htest_friedman.R'
+    'report_htest_kruskal.R'
     'report_htest_ttest.R'
     'report_htest_wilcox.R'
     'report_info.R'
@@ -143,4 +146,10 @@ Collate:
     'utils_grouped_df.R'
     'zzz.R'
 Roxygen: list(markdown = TRUE)
-Remotes: easystats/insight
+Remotes: 
+  easystats/insight,
+  easystats/datawizard,
+  easystats/parameters,
+  easystats/effectsize,
+  easystats/bayestestR,
+  easystats/performance

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2023 report authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NEWS.md

@@ -1,7 +1,13 @@
 # report 0.5.8
 
+Major Changes
+
+* This release changes the licensing model of `{see}` to an MIT license. 
+
 Minor changes 
 
+* `report` now supports variables of class `htest` for the Chi2, Friedman test, Fisher's exact test, and Kruskal-Wallis.
+
 * `report` now supports variables of class `Date`, treating them like factors.
 
 * `report` now supports objects of class `estimate_contrasts`, from easystats'
@@ -26,6 +32,8 @@ 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.
+  Gender now also supports more alternate spellings, and age converts the
+  respective column to numeric.
 
 * Fixed printing issue for intercept-only models.
 

R/cite_easystats.R

@@ -23,7 +23,7 @@
 #'   - `refs`: References or bibliography in the requested `format`
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # Cite just the 'easystats' umbrella package:
 #' cite_easystats()
 #' summary(cite_easystats(), what = "all")

R/report.aov.R

@@ -83,7 +83,7 @@ report_effectsize.aov <- function(x, ...) {
   parameters <- paste0(interpretation, " (", statistics, ")")
 
 
-  # Return output
+
   as.report_effectsize(parameters,
     summary = parameters,
     table = table,

R/report.brmsfit.R

@@ -8,7 +8,7 @@
 #' @inherit report return seealso
 #'
 #' @examplesIf require("brms", quietly = TRUE)
-#' \dontrun{
+#' \donttest{
 #' # Bayesian models
 #' library(brms)
 #' model <- suppressWarnings(brm(mpg ~ qsec + wt, data = mtcars, refresh = 0, iter = 300))

R/report.htest.R

@@ -53,22 +53,39 @@ report_effectsize.htest <- function(x, ...) {
     out <- .report_effectsize_ttest(x, table, dot_args)
   }
 
-  # For wilcox test ---------------
-
   if (model_info$is_ranktest && !model_info$is_correlation) {
-    out <- .report_effectsize_wilcox(x, table, dot_args)
+    # For friedman test ---------------
+
+    if (grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
+      out <- .report_effectsize_friedman(x, table, dot_args)
+    } else if (!is.null(x$statistic) && grepl(
+      "Kruskal", attributes(x$statistic)$names,
+      fixed = TRUE
+    )) {
+      # For Kruskal-Wallis test ---------------
+
+      out <- .report_effectsize_kruskal(x, table, dot_args)
+    } else {
+      # For wilcox test ---------------
+
+      out <- .report_effectsize_wilcox(x, table, dot_args)
+    }
   }
 
-  # For correlations ---------------
+  ## For correlations ---------------
 
   if (model_info$is_correlation) {
     out <- .report_effectsize_correlation(x, table, dot_args)
   }
 
-  # For Chi2 ---------------
+  ## For Chi2 ---------------
 
   if (model_info$is_chi2test) {
-    out <- .report_effectsize_chi2(x, table, dot_args)
+    if (chi2_type(x) == "fisher") {
+      out <- .report_effectsize_fisher(x, table, dot_args)
+    } else {
+      out <- .report_effectsize_chi2(x, table, dot_args)
+    }
   }
 
   # TODO: Chi-squared test -------------
@@ -81,7 +98,7 @@ report_effectsize.htest <- function(x, ...) {
 
   parameters <- paste0(out$interpretation, " (", out$statistics, ")")
 
-  # Return output
+
   as.report_effectsize(
     parameters,
     summary = parameters,
@@ -120,17 +137,20 @@ report_table.htest <- function(x, ...) {
     out <- .report_table_ttest(table_full, effsize)
   } else if (model_info$is_ranktest && !model_info$is_correlation) {
     # wilcox test
+    # but same function for Friedman
     out <- .report_table_wilcox(table_full, effsize)
   } else if (model_info$is_chi2test) {
     # chi2 test
     out <- .report_table_chi2(table_full, effsize)
+    attr(out$table_full, "table_footer") <- attr(attr(effsize, "table"), "table_footer")
   } else if (model_info$is_correlation) {
+    # correlation test
     out <- .report_table_correlation(table_full)
   } else {
     out <- list(table_full = table_full, table = NULL)
   }
 
-  # Return output
+
   as.report_table(out$table_full, summary = out$table, effsize = effsize)
 }
 
@@ -152,7 +172,10 @@ report_statistics.htest <- function(x, table = NULL, ...) {
   text <- NULL
 
   # Estimate
-  candidates <- c("rho", "r", "tau", "Difference", "r_rank_biserial")
+  candidates <- c(
+    "rho", "r", "tau", "Difference", "r_rank_biserial",
+    "Chi2", "Odds Ratio"
+  )
   estimate <- candidates[candidates %in% names(table)][1]
   if (!is.null(estimate) && !is.na(estimate)) {
     text <- paste0(tolower(estimate), " = ", insight::format_value(table[[estimate]]))
@@ -186,15 +209,14 @@ report_statistics.htest <- function(x, table = NULL, ...) {
     text <- paste0(text, ", z = ", insight::format_value(table$z))
   } else if ("W" %in% names(table)) {
     text <- paste0("W = ", insight::format_value(table$W))
-  } else if ("Chi2" %in% names(table)) {
-    text <- paste0(text, ", Chi2 = ", insight::format_value(table$Chi2))
   }
 
   # p-value
   text <- paste0(text, ", ", insight::format_p(table$p, stars = FALSE, digits = "apa"))
 
   # Effect size
-  if (model_info$is_ttest || (model_info$is_ranktest && !model_info$is_correlation)) {
+  if (model_info$is_ttest || (model_info$is_ranktest && !model_info$is_correlation) ||
+    model_info$is_chi2test) {
     text_full <- paste0(text, "; ", attributes(effsize)$statistics)
     text <- paste0(text, ", ", attributes(effsize)$main)
   } else {
@@ -239,13 +261,29 @@ report_parameters.htest <- function(x, table = NULL, ...) {
   # Correlations
   if (model_info$is_correlation) {
     out <- .report_parameters_correlation(table, stats, ...)
-
     # t-tests
   } else if (model_info$is_ttest) {
     out <- .report_parameters_ttest(table, stats, effsize, ...)
-
-    # TODO: default, same as t-test?
+    # Friedman
+  } else if (
+    model_info$is_ranktest &&
+      grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
+    out <- .report_parameters_friedman(table, stats, effsize, ...)
+  } else if (!is.null(x$statistic) && grepl(
+    "Kruskal", attributes(x$statistic)$names,
+    fixed = TRUE
+  )) {
+    # Kruskal
+    out <- .report_parameters_kruskal(table, stats, effsize, ...)
+    # chi2
+  } else if (model_info$is_chi2test) {
+    if (chi2_type(x) == "fisher") {
+      out <- .report_parameters_fisher(table, stats, effsize, ...)
+    } else {
+      out <- .report_parameters_chi2(table, stats, effsize, ...)
+    }
   } else {
+    # TODO: default, same as t-test?
     out <- .report_parameters_htest_default(table, stats, effsize, ...)
   }
 
@@ -286,7 +324,23 @@ report_model.htest <- function(x, table = NULL, ...) {
   }
 
   if (model_info$is_ranktest && !model_info$is_correlation) {
-    text <- .report_model_wilcox(x, table)
+    # For friedman test ---------------
+
+    if (grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
+      text <- .report_model_friedman(x, table)
+    } else {
+      # For wilcox test ---------------
+
+      text <- .report_model_wilcox(x, table)
+    }
+  }
+
+  if (model_info$is_chi2test) {
+    if (chi2_type(x) == "fisher") {
+      text <- .report_model_fisher(x, table)
+    } else {
+      text <- .report_model_chi2(x, table)
+    }
   }
 
   as.report_model(text, summary = text)

R/report.lm.R

@@ -99,21 +99,18 @@ report_effectsize.lm <- function(x, effectsize_method = "refit", ...) {
 
   if ("Component" %in% colnames(table)) {
     merge_by <- c("Parameter", "Component")
-    start_col <- 4
+    start_col <- 4L
   } else {
     merge_by <- "Parameter"
-    start_col <- 3
+    start_col <- 3L
   }
 
   table <- as.data.frame(table)[c(merge_by, estimate, "CI_low", "CI_high")]
   names(table)[start_col:ncol(table)] <- c(paste0(estimate, "_CI_low"), paste0(estimate, "_CI_high"))
 
-
   rules <- .text_effectsize(attr(attr(interpret, "rules"), "rule_name"))
   parameters <- paste0(interpretation, " (", statistics, ")")
 
-
-  # Return output
   as.report_effectsize(parameters,
     summary = parameters,
     table = table,

R/report.numeric.R

@@ -206,15 +206,15 @@ report_parameters.numeric <- function(x,
   }
 
   text_full <- c(
-    "n_Obs" = text_n,
-    "Mean" = text_mean,
-    "Dispersion_Mean" = paste0("SD = ", text_sd),
-    "Median" = text_median,
-    "Dispersion_Median" = paste0("MAD = ", text_mad),
-    "Range" = paste0("range: ", text_range),
-    "Skewness" = text_skewness,
-    "Kurtosis" = text_kurtosis,
-    "Missing" = text_missing
+    n_Obs = text_n,
+    Mean = text_mean,
+    Dispersion_Mean = paste0("SD = ", text_sd),
+    Median = text_median,
+    Dispersion_Median = paste0("MAD = ", text_mad),
+    Range = paste0("range: ", text_range),
+    Skewness = text_skewness,
+    Kurtosis = text_kurtosis,
+    Missing = text_missing
   )
 
   # Shorten ---

R/report.sessionInfo.R

@@ -129,9 +129,9 @@ report_table.sessionInfo <- function(x, include_R = TRUE, ...) {
   }
 
   data <- data.frame(
-    "Package" = names,
-    "Version" = versions,
-    "Reference" = citations,
+    Package = names,
+    Version = versions,
+    Reference = citations,
     stringsAsFactors = FALSE
   )