Format ANOVAs

DESCRIPTION

@@ -23,7 +23,9 @@ Suggests:
 Config/testthat/edition: 3
 Imports: 
     dplyr,
-    lifecycle
+    lifecycle,
+    rlang (>= 1.1.0)
 URL: https://github.com/JeffreyRStevens/cocoon, https://jeffreyrstevens.github.io/cocoon/
 BugReports: https://github.com/JeffreyRStevens/cocoon/issues
-VignetteBuilder: knitr
+VignetteBuilder: 
+    knitr

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(format_stats,BFBayesFactor)
+S3method(format_stats,aov)
 S3method(format_stats,default)
 S3method(format_stats,easycorrelation)
 S3method(format_stats,htest)
@@ -21,3 +22,5 @@ export(format_sub)
 export(format_summary)
 export(format_ttest)
 importFrom(lifecycle,deprecated)
+importFrom(rlang,ffi_standalone_check_number_1.0.7)
+importFrom(rlang,ffi_standalone_is_bool_1.0.7)

R/cocoon-package.R

@@ -3,5 +3,7 @@
 
 ## usethis namespace: start
 #' @importFrom lifecycle deprecated
+#' @importFrom rlang ffi_standalone_check_number_1.0.7
+#' @importFrom rlang ffi_standalone_is_bool_1.0.7
 ## usethis namespace: end
 NULL

R/format_numbers.R

@@ -17,9 +17,8 @@ format_num <- function(x,
                        digits = 1,
                        pzero = TRUE) {
   # Check arguments
-  stopifnot("Input must be a numeric vector." = is.numeric(x))
-  stopifnot("Argument `digits` must be a non-negative numeric vector." = is.numeric(digits))
-  stopifnot("Argument `digits` must be a non-negative numeric vector." = digits >= 0)
+  check_numeric(x)
+  check_number_whole(digits, min = 0)
 
   # Format number
   dplyr::case_when(
@@ -48,10 +47,9 @@ format_scientific <- function(x,
                               digits = 1,
                               type = "md") {
   # Check arguments
-  stopifnot("Input must be a numeric vector." = is.numeric(x))
-  stopifnot("Argument `digits` must be a non-negative numeric vector." = is.numeric(digits))
-  stopifnot("Argument `digits` must be a non-negative numeric vector." = digits >= 0)
-  stopifnot("Argument `type` must be 'md' or 'latex'." = type %in% c("md", "latex"))
+  check_numeric(x)
+  check_number_whole(digits, min = 1)
+  check_match(type, c("md", "latex"))
 
   # Format number
   num <- formatC(x, digits = digits, format = "e")
@@ -91,9 +89,9 @@ format_chr <- function(x,
                        italics = TRUE,
                        type = "md") {
   # Check arguments
-  stopifnot("Input must be a character string." = is.character(x))
-  stopifnot("Argument `italics` must be TRUE or FALSE." = is.logical(italics))
-  stopifnot("Argument `type` must be 'md' or 'latex'." = type %in% c("md", "latex"))
+  check_string(x)
+  check_bool(italics)
+  check_match(type, c("md", "latex"))
   dplyr::case_when(
     italics & type == "md" ~ paste0("_", x, "_"),
     italics & type == "latex" ~ paste0("$", x, "$"),
@@ -119,8 +117,8 @@ format_chr <- function(x,
 format_sub <- function(subscript = NULL,
                        type = "md") {
   # Check arguments
-  stopifnot("Input must be a character string or NULL." = is.character(subscript) | is.null(subscript))
-  stopifnot("Argument `type` must be 'md' or 'latex'." = type %in% c("md", "latex"))
+  check_string(subscript, allow_null = TRUE)
+  check_match(type, c("md", "latex"))
   dplyr::case_when(
     subscript == "" ~ "",
     !is.null(subscript) & type == "md" ~ paste0("~", subscript, "~"),

R/format_stats.R

@@ -7,6 +7,7 @@
 #' 1. `htest` objects of correlations, t-tests, and Wilcoxon tests
 #' 1. correlations from the
 #' \{[correlation](https://cran.r-project.org/package=correlation)\} package.
+#' 1. `aov` objects for ANOVAs
 #' 1. Bayes factors from the
 #' \{[BayesFactor](https://cran.r-project.org/package=BayesFactor)\} package.
 #' The function invokes specific methods that depend on the class of the
@@ -69,293 +70,3 @@ format_stats.default <- function(x, ...) {
     )
   }
 }
-
-#' Format hypothesis test statistics
-#'
-#' This method formats hypothesis test statistics from the class `htest`.
-#' Currently, this includes correlations from [cor.test()] and t-tests and
-#' Wilcoxon tests from [t.test()] and [wilcox.test()]. For correlations, the
-#' function detects whether the object is from a Pearson,
-#' Spearman, or Kendall correlation and reports the appropriate correlation
-#' label (r, \eqn{\tau}, \eqn{\rho}). The default output is APA formatted, but
-#' this function allows control over numbers of
-#' digits, leading zeros, the presence of means and confidence intervals,
-#' italics, degrees of freedom, and mean labels, and output format of
-#' Markdown or LaTeX.
-#'
-#' @param x An `htest` object
-#' @param digits Number of digits after the decimal for means, confidence
-#' intervals, and test statistics
-#' @param pdigits Number of digits after the decimal for p-values, ranging
-#' between 1-5 (also controls cutoff for small p-values)
-#' @param pzero Logical value (default = FALSE) for whether to include
-#' leading zero for p-values
-#' @param full Logical value (default = TRUE) for whether to include means
-#' and confidence intervals or just test statistic and p-value
-#' @param italics Logical value (default = TRUE) for whether _p_ label should be
-#' italicized
-#' @param dfs Formatting for degrees of freedom ("par" = parenthetical,
-#' "sub" = subscript, "none" = do not print degrees of freedom)
-#' @param mean Formatting for mean label ("abbr" = M, "word" = Mean)
-#' @param type Type of formatting ("md" = markdown, "latex" = LaTeX)
-#' @param ... Additional arguments passed to methods.
-#'
-#' @return
-#' A character string of statistical information formatted in Markdown or LaTeX.
-#'
-#' @method format_stats htest
-#' @family functions for printing statistical objects
-#' @export
-#'
-#' @examples
-#' # Prepare statistical objects
-#' test_corr <- cor.test(mtcars$mpg, mtcars$cyl)
-#' test_corr2 <- cor.test(mtcars$mpg, mtcars$cyl, method = "kendall")
-#' test_ttest <- t.test(mtcars$vs, mtcars$am)
-#' test_ttest2 <- wilcox.test(mtcars$vs, mtcars$am)
-#'
-#' # Format correlation
-#' format_stats(test_corr)
-#'
-#' # Remove confidence intervals and italics
-#' format_stats(test_corr, full = FALSE, italics = FALSE)
-#'
-#' # Change digits and add leading zero to p-value
-#' format_stats(test_corr, digits = 3, pdigits = 4, pzero = TRUE)
-#'
-#' # Format Kendall's tau
-#' format_stats(test_corr2)
-#'
-#' # Format t-test
-#'   format_stats(test_ttest)
-#'
-#' # Remove mean and confidence interval
-#' format_stats(test_ttest, full = FALSE)
-#'
-#' # Remove degrees of freedom and spell out "Mean"
-#' format_stats(test_ttest, dfs = "none", mean = "word")
-#'
-#' # Format for LaTeX
-#' format_stats(test_ttest2, type = "latex")
-format_stats.htest <- function(x,
-                               digits = NULL,
-                               pdigits = 3,
-                               pzero = FALSE,
-                               full = TRUE,
-                               italics = TRUE,
-                               dfs = "par",
-                               mean = "abbr",
-                               type = "md",
-                               ...) {
-  # Validate arguments
-  if (!is.null(digits)) {
-    stopifnot("Argument `digits` must be a non-negative numeric vector." = is.numeric(digits))
-    stopifnot("Argument `digits` must be a non-negative numeric vector." = digits >= 0)
-  }
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = is.numeric(pdigits))
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = pdigits > 0)
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = pdigits < 6)
-  stopifnot("Argument `pzero` must be TRUE or FALSE." = is.logical(pzero))
-  stopifnot("Argument `full` must be TRUE or FALSE." = is.logical(full))
-  stopifnot("Argument `italics` must be TRUE or FALSE." = is.logical(italics))
-  stopifnot("Argument `dfs` must be 'par', 'sub', or 'none'." = dfs %in% c("par", "sub", "none"))
-  stopifnot("Argument `mean` must be 'abbr' or 'word'." = mean %in% c("abbr", "word"))
-  stopifnot("Argument `type` must be 'md' or 'latex'." = type %in% c("md", "latex"))
-
-  if (grepl("correlation", x$method)) {
-    if (is.null(digits)) {
-      digits <- 2
-    } else {
-      digits <- digits
-    }
-    format_corr(x,
-                digits = digits,
-                pdigits = pdigits,
-                pzero = pzero,
-                full = full,
-                italics = italics,
-                type = type)
-  } else if (grepl("t-test", x$method) | grepl("Wilcoxon", x$method)) {
-    if (is.null(digits)) {
-      digits <- 1
-    } else {
-      digits <- digits
-    }
-    format_ttest(x,
-                 digits = digits,
-                 pdigits = pdigits,
-                 pzero = pzero,
-                 full = full,
-                 italics = italics,
-                 dfs = dfs,
-                 mean = mean,
-                 type = type)
-  } else {
-    stop(
-      "Objects of method '"
-      , x$method
-      , "' are currently not supported."
-      , "\nVisit https://github.com/JeffreyRStevens/cocoon/issues to request support for this method."
-      , call. = FALSE
-    )
-  }
-}
-
-#' Format correlation statistics
-#'
-#' @description
-#' This functions formats correlation statistics generated from the
-#' \{[correlation](https://cran.r-project.org/package=correlation)\} package.
-#' This detects whether the object is from a Pearson, Spearman, or Kendall
-#' correlation and reports the appropriate correlation label
-#' (r, \eqn{\tau}, \eqn{\rho}). The default output is APA formatted, but
-#' numbers of digits, leading zeros, the presence of confidence intervals,
-#' and italics are all customizable.
-
-#' @inheritParams format_stats.htest
-#'
-#' @return
-#' A character string of statistical information formatted in Markdown or LaTeX.
-#'
-#' @method format_stats easycorrelation
-#' @family functions for printing statistical objects
-
-#' @export
-#'
-#' @examples
-#' # Prepare statistical objects
-#' test_corr <- correlation::correlation(mtcars, select = "mpg", select2 = "disp")
-#' test_corr2 <- correlation::correlation(mtcars, select = "mpg", select2 = "disp", method = "kendall")
-#'
-#' # Format correlation
-#' format_stats(test_corr)
-#'
-#' # Remove confidence intervals and italics
-#' format_stats(test_corr, full = FALSE, italics = FALSE)
-#'
-#' # Change digits and add leading zero to p-value
-#' format_stats(test_corr, digits = 3, pdigits = 4, pzero = TRUE)
-#'
-#' # Format Kendall's tau for LaTeX
-#' format_stats(test_corr2, type = "latex")
-format_stats.easycorrelation <- function(x,
-                                         digits = 2,
-                                         pdigits = 3,
-                                         pzero = FALSE,
-                                         full = TRUE,
-                                         italics = TRUE,
-                                         type = "md",
-                                         ...) {
-  # Validate arguments
-  if (!is.null(digits)) {
-    stopifnot("Argument `digits` must be a non-negative numeric vector." = is.numeric(digits))
-    stopifnot("Argument `digits` must be a non-negative numeric vector." = digits >= 0)
-  }
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = is.numeric(pdigits))
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = pdigits > 0)
-  stopifnot("Argument `pdigits` must be a numeric between 1 and 5." = pdigits < 6)
-  stopifnot("Argument `pzero` must be TRUE or FALSE." = is.logical(pzero))
-  stopifnot("Argument `full` must be TRUE or FALSE." = is.logical(full))
-  stopifnot("Argument `italics` must be TRUE or FALSE." = is.logical(italics))
-  stopifnot("Argument `type` must be 'md' or 'latex'." = type %in% c("md", "latex"))
-
-  if ("r" %in% names(x)) {
-    method <- "Pearson correlation"
-  } else if ("rho" %in% names(x)) {
-    method <- "Spearman correlation"
-    x$r <- x$rho
-  }  else if ("tau" %in% names(x)) {
-    method <- "Kendall correlation"
-    x$r <- x$tau
-  } else {
-    stop("Correlation method is not Pearson, Spearman, or Kendall.")
-  }
-
-  y <- list(statistic = x$t,
-            parameter = x$df_error,
-            p.value = x$p,
-            estimate = x$r,
-            data.name = paste0(x$Parameter1, " and ", x$Parameter2),
-            method = method,
-            conf.int = c(x$CI_low, x$CI_high))
-  class(y) <- "htest"
-  format_corr(y,
-              digits = digits,
-              pdigits = pdigits,
-              pzero = pzero,
-              full = full,
-              italics = italics,
-              type = type)
-}
-
-#' Format Bayes factors
-#'
-#' This method formats Bayes factors from the
-#' \{[BayesFactor](https://cran.r-project.org/package=BayesFactor)\} package.
-#' By default, this function rounds Bayes factors greater than 1 to one decimal
-#' place and Bayes factors less than 1 to two decimal places. Values greater
-#' than 1000 or less than 1/1000 are formatted using scientific notation.
-#' Cutoffs can be set that format the values as greater than or less than the
-#' cutoffs (e.g., BF > 1000 or BF < 0.001). Numbers of digits, cutoffs,
-#' italics, and label subscripts are all customizable.
-#'
-#' @param x BayesFactor object or vector of numeric Bayes factor values
-#' @param digits1 Number of digits after the decimal for Bayes factors > 1
-#' @param digits2 Number of digits after the decimal for Bayes factors < 1
-#' @param cutoff Cutoff for using `_BF_~10~ > <cutoff>` or
-#' `_BF_~10~ < 1 / <cutoff>` (value must be > 1)
-#' @param label Character string for label before Bayes factor. Default is BF.
-#' Set `label = ""` to return just the formatted Bayes factor value with no
-#' label or operator (`=`, `<`, `>`)
-#' @param italics Logical value (default = TRUE) for whether label should be
-#' italicized (_BF_ or BF)
-#' @param subscript Subscript to include with _BF_ label (`"10"`, `"01"`, or
-#' `""` for no subscript)
-#' @param type Type of formatting (`"md"` = markdown, `"latex"` = LaTeX)
-#' @param ... Additional arguments passed to methods.
-#'
-#'
-#' @return
-#' A character string of statistical information formatted in Markdown or LaTeX.
-#'
-#' @method format_stats BFBayesFactor
-#' @family functions for printing statistical objects
-#' @export
-#'
-#' @examples
-#' # Prepare statistical object
-#' test_bf <- BayesFactor::ttestBF(mtcars$vs, mtcars$am)
-#'
-#' # Format Bayes factor
-#' format_stats(test_bf)
-#'
-#' # Control cutoff for output
-#' format_stats(test_bf, cutoff = 3)
-#'
-#' # Change digits, remove italics and subscript
-#' format_stats(test_bf, digits2 = 1, italics = FALSE, subscript = "")
-#'
-#' # Return only Bayes factor value (no label)
-#' format_stats(test_bf, label = "")
-#'
-#' # Format for LaTeX
-#' format_stats(test_bf, type = "latex")
-format_stats.BFBayesFactor <- function(x,
-                                       digits1 = 1,
-                                       digits2 = 2,
-                                       cutoff = NULL,
-                                       label = "BF",
-                                       italics = TRUE,
-                                       subscript = "10",
-                                       type = "md",
-                                       ...) {
-
-  format_bf(x,
-            digits1 = digits1,
-            digits2 = digits2,
-            cutoff = cutoff,
-            label = label,
-            italics = italics,
-            subscript = subscript,
-            type = type)
-}