air

Author: mattansb

.Rbuildignore

@@ -53,3 +53,5 @@ hextools
 # ^vignettes/(?!additional).*
 ^vignettes/additional
 ^LICENSE\.md$
+^\.vscode$
+^[.]?air[.]toml$

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    },
+    "[quarto]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "quarto.quarto"
+    }
+}

R/cohens_d.R

@@ -136,34 +136,57 @@
 #' Correcting error and bias in research findings. Sage.
 #'
 #' @export
-cohens_d <- function(x, y = NULL, data = NULL,
-                     pooled_sd = TRUE, mu = 0, paired = FALSE,
-                     reference = NULL,
-                     adjust = FALSE,
-                     ci = 0.95, alternative = "two.sided",
-                     verbose = TRUE, ...) {
+cohens_d <- function(
+  x,
+  y = NULL,
+  data = NULL,
+  pooled_sd = TRUE,
+  mu = 0,
+  paired = FALSE,
+  reference = NULL,
+  adjust = FALSE,
+  ci = 0.95,
+  alternative = "two.sided",
+  verbose = TRUE,
+  ...
+) {
   var.equal <- eval.parent(match.call()[["var.equal"]])
-  if (!is.null(var.equal)) pooled_sd <- var.equal
+  if (!is.null(var.equal)) {
+    pooled_sd <- var.equal
+  }
 
   .effect_size_difference(
     x,
-    y = y, data = data,
-    type = "d", adjust = adjust,
-    pooled_sd = pooled_sd, mu = mu, paired = paired,
+    y = y,
+    data = data,
+    type = "d",
+    adjust = adjust,
+    pooled_sd = pooled_sd,
+    mu = mu,
+    paired = paired,
     reference = reference,
-    ci = ci, alternative = alternative,
+    ci = ci,
+    alternative = alternative,
     verbose = verbose,
     ...
   )
 }
 
 #' @rdname cohens_d
 #' @export
-hedges_g <- function(x, y = NULL, data = NULL,
-                     pooled_sd = TRUE, mu = 0, paired = FALSE,
-                     reference = NULL,
-                     ci = 0.95, alternative = "two.sided",
-                     verbose = TRUE, ...) {
+hedges_g <- function(
+  x,
+  y = NULL,
+  data = NULL,
+  pooled_sd = TRUE,
+  mu = 0,
+  paired = FALSE,
+  reference = NULL,
+  ci = 0.95,
+  alternative = "two.sided",
+  verbose = TRUE,
+  ...
+) {
   cl <- match.call()
   cl[[1]] <- quote(effectsize::cohens_d)
   cl$adjust <- TRUE
@@ -172,47 +195,77 @@ hedges_g <- function(x, y = NULL, data = NULL,
 
 #' @rdname cohens_d
 #' @export
-glass_delta <- function(x, y = NULL, data = NULL,
-                        mu = 0, adjust = TRUE,
-                        reference = NULL,
-                        ci = 0.95, alternative = "two.sided",
-                        verbose = TRUE, ...) {
+glass_delta <- function(
+  x,
+  y = NULL,
+  data = NULL,
+  mu = 0,
+  adjust = TRUE,
+  reference = NULL,
+  ci = 0.95,
+  alternative = "two.sided",
+  verbose = TRUE,
+  ...
+) {
   .effect_size_difference(
     x,
-    y = y, data = data,
+    y = y,
+    data = data,
     type = "delta",
-    mu = mu, adjust = adjust,
+    mu = mu,
+    adjust = adjust,
     reference = reference,
-    ci = ci, alternative = alternative,
+    ci = ci,
+    alternative = alternative,
     verbose = verbose,
-    pooled_sd = NULL, paired = FALSE,
+    pooled_sd = NULL,
+    paired = FALSE,
     ...
   )
 }
 
 
-
 #' @keywords internal
-.effect_size_difference <- function(x, y = NULL, data = NULL,
-                                    type = "d", adjust = FALSE,
-                                    mu = 0, pooled_sd = TRUE, paired = FALSE,
-                                    reference = NULL,
-                                    ci = 0.95, alternative = "two.sided",
-                                    verbose = TRUE, ...) {
-  if (type == "d" && adjust) type <- "g"
+.effect_size_difference <- function(
+  x,
+  y = NULL,
+  data = NULL,
+  type = "d",
+  adjust = FALSE,
+  mu = 0,
+  pooled_sd = TRUE,
+  paired = FALSE,
+  reference = NULL,
+  ci = 0.95,
+  alternative = "two.sided",
+  verbose = TRUE,
+  ...
+) {
+  if (type == "d" && adjust) {
+    type <- "g"
+  }
 
   # TODO: Check if we can do anything with `reference` for these classes
   if (type != "delta") {
     if (.is_htest_of_type(x, "t-test")) {
       return(effectsize(x, type = type, verbose = verbose, data = data, ...))
-    } else if (.is_BF_of_type(x, c("BFoneSample", "BFindepSample"), "t-squared")) {
+    } else if (
+      .is_BF_of_type(x, c("BFoneSample", "BFindepSample"), "t-squared")
+    ) {
       return(effectsize(x, ci = ci, verbose = verbose, ...))
     }
   }
 
-
   alternative <- .match.alt(alternative)
-  out <- .get_data_2_samples(x, y, data, paired = paired, reference = reference, verbose = verbose, ...)
+  out <- .get_data_2_samples(
+    x,
+    y,
+    data,
+    paired = paired,
+    reference = reference,
+    verbose = verbose,
+    ...
+  )
   x <- out[["x"]]
   y <- out[["y"]]
   paired <- out[["paired"]]
@@ -225,7 +278,9 @@ glass_delta <- function(x, y = NULL, data = NULL,
 
   if (is.null(y)) {
     if (type == "delta") {
-      insight::format_error("For Glass' Delta, please provide data from two samples.")
+      insight::format_error(
+        "For Glass' Delta, please provide data from two samples."
+      )
     }
     y <- 0
     is_paired_or_onesample <- TRUE
@@ -236,7 +291,9 @@ glass_delta <- function(x, y = NULL, data = NULL,
   # Compute index
   if (is_paired_or_onesample) {
     if (type == "delta") {
-      insight::format_error("This effect size is only applicable for two independent samples.")
+      insight::format_error(
+        "This effect size is only applicable for two independent samples."
+      )
     }
 
     d <- mean(x - y)
@@ -304,17 +361,31 @@ glass_delta <- function(x, y = NULL, data = NULL,
 
   if (adjust) {
     J <- .J(df1)
-    col_to_adjust <- intersect(colnames(out), c(types[type], "CI_low", "CI_high"))
+    col_to_adjust <- intersect(
+      colnames(out),
+      c(types[type], "CI_low", "CI_high")
+    )
     out[, col_to_adjust] <- out[, col_to_adjust] * J
 
     if (type == "delta") {
       colnames(out)[1] <- "Glass_delta_adjusted"
     }
   }
 
-  class(out) <- c("effectsize_difference", "effectsize_table", "see_effectsize_table", class(out))
+  class(out) <- c(
+    "effectsize_difference",
+    "effectsize_table",
+    "see_effectsize_table",
+    class(out)
+  )
   .someattributes(out) <- .nlist(
-    paired, pooled_sd, mu, ci, ci_method, alternative, adjust,
+    paired,
+    pooled_sd,
+    mu,
+    ci,
+    ci_method,
+    alternative,
+    adjust,
     approximate = FALSE
   )
   out

R/cohens_g.R

@@ -52,16 +52,13 @@
 #' # Test 2 gives a negative result more than test 1!
 #'
 #' @export
-cohens_g <- function(x, y = NULL,
-                     ci = 0.95, alternative = "two.sided",
-                     ...) {
+cohens_g <- function(x, y = NULL, ci = 0.95, alternative = "two.sided", ...) {
   alternative <- .match.alt(alternative)
 
   if (.is_htest_of_type(x, "McNemar")) {
     return(effectsize(x, ci = ci, alternative = alternative))
   }
 
-
   if (!is.matrix(x)) {
     if (is.null(y)) {
       insight::format_error("if 'x' is not a matrix, 'y' must be given")
@@ -73,14 +70,17 @@ cohens_g <- function(x, y = NULL,
     x <- as.factor(x[OK])
     y <- as.factor(y[OK])
     if ((nlevels(x) < 2) || (nlevels(y) != nlevels(x))) {
-      insight::format_error("'x' and 'y' must have the same number of levels (minimum 2)")
+      insight::format_error(
+        "'x' and 'y' must have the same number of levels (minimum 2)"
+      )
     }
     x <- table(x, y)
   } else if ((nrow(x) < 2) || (ncol(x) != nrow(x))) {
-    insight::format_error("'x' must be square with at least two rows and columns")
+    insight::format_error(
+      "'x' must be square with at least two rows and columns"
+    )
   }
 
-
   a <- x[upper.tri(x)]
   b <- t(x)[upper.tri(x)]
 
@@ -95,7 +95,9 @@ cohens_g <- function(x, y = NULL,
     n <- sum(a) + sum(b)
     k <- P * n
 
-    res <- stats::prop.test(k, n,
+    res <- stats::prop.test(
+      k,
+      n,
       p = 0.5,
       alternative = alternative,
       conf.level = ci,