Merge branch 'main' into main

easystats · Oct 24, 2023 · 6a12bde · 6a12bde
2 parents 397c4cc + bf6cb28
commit 6a12bde
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diff --git a/.github/workflows/html-5-check.yaml b/.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
diff --git a/.github/workflows/update-to-latest-easystats.yaml b/.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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: effectsize
 Title: Indices of Effect Size
-Version: 0.8.6
+Version: 0.8.6.1
 Authors@R: 
     c(person(given = "Mattan S.",
              family = "Ben-Shachar",
@@ -65,7 +65,7 @@ Description: Provide utilities to work with indices of effect size for a wide
     the function 'insight::supported_models()'), allowing computation of and 
     conversion between indices such as Cohen's d, r, odds, etc.
     References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
-License: GPL-3
+License: MIT + file LICENSE
 URL: https://easystats.github.io/effectsize/
 BugReports: https://github.com/easystats/effectsize/issues/
 Depends:

diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
@@ -139,6 +139,7 @@ export(interpret_direction)
 export(interpret_epsilon_squared)
 export(interpret_ess)
 export(interpret_eta_squared)
+export(interpret_fei)
 export(interpret_g)
 export(interpret_gfi)
 export(interpret_glass_delta)
@@ -247,14 +248,8 @@ importFrom(bayestestR,equivalence_test)
 importFrom(datawizard,standardise)
 importFrom(datawizard,standardize)
 importFrom(insight,display)
-importFrom(insight,find_predictors)
 importFrom(insight,print_html)
 importFrom(insight,print_md)
-importFrom(parameters,model_parameters)
 importFrom(parameters,standardize_info)
 importFrom(parameters,standardize_parameters)
 importFrom(parameters,standardize_posteriors)
-importFrom(stats,anova)
-importFrom(stats,aov)
-importFrom(stats,na.omit)
-importFrom(utils,packageVersion)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# effectsize 0.8.7.xxx
+
+- This release changes the licensing model of `{effectsize}` to an MIT license.
+
+# effectsize 0.8.7
+
+## New features
+
+- New function: `interpret_fei()`
+
 # effectsize 0.8.6
 
 This is a minor update to bring `effectsize` in-line with the formula methods 

diff --git a/R/cohens_d.R b/R/cohens_d.R
@@ -266,7 +266,7 @@ glass_delta <- function(x, y = NULL, data = NULL,
   }
 
   out <- data.frame(d = (d - mu) / s)
-  types <- c("d" = "Cohens_d", "g" = "Hedges_g", "delta" = "Glass_delta")
+  types <- c(d = "Cohens_d", g = "Hedges_g", delta = "Glass_delta")
   colnames(out) <- types[type]
 
   if (.test_ci(ci)) {

diff --git a/R/convert_stat_chisq.R b/R/convert_stat_chisq.R
@@ -48,7 +48,8 @@
 #'
 #' \deqn{\textrm{Pearson's } C = \sqrt{\chi^2 / (\chi^2 + n)}}{Pearson's C = sqrt(\chi^2 / (\chi^2 + n))}
 #'
-#' For versions adjusted for small-sample bias of \eqn{\phi}, \eqn{V}, and \eqn{T}, see [Bergsma, 2013](https://en.wikipedia.org/wiki/Cram%C3%A9r%27s_V#Bias_correction).
+#' For versions adjusted for small-sample bias of \eqn{\phi}, \eqn{V}, and \eqn{T},
+#' see [Bergsma, 2013](https://en.wikipedia.org/wiki/Cram%C3%A9r%27s_V#Bias_correction).
 #'
 #' @inheritSection effectsize_CIs Confidence (Compatibility) Intervals (CIs)
 #' @inheritSection effectsize_CIs CIs and Significance Tests

diff --git a/R/effectsize-package.R b/R/effectsize-package.R
@@ -18,8 +18,9 @@
 #' and hypothesis tests, such as [cohens_d()], [phi()], [eta_squared()], and
 #' many more.
 #'
-#' See [`vignette("effectsize", package = "effectsize")`](https://easystats.github.io/effectsize/articles/effectsize.html) for more details,
-#' or [`vignette(package = "effectsize")`](https://easystats.github.io/effectsize/articles/) for a full list of vignettes.
+#' See [`vignette("effectsize", package = "effectsize")`](https://easystats.github.io/effectsize/articles/effectsize.html)
+#' for more details, or [`vignette(package = "effectsize")`](https://easystats.github.io/effectsize/articles/)
+#' for a full list of vignettes.
 #'
 #' References: Ben-Shachar et al. (2020) \doi{10.21105/joss.02815}.
 #'

diff --git a/R/eta_squared-main.R b/R/eta_squared-main.R
@@ -764,7 +764,6 @@ cohens_f_squared <- function(model,
 
 
 #' @keywords internal
-#' @importFrom stats anova
 .anova_es.default <- function(model, ...) {
   .anova_es.anova(stats::anova(model), ...)
 }
@@ -842,8 +841,6 @@ cohens_f_squared <- function(model,
 }
 
 #' @keywords internal
-#' @importFrom parameters model_parameters
-#' @importFrom stats anova
 .anova_es.aov <- function(model,
                           type = c("eta", "omega", "epsilon"),
                           partial = TRUE,
@@ -885,8 +882,6 @@ cohens_f_squared <- function(model,
 .anova_es.glm <- .anova_es.lm
 
 #' @keywords internal
-#' @importFrom parameters model_parameters
-#' @importFrom insight find_predictors
 .anova_es.aovlist <- function(model,
                               type = c("eta", "omega", "epsilon"),
                               partial = TRUE,

diff --git a/R/eta_squared-methods.R b/R/eta_squared-methods.R
@@ -110,7 +110,7 @@
     within <- names(model$idata)
     within <- lapply(within, function(x) c(NA, x))
     within <- do.call(expand.grid, within)
-    within <- apply(within, 1, na.omit)
+    within <- apply(within, 1, stats::na.omit)
     ns <- sapply(within, length)
     within <- sapply(within, paste, collapse = ":")
     within <- within[order(ns)]
@@ -179,7 +179,6 @@
 #' @keywords internal
 .anova_es.anova.lme <- .anova_es.anova
 
-#' @importFrom stats na.omit
 #' @keywords internal
 .anova_es.parameters_model <- function(model,
                                        type = c("eta", "omega", "epsilon"),
@@ -249,8 +248,6 @@
 # Specific models ---------------------------------------------------------
 
 #' @keywords internal
-#' @importFrom stats aov
-#' @importFrom utils packageVersion
 .anova_es.maov <- function(model,
                            type = c("eta", "omega", "epsilon"),
                            partial = TRUE,

diff --git a/R/interpret.R b/R/interpret.R
@@ -36,7 +36,7 @@ rules <- function(values, labels = NULL, name = NULL, right = TRUE) {
     }
   }
 
-  # Sanity checks
+  # validation checks
   if (length(labels) < length(values)) {
     insight::format_error("There cannot be less labels than reference values!")
   } else if (length(labels) > length(values) + 1) {
@@ -178,7 +178,7 @@ interpret.effectsize_table <- function(x, rules, ...) {
     Cohens_w = ,
     Tschuprows_t = ,
     Tschuprows_t_adjusted = ,
-    fei = interpret_cramers_v(value, rules = rules),
+    Fei = interpret_fei(value, rules = rules),
 
     ## xtab 2x2
     Cohens_h = interpret_cohens_d(value, rules = rules),

diff --git a/R/interpret_r.R b/R/interpret_r.R
@@ -109,3 +109,7 @@ interpret_cramers_v <- interpret_r
 #' @export
 #' @rdname interpret_r
 interpret_rank_biserial <- interpret_r
+
+#' @export
+#' @rdname interpret_r
+interpret_fei <- interpret_r
diff --git a/R/xtab_diff.R b/R/xtab_diff.R
@@ -295,7 +295,7 @@ arr <- function(x, y = NULL, ci = 0.95, alternative = "two.sided", ...) {
 nnt <- function(x, y = NULL, ci = 0.95, alternative = "two.sided", ...) {
   alternative <- .match.alt(alternative)
 
-  flip_alt <- c("less" = "greater", "greater" = "less", "two.sided" = "two.sided")
+  flip_alt <- c(less = "greater", greater = "less", two.sided = "two.sided")
   alternative2 <- unname(flip_alt[alternative])
 
   if (.is_htest_of_type(x, "Pearson's Chi-squared", "Chi-squared-test")) {

diff --git a/man/convert_chisq.Rd b/man/convert_chisq.Rd
diff --git a/man/effectsize-package.Rd b/man/effectsize-package.Rd
diff --git a/man/effectsize.Rd b/man/effectsize.Rd
diff --git a/man/interpret_r.Rd b/man/interpret_r.Rd
diff --git a/tests/testthat/test-effectsize.R b/tests/testthat/test-effectsize.R
@@ -252,14 +252,56 @@ test_that("htest | rank", {
 })
 
 test_that("htest | Get args from htest", {
-  tt <- t.test(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3, conf.level = 0.8, var.equal = TRUE)
-  expect_equal(cohens_d(tt), cohens_d(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3, ci = 0.8), ignore_attr = TRUE)
+  tt <- t.test(
+    mtcars$hp,
+    mtcars$mpg,
+    alternative = "l",
+    mu = -3,
+    conf.level = 0.8,
+    var.equal = TRUE
+  )
+  expect_equal(
+    cohens_d(tt),
+    cohens_d(
+      mtcars$hp,
+      mtcars$mpg,
+      alternative = "l",
+      mu = -3,
+      ci = 0.8
+    ),
+    ignore_attr = TRUE
+  )
 
-  suppressWarnings(ww1 <- wilcox.test(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3))
-  expect_equal(rank_biserial(ww1), rank_biserial(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3), ignore_attr = TRUE)
+  suppressWarnings({
+    ww1 <- wilcox.test(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3)
+  })
+  expect_equal(
+    rank_biserial(ww1),
+    rank_biserial(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3),
+    ignore_attr = TRUE
+  )
 
-  suppressWarnings(ww2 <- wilcox.test(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3, conf.int = TRUE, conf.level = 0.8))
-  expect_equal(rank_biserial(ww2), rank_biserial(mtcars$hp, mtcars$mpg, alternative = "l", mu = -3, ci = 0.8), ignore_attr = TRUE)
+  suppressWarnings({
+    ww2 <- wilcox.test(
+      mtcars$hp,
+      mtcars$mpg,
+      alternative = "l",
+      mu = -3,
+      conf.int = TRUE,
+      conf.level = 0.8
+    )
+  })
+  expect_equal(
+    rank_biserial(ww2),
+    rank_biserial(
+      mtcars$hp,
+      mtcars$mpg,
+      alternative = "l",
+      mu = -3,
+      ci = 0.8
+    ),
+    ignore_attr = TRUE
+  )
 })