From 73b0f3b7a592855c2734bc48c428ea14311202b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
<13123390+rempsyc@users.noreply.github.com>
Date: Sun, 1 Oct 2023 12:25:08 -0400
Subject: [PATCH 1/5] add kruskal method
---
DESCRIPTION | 1 +
NEWS.md | 2 +-
R/report.htest.R | 13 ++-
R/report_htest_kruskal.R | 89 +++++++++++++++++++
.../_snaps/windows/report.htest-chi2.md | 6 +-
.../_snaps/windows/report.htest-kruskal.md | 12 +++
tests/testthat/test-report.htest-kruskal.R | 9 ++
7 files changed, 125 insertions(+), 7 deletions(-)
create mode 100644 R/report_htest_kruskal.R
create mode 100644 tests/testthat/_snaps/windows/report.htest-kruskal.md
create mode 100644 tests/testthat/test-report.htest-kruskal.R
diff --git a/DESCRIPTION b/DESCRIPTION
index 55425d6d..dd2783e9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -126,6 +126,7 @@ Collate:
'report_htest_chi2.R'
'report_htest_cor.R'
'report_htest_friedman.R'
+ 'report_htest_kruskal.R'
'report_htest_ttest.R'
'report_htest_wilcox.R'
'report_info.R'
diff --git a/NEWS.md b/NEWS.md
index 2a6ba0a8..0f87fde9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,7 +6,7 @@ Major Changes
Minor changes
-* `report` now supports variables of class `htest` for the Friedman test.
+* `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.
diff --git a/R/report.htest.R b/R/report.htest.R
index adb28a34..ed3974fa 100644
--- a/R/report.htest.R
+++ b/R/report.htest.R
@@ -58,6 +58,10 @@ report_effectsize.htest <- function(x, ...) {
if (grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
out <- .report_effectsize_friedman(x, table, dot_args)
+ } else if (grepl("Kruskal", attributes(x$statistic)$names, fixed = TRUE)) {
+ # For Kruskal-Wallis test ---------------
+
+ out <- .report_effectsize_kruskal(x, table, dot_args)
} else {
# For wilcox test ---------------
@@ -247,14 +251,17 @@ 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, ...)
# Friedman
- } else if (model_info$is_ranktest &&
- grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
+ } else if (
+ model_info$is_ranktest &&
+ grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
out <- .report_parameters_friedman(table, stats, effsize, ...)
+ } else if (grepl("Kruskal", attributes(x$statistic)$names, fixed = TRUE)) {
+ # Kruskal
+ out <- .report_parameters_kruskal(table, stats, effsize, ...)
# chi2
} else if (model_info$is_chi2test) {
out <- .report_parameters_chi2(table, stats, effsize, ...)
diff --git a/R/report_htest_kruskal.R b/R/report_htest_kruskal.R
new file mode 100644
index 00000000..05681e53
--- /dev/null
+++ b/R/report_htest_kruskal.R
@@ -0,0 +1,89 @@
+# report_table -----------------
+
+.report_table_kruskal <- function(table_full, effsize) {
+ table_full <- cbind(table_full, attributes(effsize)$table)
+ list(table = NULL, table_full = table_full)
+}
+
+
+# report_effectsize ---------------------
+
+.report_effectsize_kruskal <- function(x, table, dot_args, rules = "funder2019") {
+ args <- c(list(x), dot_args)
+ table <- do.call(effectsize::effectsize, args)
+ ci <- attributes(table)$ci
+ estimate <- names(table)[1]
+
+ rules <- ifelse(is.null(dot_args$rules), rules, dot_args$rules)
+
+ # same as Pearson's r
+ args <- c(list(table$rank_epsilon_squared), dot_args)
+ interpretation <- do.call(effectsize::interpret_epsilon_squared, args)
+ rules <- .text_effectsize(attr(attr(interpretation, "rules"), "rule_name"))
+
+ main <- paste0("Epsilon squared (rank) = ", insight::format_value(table$rank_epsilon_squared))
+ statistics <- paste0(
+ main,
+ ", ",
+ insight::format_ci(table$CI_low, table$CI_high, ci)
+ )
+
+ table <- table[names(table)[-2]]
+
+ list(
+ table = table, statistics = statistics, interpretation = interpretation,
+ rules = rules, ci = ci, main = main
+ )
+}
+
+
+# report_model ----------------------------
+
+.report_model_kruskal <- function(x, table) {
+ # two-sample
+ if ("Parameter1" %in% names(table)) {
+ vars_full <- paste0(table$Parameter1[[1]], ", and ", table$Parameter2[[1]])
+
+ text <- paste0(
+ trimws(x$method),
+ " testing the difference in ranks between ",
+ vars_full
+ )
+ } else {
+ # one-sample
+ vars_full <- paste0(table$Parameter[[1]])
+
+ text <- paste0(
+ trimws(x$method),
+ " testing the difference in rank for ",
+ vars_full,
+ " and true location of 0"
+ )
+ }
+
+ text
+}
+
+.report_parameters_kruskal <- function(table, stats, effsize, ...) {
+ text_full <- paste0(
+ "statistically ",
+ effectsize::interpret_p(table$p, rules = "default"),
+ ", and ",
+ attributes(effsize)$interpretation,
+ " (",
+ paste0("Kruskal-Wallis ", stats),
+ ")"
+ )
+
+ text_short <- paste0(
+ "statistically ",
+ effectsize::interpret_p(table$p, rules = "default"),
+ ", and ",
+ attributes(effsize)$interpretation,
+ " (",
+ paste0("Kruskal-Wallis ", summary(stats)),
+ ")"
+ )
+
+ list(text_short = text_short, text_full = text_full)
+}
diff --git a/tests/testthat/_snaps/windows/report.htest-chi2.md b/tests/testthat/_snaps/windows/report.htest-chi2.md
index 618bb13b..d0d2bff3 100644
--- a/tests/testthat/_snaps/windows/report.htest-chi2.md
+++ b/tests/testthat/_snaps/windows/report.htest-chi2.md
@@ -318,10 +318,10 @@
Code
report(x)
Output
-
+ Effect sizes were labelled following Funder's (2019) recommendations.
The Chi-squared test for given probabilities / goodness of fit of
table(mtcars$cyl) to a distribution of [4: n=3.2, 6: n=9.6, 8: n=19.2] suggests
- that the effect is statistically significant, and (chi2 = 21.12, p < .001; Fei
- = 0.27, 95% CI [0.17, 1.00])
+ that the effect is statistically significant, and medium (chi2 = 21.12, p <
+ .001; Fei = 0.27, 95% CI [0.17, 1.00])
diff --git a/tests/testthat/_snaps/windows/report.htest-kruskal.md b/tests/testthat/_snaps/windows/report.htest-kruskal.md
new file mode 100644
index 00000000..2fd07386
--- /dev/null
+++ b/tests/testthat/_snaps/windows/report.htest-kruskal.md
@@ -0,0 +1,12 @@
+# report.htest-kruskal report
+
+ Code
+ report(x, verbose = FALSE)
+ Output
+ Effect sizes were labelled following Field's (2013) recommendations.
+
+ The Kruskal-Wallis rank sum test testing the difference in ranks between
+ airquality$Ozone and as.factor(airquality$Month) suggests that the effect is
+ statistically significant, and large (Kruskal-Wallis chi2 = 29.27, p < .001;
+ Epsilon squared (rank) = 0.25, 95% CI [0.15, 1.00])
+
diff --git a/tests/testthat/test-report.htest-kruskal.R b/tests/testthat/test-report.htest-kruskal.R
new file mode 100644
index 00000000..4d518adf
--- /dev/null
+++ b/tests/testthat/test-report.htest-kruskal.R
@@ -0,0 +1,9 @@
+test_that("report.htest-kruskal report", {
+ x <- kruskal.test(airquality$Ozone ~ as.factor(airquality$Month))
+
+ set.seed(100)
+ expect_snapshot(
+ variant = "windows",
+ report(x, verbose = FALSE)
+ )
+})
From 40d308075379c728a41139c3b20971fecb187636 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
<13123390+rempsyc@users.noreply.github.com>
Date: Sun, 5 Nov 2023 13:06:50 -0500
Subject: [PATCH 2/5] fix tests errors, add tests/testthat/helper-state.R
---
R/report.htest.R | 10 ++++++++--
tests/testthat/helper-state.R | 13 +++++++++++++
2 files changed, 21 insertions(+), 2 deletions(-)
create mode 100644 tests/testthat/helper-state.R
diff --git a/R/report.htest.R b/R/report.htest.R
index 762c9160..77dc1d69 100644
--- a/R/report.htest.R
+++ b/R/report.htest.R
@@ -58,7 +58,10 @@ report_effectsize.htest <- function(x, ...) {
if (grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
out <- .report_effectsize_friedman(x, table, dot_args)
- } else if (grepl("Kruskal", attributes(x$statistic)$names, fixed = TRUE)) {
+ } else if (!is.null(x$statistic) && grepl(
+ "Kruskal", attributes(x$statistic)$names,
+ fixed = TRUE
+ )) {
# For Kruskal-Wallis test ---------------
out <- .report_effectsize_kruskal(x, table, dot_args)
@@ -266,7 +269,10 @@ report_parameters.htest <- function(x, table = NULL, ...) {
model_info$is_ranktest &&
grepl("Friedman", attributes(x$statistic)$names, fixed = TRUE)) {
out <- .report_parameters_friedman(table, stats, effsize, ...)
- } else if (grepl("Kruskal", attributes(x$statistic)$names, fixed = TRUE)) {
+ } else if (!is.null(x$statistic) && grepl(
+ "Kruskal", attributes(x$statistic)$names,
+ fixed = TRUE
+ )) {
# Kruskal
out <- .report_parameters_kruskal(table, stats, effsize, ...)
# chi2
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
new file mode 100644
index 00000000..bb2e83e1
--- /dev/null
+++ b/tests/testthat/helper-state.R
@@ -0,0 +1,13 @@
+testthat::set_state_inspector(function() {
+ list(
+ attached = search(),
+ connections = nrow(showConnections()),
+ cwd = getwd(),
+ envvars = Sys.getenv(),
+ libpaths = .libPaths(),
+ locale = Sys.getlocale(),
+ options = .Options,
+ packages = .packages(all.available = TRUE),
+ NULL
+ )
+})
\ No newline at end of file
From c0c58c137a32272fe358951a90c435d58fc2b141 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
<13123390+rempsyc@users.noreply.github.com>
Date: Sun, 5 Nov 2023 13:27:29 -0500
Subject: [PATCH 3/5] style and skip helper-state.R for this PR
---
tests/testthat/helper-state.R | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
index bb2e83e1..57ea9dcb 100644
--- a/tests/testthat/helper-state.R
+++ b/tests/testthat/helper-state.R
@@ -1,4 +1,5 @@
testthat::set_state_inspector(function() {
+ skip()
list(
attached = search(),
connections = nrow(showConnections()),
@@ -10,4 +11,4 @@ testthat::set_state_inspector(function() {
packages = .packages(all.available = TRUE),
NULL
)
-})
\ No newline at end of file
+})
From 35def102b1ea18fabac83f5df30b36501715d0ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
<13123390+rempsyc@users.noreply.github.com>
Date: Sun, 5 Nov 2023 13:43:21 -0500
Subject: [PATCH 4/5] comment helper-state.R
---
DESCRIPTION | 2 +-
tests/testthat/helper-state.R | 28 ++++++++++++++--------------
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 55cbb07f..1b75273a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: report
Type: Package
Title: Automated Reporting of Results and Statistical Models
-Version: 0.5.7.12
+Version: 0.5.7.13
Authors@R:
c(person(given = "Dominique",
family = "Makowski",
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
index 57ea9dcb..41549a95 100644
--- a/tests/testthat/helper-state.R
+++ b/tests/testthat/helper-state.R
@@ -1,14 +1,14 @@
-testthat::set_state_inspector(function() {
- skip()
- list(
- attached = search(),
- connections = nrow(showConnections()),
- cwd = getwd(),
- envvars = Sys.getenv(),
- libpaths = .libPaths(),
- locale = Sys.getlocale(),
- options = .Options,
- packages = .packages(all.available = TRUE),
- NULL
- )
-})
+# testthat::set_state_inspector(function() {
+# list(
+# attached = search(),
+# connections = nrow(showConnections()),
+# cwd = getwd(),
+# envvars = Sys.getenv(),
+# libpaths = .libPaths(),
+# locale = Sys.getlocale(),
+# options = .Options,
+# packages = .packages(all.available = TRUE),
+# NULL
+# )
+# })
+#
From 0b7592a6fa08e6b91fb84c5941382162afd9f193 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
<13123390+rempsyc@users.noreply.github.com>
Date: Sun, 5 Nov 2023 14:41:34 -0500
Subject: [PATCH 5/5] trigger tests again
---
tests/testthat/helper-state.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tests/testthat/helper-state.R b/tests/testthat/helper-state.R
index 41549a95..6fcd92ae 100644
--- a/tests/testthat/helper-state.R
+++ b/tests/testthat/helper-state.R
@@ -11,4 +11,4 @@
# NULL
# )
# })
-#
+##