safer tests because it fails on some distribution

easystats · Sep 26, 2020 · ab44523 · ab44523
1 parent 9ebe2e6
commit ab44523
Show file tree

Hide file tree

Showing 2 changed files with 56 additions and 40 deletions.
diff --git a/tests/testthat/test-cor_test.R b/tests/testthat/test-cor_test.R
@@ -1,22 +1,30 @@
 context("cor_test")
 
 
-
 test_that("cor_test frequentist", {
- if (requireNamespace("psych")) {
- data <- iris
- data$Sepal.Width_binary <- ifelse(data$Sepal.Width > 3, 1, 0)
- data$Petal.Width_binary <- ifelse(data$Petal.Width > 1.2, 1, 0)
 
+ testthat::expect_error(cor_test(iris, Petal.Length, Petal.Width))
 
- testthat::expect_error(cor_test(data, Petal.Length, Petal.Width))
+ out <- cor_test(iris, "Petal.Length", "Petal.Width")
+ testthat::expect_equal(out$r, 0.962, tol = 0.01)
+
+})
 
- out <- cor_test(data, "Petal.Length", "Petal.Width")
- testthat::expect_equal(out$r, 0.962, tol = 0.01)
 
- out <- cor_test(data, "Petal.Length", "Petal.Width", bayesian = TRUE)
-  testthat::expect_equal(out$r, 0.962, tol = 0.01)
+test_that("cor_test bayesian", {
+ if (requireNamespace("BayesFactor")) {
 
+ out <- cor_test(iris, "Petal.Length", "Petal.Width", bayesian = TRUE)
+ testthat::expect_equal(out$r, 0.962, tol = 0.01)
+
+ }
+})
+
+test_that("cor_test tetrachoric", {
+ if (requireNamespace("psych")) {
+ data <- iris
+ data$Sepal.Width_binary <- ifelse(data$Sepal.Width > 3, 1, 0)
+ data$Petal.Width_binary <- ifelse(data$Petal.Width > 1.2, 1, 0)
 
  # With Factors / Binary
  out <- cor_test(data, "Sepal.Width_binary", "Petal.Width_binary", method = "tetrachoric")
@@ -85,9 +93,11 @@ test_that("cor_test blomqvist", {
 })
 
 test_that("cor_test hoeffding", {
+ if (requireNamespace("Hmisc")) {
  set.seed(333)
  out <- cor_test(iris, "Petal.Length", "Petal.Width", method = "hoeffding")
  testthat::expect_equal(out$r, as.numeric(0.5629277), tol = 0.01)
+ }
 })
 
 test_that("cor_test gamma", {
@@ -101,8 +111,10 @@ test_that("cor_test gaussian", {
  out <- cor_test(iris, "Petal.Length", "Petal.Width", method = "gaussian")
  testthat::expect_equal(out$r, as.numeric(0.87137), tol = 0.01)
 
- out <- cor_test(iris, "Petal.Length", "Petal.Width", method = "gaussian", bayesian = TRUE)
- testthat::expect_equal(out$r, as.numeric(0.8620878), tol = 0.01)
+ if (requireNamespace("BayesFactor")) {
+ out <- cor_test(iris, "Petal.Length", "Petal.Width", method = "gaussian", bayesian = TRUE)
+ testthat::expect_equal(out$r, as.numeric(0.8620878), tol = 0.01)
+ }
 })
 
 

diff --git a/tests/testthat/test-correlation.R b/tests/testthat/test-correlation.R
@@ -68,40 +68,42 @@ test_that("comparison with other packages", {
 
 
  # Bayesian
- out <- correlation(iris, include_factors = FALSE, bayesian = TRUE)
- rez <- as.data.frame(as.table(out))
+ if (requireNamespace("BayesFactor")) {
+ out <- correlation(iris, include_factors = FALSE, bayesian = TRUE)
+ rez <- as.data.frame(as.table(out))
 
- r <- as.matrix(rez[2:5])
- testthat::expect_equal(mean(r - cor(iris[1:4])), 0, tol = 0.01)
+  r <- as.matrix(rez[2:5])
+  testthat::expect_equal(mean(r - cor(iris[1:4])), 0, tol = 0.01)
 
- hmisc <- Hmisc::rcorr(as.matrix(iris[1:4]), type = c("pearson"))
- testthat::expect_equal(mean(r - hmisc$r), 0, tol = 0.01)
+  hmisc <- Hmisc::rcorr(as.matrix(iris[1:4]), type = c("pearson"))
+  testthat::expect_equal(mean(r - hmisc$r), 0, tol = 0.01)
 
- pd <- as.matrix(attributes(rez)$pd[2:5])
- p <- bayestestR::pd_to_p(pd)
- testthat::expect_equal(mean(p - hmisc$P, na.rm = TRUE), 0, tol = 0.01)
+  pd <- as.matrix(attributes(rez)$pd[2:5])
+  p <- bayestestR::pd_to_p(pd)
+  testthat::expect_equal(mean(p - hmisc$P, na.rm = TRUE), 0, tol = 0.01)
 
 
- # Bayesian - Partial
- out <- correlation(iris, include_factors = FALSE, bayesian = TRUE, partial = TRUE)
- rez <- as.data.frame(as.table(out))
+  # Bayesian - Partial
+  out <- correlation(iris, include_factors = FALSE, bayesian = TRUE, partial = TRUE)
+  rez <- as.data.frame(as.table(out))
 
- r <- as.matrix(rez[2:5])
- ppcor <- ppcor::pcor(iris[1:4])
- testthat::expect_equal(max(r - as.matrix(ppcor$estimate)), 0, tol = 0.02)
+  r <- as.matrix(rez[2:5])
+  ppcor <- ppcor::pcor(iris[1:4])
+  testthat::expect_equal(max(r - as.matrix(ppcor$estimate)), 0, tol = 0.02)
 
- pd <- as.matrix(attributes(rez)$pd[2:ncol(rez)])
- p <- bayestestR::pd_to_p(pd)
- testthat::expect_equal(mean(abs(p - as.matrix(ppcor$p.value))), 0, tol = 0.001)
+  pd <- as.matrix(attributes(rez)$pd[2:ncol(rez)])
+  p <- bayestestR::pd_to_p(pd)
+  testthat::expect_equal(mean(abs(p - as.matrix(ppcor$p.value))), 0, tol = 0.001)
 
 
- # Bayesian (Full) - Partial
- out <- correlation(iris, include_factors = FALSE, bayesian = TRUE, partial = TRUE, partial_bayesian = TRUE)
- rez <- as.data.frame(as.table(out))
+  # Bayesian (Full) - Partial
+  out <- correlation(iris, include_factors = FALSE, bayesian = TRUE, partial = TRUE, partial_bayesian = TRUE)
+  rez <- as.data.frame(as.table(out))
 
- r <- as.matrix(rez[2:5])
- ppcor <- ppcor::pcor(iris[1:4])
- testthat::expect_equal(max(r - as.matrix(ppcor$estimate)), 0, tol = 0.02)
+ r <- as.matrix(rez[2:5])
+ ppcor <- ppcor::pcor(iris[1:4])
+ testthat::expect_equal(max(r - as.matrix(ppcor$estimate)), 0, tol = 0.02)
+ }
  }
 })
 
@@ -140,10 +142,12 @@ test_that("format checks", {
  }
 
  # Bayesian full partial
- out <- correlation(iris, include_factors = TRUE, multilevel = TRUE, bayesian = TRUE, partial = TRUE, partial_bayesian = TRUE)
- testthat::expect_equal(c(nrow(out), ncol(out)), c(6, 13))
- testthat::expect_equal(c(nrow(as.table(out)), ncol(as.table(out))), c(4, 5))
- testthat::expect_equal(c(nrow(summary(out)), ncol(summary(out))), c(3, 4))
+ if (requireNamespace("BayesFactor")) {
+ out <- correlation(iris, include_factors = TRUE, multilevel = TRUE, bayesian = TRUE, partial = TRUE, partial_bayesian = TRUE)
+ testthat::expect_equal(c(nrow(out), ncol(out)), c(6, 13))
+ testthat::expect_equal(c(nrow(as.table(out)), ncol(as.table(out))), c(4, 5))
+ testthat::expect_equal(c(nrow(summary(out)), ncol(summary(out))), c(3, 4))
+ }
 })