added ui tests for assumptiopns, correlations, statisticla tests, tte…

…st and visualisation

bs/inst/tinytest/Assumptions.R

@@ -0,0 +1,50 @@
+library(shinytest2)
+library(tinytest)
+app <- bs::app()
+app <- shiny::shinyApp(app$ui, app$server)
+app <- AppDriver$new(app)
+app$upload_file(
+  file = system.file("/test_data/CO2.csv", package = "bs")
+)
+app$set_inputs(conditionedPanels = "Assumption")
+app$set_window_size(width = 2259, height = 1326)
+app$click("ASS-open_formula_editor")
+app$set_inputs(`FO-colnames-dropdown_0` = "uptake")
+app$click("FO-colnames_Treatment_0")
+app$click("FO-create_formula")
+app$run_js("$('.modal-footer button:contains(\"Close\")').click();")
+app$click("ASS-shapiro")
+res <- app$get_values()$export
+expected <- rbind(
+  broom::tidy(shapiro.test(CO2[CO2$Treatment == "nonchilled", "uptake"])),
+  broom::tidy(shapiro.test(CO2[CO2$Treatment == "chilled", "uptake"]))
+)
+expected$variable <- c("nonchilled", "chilled")
+expected$`Normal distributed` <- expected$p.value > 0.05
+expected
+tinytest::expect_equal(res[[1]], expected)
+
+# Update output value
+app$click("ASS-shapiroResiduals")
+res <- app$get_values()$export
+fit <- lm(uptake ~ Treatment, data = CO2)
+r <- resid(fit)
+expected <- broom::tidy(shapiro.test(r))
+expected$`Residuals normal distributed` <- expected$p.value > 0.05
+tinytest::expect_equal(res[[1]], expected)
+
+# Update output value
+app$click("ASS-levene")
+res <- app$get_values()$export
+expected <- broom::tidy(car::leveneTest(uptake ~ Treatment,
+  data = CO2, center = "mean"))
+expected$`Variance homogenity` <- expected$p.value > 0.05
+tinytest::expect_equal(res[[1]], expected)
+
+# Update output value
+app$click("ASS-DiagnosticPlot")
+res <- app$get_values()$export
+tinytest::expect_equal(inherits(res[[1]], "ggplot"), TRUE)
+# TODO: add internal backend test for diagnostic plot functions
+
+app$stop()

bs/inst/tinytest/Correlation.R

@@ -0,0 +1,31 @@
+library(shinytest2)
+library(tinytest)
+app <- bs::app()
+app <- shiny::shinyApp(app$ui, app$server)
+app <- AppDriver$new(app)
+app$upload_file(
+  file = system.file("/test_data/CO2.csv", package = "bs")
+)
+app$set_window_size(width = 2259, height = 1326)
+app$set_inputs(conditionedPanels = "Correlation")
+app$click("CORR-open_formula_editor")
+app$set_inputs(`FO-colnames-dropdown_0` = "uptake")
+app$click("FO-colnames_conc_0")
+app$click("FO-create_formula")
+app$run_js("$('.modal-footer button:contains(\"Close\")').click();")
+app$click("CORR-pear")
+res <- app$get_values()$export
+expected <- cor.test(CO2$uptake, CO2$conc, method = "pearson")
+expected <- broom::tidy(expected)
+tinytest::expect_equal(res[[1]], expected)
+app$click("CORR-spear")
+res <- app$get_values()$export
+expected <- cor.test(CO2$uptake, CO2$conc, method = "spearman")
+expected <- broom::tidy(expected)
+tinytest::expect_equal(res[[1]], expected)
+app$click("CORR-kendall")
+res <- app$get_values()$export
+expected <- cor.test(CO2$uptake, CO2$conc, method = "kendall")
+expected <- broom::tidy(expected)
+tinytest::expect_equal(res[[1]], expected)
+app$stop()

bs/inst/tinytest/StatisticalTests.R

@@ -0,0 +1,96 @@
+library(shinytest2)
+library(tinytest)
+app <- bs::app()
+app <- shiny::shinyApp(app$ui, app$server)
+app <- AppDriver$new(app)
+app$upload_file(
+  file = system.file("/test_data/CO2.csv", package = "bs")
+)
+app$set_window_size(width = 2259, height = 1326)
+app$set_inputs(conditionedPanels = "Tests")
+
+# Define formula
+app$click("TESTS-open_formula_editor")
+app$set_inputs(`FO-colnames-dropdown_0` = "uptake")
+app$set_inputs(`FO-editable_code` = "conc * Treatment + Type")
+app$click("FO-create_formula")
+app$run_js("$('.modal-footer button:contains(\"Close\")').click();")
+
+# ANOVA
+app$set_inputs(TestsConditionedPanels  = "More than two groups")
+app$click("TESTS-aovTest")
+res <- app$get_values()$export
+CO2$Treatment <- as.character(CO2$Treatment)
+CO2$Type <- as.character(CO2$Type)
+expected <- broom::tidy(aov(uptake ~ conc*Treatment + Type, data = CO2))
+expected <- cbind(expected, row.names(expected))
+names(expected)[ncol(expected)] <- paste0("conc * Treatment + Type", collapse = ".")
+tinytest::expect_equal(res[[1]], expected)
+
+# Kruskal-Wallis
+app$click("TESTS-open_formula_editor")
+app$set_inputs(`FO-colnames-dropdown_0` = "uptake")
+app$set_inputs(`FO-editable_code` = "conc")
+app$click("FO-create_formula")
+app$run_js("$('.modal-footer button:contains(\"Close\")').click();")
+
+app$click("TESTS-kruskalTest")
+res <- app$get_values()$export
+CO2$Treatment <- as.character(CO2$Treatment)
+expected <- broom::tidy(kruskal.test(uptake ~conc, data = CO2))
+expected <- cbind(expected, row.names(expected))
+names(expected)[ncol(expected)] <- paste0("conc", collapse = ".")
+tinytest::expect_equal(res[[1]], expected)
+
+# PostHoc tests
+# TukeyHSD
+app$set_inputs(TestsConditionedPanels  = "Posthoc tests")
+app$set_inputs(`TESTS-PostHocTests` = "HSD")
+app$click("TESTS-PostHocTest")
+res <- app$get_values()$export
+fit <- aov(uptake ~ conc, data = CO2)
+fit <- agricolae::HSD.test(fit,
+  trt = "conc",
+  alpha = 0.05, group = TRUE, unbalanced = TRUE
+)$groups
+expected <- cbind(fit, row.names(fit))
+names(expected)[ncol(expected)] <- paste0("conc", collapse = ".")
+tinytest::expect_equal(res[[1]], expected)
+
+app$set_inputs(TestsConditionedPanels  = "Posthoc tests")
+app$set_inputs(`TESTS-PostHocTests` = "HSD")
+app$set_inputs(`TESTS-design` = "ub")
+app$click("TESTS-PostHocTest")
+res <- app$get_values()$export
+fit <- aov(uptake ~ conc, data = CO2)
+fit <- agricolae::HSD.test(fit,
+  trt = "conc",
+  alpha = 0.05, group = TRUE, unbalanced = FALSE
+)$groups
+expected <- cbind(fit, row.names(fit))
+names(expected)[ncol(expected)] <- paste0("conc", collapse = ".")
+tinytest::expect_equal(res[[1]], expected)
+
+# Kruskal-Wallis test
+app$set_inputs(`TESTS-PostHocTests` = "kruskalTest")
+app$click("TESTS-PostHocTest")
+res <- app$get_values()$export
+df <- CO2
+dep <- "uptake"
+fit <- with(df, agricolae::kruskal(df[, dep],df[, "conc"]),
+  alpha = 0.05, p.adj = 0.05, group = TRUE
+)$groups
+expected <- cbind(fit, row.names(fit))
+names(expected)[ncol(expected)] <- paste0("conc", collapse = ".")
+tinytest::expect_equal(res[[1]], expected)
+
+# LSD
+
+
+# scheffe
+
+
+# REGW
+
+app$view()
+

bs/inst/tinytest/TTest.R

@@ -0,0 +1,64 @@
+library(shinytest2)
+library(tinytest)
+app <- bs::app()
+app <- shiny::shinyApp(app$ui, app$server)
+app <- AppDriver$new(app)
+app$upload_file(
+  file = system.file("/test_data/CO2.csv", package = "bs")
+)
+app$set_window_size(width = 2259, height = 1326)
+app$set_inputs(conditionedPanels = "Tests")
+app$click("TESTS-open_formula_editor")
+app$set_inputs(`FO-colnames-dropdown_0` = "uptake")
+app$click("FO-colnames_Treatment_0")
+app$click("FO-create_formula")
+app$run_js("$('.modal-footer button:contains(\"Close\")').click();")
+
+app$click("TESTS-tTest")
+res <- app$get_values()$export
+CO2$Treatment <- as.character(CO2$Treatment)
+expected <- broom::tidy(
+  t.test(
+    uptake ~ Treatment, data = CO2,
+    var.equal = TRUE, conf.level = 0.95,
+    alternative = "two.sided"
+  )
+)
+tinytest::expect_equal(res[[1]], expected)
+# Update output value
+app$set_inputs(`TESTS-altHyp` = "less")
+app$click("TESTS-tTest")
+res <- app$get_values()$export
+expected <- broom::tidy(
+  t.test(
+    uptake ~ Treatment, data = CO2,
+    var.equal = TRUE, conf.level = 0.95,
+    alternative = "less"
+  )
+)
+tinytest::expect_equal(res[[1]], expected)
+# Update output value
+app$set_inputs(`TESTS-altHyp` = "greater")
+app$click("TESTS-tTest")
+res <- app$get_values()$export
+expected <- broom::tidy(
+  t.test(
+    uptake ~ Treatment, data = CO2,
+    var.equal = TRUE, conf.level = 0.95,
+    alternative = "greater"
+  )
+)
+tinytest::expect_equal(res[[1]], expected)
+# Update output value
+app$set_inputs(`TESTS-varEq` = "noeq")
+app$click("TESTS-tTest")
+res <- app$get_values()$export
+expected <- broom::tidy(
+  t.test(
+    uptake ~ Treatment, data = CO2,
+    var.equal = FALSE, conf.level = 0.95,
+    alternative = "greater"
+  )
+)
+tinytest::expect_equal(res[[1]], expected)
+app$stop()