From 418b2c7e6dc5980ce1a60764cfb1eb4692ef944f Mon Sep 17 00:00:00 2001 From: Julius Pfadt <38500953+juliuspfadt@users.noreply.github.com> Date: Fri, 6 Dec 2024 15:35:10 +0100 Subject: [PATCH] Fix test release issues jaspFactor (#248) * add seed stuff * add varCovData to check Errors * also adjust the tests * renv lock file --- R/exploratoryfactoranalysis.R | 22 +- R/principalcomponentanalysis.R | 2 +- inst/qml/ExploratoryFactorAnalysis.qml | 12 +- inst/qml/PrincipalComponentAnalysis.qml | 11 +- renv.lock | 1307 ++++++++++++----- renv/activate.R | 10 +- .../testthat/test-exploratoryfactoranalysis.R | 32 +- .../test-principalcomponentanalysis.R | 12 +- 8 files changed, 969 insertions(+), 439 deletions(-) diff --git a/R/exploratoryfactoranalysis.R b/R/exploratoryfactoranalysis.R index e87f9a8..13e39f3 100644 --- a/R/exploratoryfactoranalysis.R +++ b/R/exploratoryfactoranalysis.R @@ -101,7 +101,7 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... ) if (options[["dataType"]] == "raw") { - error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksEFA, + error <- .hasErrors(dataset = dataset, type = c("infinity", "variance", "varCovData"), custom = customChecksEFA, exitAnalysisIfErrors = TRUE) } @@ -192,7 +192,8 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") { polyTetraCor <- psych::mixedCor(dataset) - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(polyTetraCor$rho, plot = FALSE, fa = ifelse(options[["parallelAnalysisMethod"]] == "principalComponentBased", @@ -200,7 +201,8 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... n.obs = nrow(dataset))) } else { - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(dataset, plot = FALSE, fa = ifelse(options[["parallelAnalysisMethod"]] == "principalComponentBased", "pc", "fa"))) @@ -600,14 +602,16 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") { polyTetraCor <- psych::mixedCor(dataset) - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(polyTetraCor$rho, plot = FALSE, fa = ifelse(options[["parallelAnalysisTableMethod"]] == "principalComponentBased", "pc", "fa"), n.obs = nrow(dataset))) } else { - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(dataset, plot = FALSE, fa = ifelse(options[["parallelAnalysisTableMethod"]] == "principalComponentBased", "pc", "fa"))) @@ -628,7 +632,7 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... } parallelTable <- createJaspTable(gettext("Parallel Analysis")) - parallelTable$dependOn(c("parallelAnalysisTable", "parallelAnalysisTableMethod", "parallelAnalysisSeed")) + parallelTable$dependOn(c("parallelAnalysisTable", "parallelAnalysisTableMethod")) parallelTable$addColumnInfo(name = "col", title = "", type = "string") parallelTable$addColumnInfo(name = "val1", title = eigTitle, type = "number", format = "dp:3") @@ -679,14 +683,16 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") { polyTetraCor <- psych::mixedCor(dataset) - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(polyTetraCor$rho, plot = FALSE, fa = ifelse(options[["parallelAnalysisTableMethod"]] == "principalComponentBased", "pc", "fa"), n.obs = nrow(dataset))) } else { - set.seed(options[["parallelAnalysisSeed"]]) + .setSeedJASP(options) + parallelResult <- try(psych::fa.parallel(dataset, plot = FALSE, fa = ifelse(options[["parallelAnalysisTableMethod"]] == "principalComponentBased", "pc", "fa"))) diff --git a/R/principalcomponentanalysis.R b/R/principalcomponentanalysis.R index 432e1c1..4945b5c 100644 --- a/R/principalcomponentanalysis.R +++ b/R/principalcomponentanalysis.R @@ -157,7 +157,7 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. ) if (options[["dataType"]] == "raw") { - error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksPCAEFA, + error <- .hasErrors(dataset = dataset, type = c("infinity", "variance", "varCovData"), custom = customChecksPCAEFA, exitAnalysisIfErrors = TRUE) } diff --git a/inst/qml/ExploratoryFactorAnalysis.qml b/inst/qml/ExploratoryFactorAnalysis.qml index 4b77e19..0915d1d 100644 --- a/inst/qml/ExploratoryFactorAnalysis.qml +++ b/inst/qml/ExploratoryFactorAnalysis.qml @@ -81,15 +81,9 @@ Form label: qsTr("Based on FA") } } - IntegerField - { - name: "parallelAnalysisSeed" - label: "Seed" - defaultValue: 1234 - fieldWidth: 60 - min: 1 - max: 1e6 - } + + SetSeed{} + } RadioButton diff --git a/inst/qml/PrincipalComponentAnalysis.qml b/inst/qml/PrincipalComponentAnalysis.qml index 523122d..4057a09 100644 --- a/inst/qml/PrincipalComponentAnalysis.qml +++ b/inst/qml/PrincipalComponentAnalysis.qml @@ -78,15 +78,8 @@ Form label: qsTr("Based on factors") } } - IntegerField - { - name: "parallelAnalysisSeed" - label: "Seed" - defaultValue: 1234 - fieldWidth: 60 - min: 1 - max: 1e6 - } + SetSeed{} + } RadioButton { diff --git a/renv.lock b/renv.lock index d827bc2..afc95a7 100644 --- a/renv.lock +++ b/renv.lock @@ -13,316 +13,396 @@ "Package": "BH", "Version": "1.84.0-0", "Source": "Repository", - "Requirements": [] + "Repository": "CRAN", + "Hash": "a8235afbcd6316e6e91433ea47661013" }, "Formula": { "Package": "Formula", "Version": "1.2-5", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "stats" - 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"cpp11" - ] + "magrittr", + "methods", + "pkgload", + "praise", + "processx", + "ps", + "rlang", + "utils", + "waldo", + "withr" + ], + "Hash": "3f6e7e5e2220856ff865e4834766bf2b" }, "textshaping": { "Package": "textshaping", "Version": "0.4.0", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", + "cpp11", "lifecycle", - "systemfonts", - "cpp11" - ] + "systemfonts" + ], + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", "Version": "3.2.1", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "fansi", @@ -1838,15 +2314,18 @@ "rlang", "utils", "vctrs" - ] + ], + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" }, "tidyr": { "Package": "tidyr", "Version": "1.3.1", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "cli", + "cpp11", "dplyr", "glue", "lifecycle", @@ -1857,14 +2336,15 @@ "tibble", "tidyselect", "utils", - "vctrs", - "cpp11" - ] + "vctrs" + ], + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", "Version": "1.2.1", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "cli", @@ -1873,116 +2353,173 @@ "rlang", "vctrs", "withr" - 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] + ], + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" }, "xtable": { "Package": "xtable", "Version": "1.8-4", "Source": "Repository", + "Repository": "CRAN", "Requirements": [ "R", "stats", "utils" - ] + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", "Version": "2.3.10", "Source": "Repository", - "Requirements": [] + "Repository": "CRAN", + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" }, "zip": { "Package": "zip", "Version": "2.3.1", "Source": "Repository", - "Requirements": [] + "Repository": "CRAN", + "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab" } } } diff --git a/renv/activate.R b/renv/activate.R index c19fc3e..0eb5108 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.10" + version <- "1.0.11" attr(version, "sha") <- NULL # the project directory @@ -368,8 +368,7 @@ local({ quiet = TRUE ) - if ("headers" %in% names(formals(utils::download.file))) - { + if ("headers" %in% names(formals(utils::download.file))) { headers <- renv_bootstrap_download_custom_headers(url) if (length(headers) && is.character(headers)) args$headers <- headers @@ -457,9 +456,8 @@ local({ # add custom headers if available -- note that # utils::available.packages() will pass this to download.file() - if ("headers" %in% names(formals(utils::download.file))) - { - headers <- renv_bootstrap_download_custom_headers(url) + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) if (length(headers) && is.character(headers)) args$headers <- headers } diff --git a/tests/testthat/test-exploratoryfactoranalysis.R b/tests/testthat/test-exploratoryfactoranalysis.R index 8d197d3..de47093 100644 --- a/tests/testthat/test-exploratoryfactoranalysis.R +++ b/tests/testthat/test-exploratoryfactoranalysis.R @@ -201,7 +201,7 @@ options$orthogonalSelector <- "none" options$rotationMethod <- "orthogonal" options$variables <- paste0("x", 1:9) set.seed(1) -results <- runAnalysis("exploratoryFactorAnalysis", "holzingerswineford.csv", options) +results <- runAnalysis("exploratoryFactorAnalysis", testthat::test_path("holzingerswineford.csv"), options) test_that("Factor Characteristics table results match", { @@ -257,13 +257,15 @@ options$factoringMethod <- "minimumResidual" options$variables <- list("contcor1", "contcor2", "facFifty", "facFive","contNormal", "debMiss1") set.seed(1) -results <- runAnalysis("exploratoryFactorAnalysis", "test.csv", options) +results <- runAnalysis("exploratoryFactorAnalysis", "test.csv", options, makeTests = F) test_that("Factor Characteristics table results match with poly cor", { table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_eigenTable"]][["data"]] jaspTools::expect_equal_tables(table, - list("Factor 1", 0.237661902584815, 0.237661825764328, 1.78311572348898, - 0.237661902584815, 0.237661825764328, 1.42597141550889, 1.42597095458596 + list("Factor 1", 0.237444621938795, 0.238183139137491, 1.78311572348898, + 0.237444621938795, 0.238183139137491, 1.42466773163277, 1.42909883482494, + "Factor 2", 0.411139518227707, 0.411182023092321, 1.28924116893078, + 0.173694896288912, 0.17299888395483, 1.04216937773347, 1.03799330372898 )) }) @@ -280,11 +282,11 @@ test_that("Mardia's Test of Multivariate Normality table results match with poly test_that("Parallel Analysis table results match with poly cor", { table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_parallelTable"]][["data"]] jaspTools::expect_equal_tables(table, - list("Factor 1*", 1.78311572348898, 1.35019729324916, "Factor 2*", - 1.28924116893078, 1.18561012192069, "Factor 3*", 1.08833059622023, - 1.03479212515924, "Factor 4", 0.845932695389084, 0.916703296293484, - "Factor 5", 0.688011322780564, 0.816974205065407, "Factor 6", - 0.305368493190363, 0.695722958312017)) + list("Factor 1*", 1.78311572348898, 1.34293486623467, "Factor 2*", + 1.28924116893078, 1.18287911279811, "Factor 3*", 1.08833059622023, + 1.05066617046688, "Factor 4", 0.845932695389084, 0.925279735884113, + "Factor 5", 0.688011322780564, 0.809825771393728, "Factor 6", + 0.305368493190363, 0.688414343222493)) }) @@ -298,16 +300,16 @@ options$variables <- list("contcor1", "contcor2", "facFifty", "facFive","contNor options("mc.cores" = 1L) set.seed(1) -results <- runAnalysis("exploratoryFactorAnalysis", "test.csv", options) +results <- runAnalysis("exploratoryFactorAnalysis", "test.csv", options, makeTests = F) test_that("Parallel Analysis table results match", { table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_parallelTable"]][["data"]] jaspTools::expect_equal_tables(table, - list("Factor 1*", 1.7795916550878, 1.3666469872842, "Factor 2*", 1.28644706023115, - 1.16634731028432, "Factor 3*", 1.08333785331839, 1.04662919278838, - "Factor 4", 0.848949206589453, 0.937115883176427, "Factor 5", - 0.696170865182367, 0.806896345892467, "Factor 6", 0.305503359590833, - 0.676364280574212)) + list("Factor 1*", 1.7795916550878, 1.33053625507377, "Factor 2*", 1.28644706023115, + 1.17402737320915, "Factor 3*", 1.08333785331839, 1.0367445878489, + "Factor 4", 0.848949206589453, 0.923477592629848, "Factor 5", + 0.696170865182367, 0.837720518530386, "Factor 6", 0.305503359590833, + 0.697493672707948)) }) diff --git a/tests/testthat/test-principalcomponentanalysis.R b/tests/testthat/test-principalcomponentanalysis.R index e46ab0f..f1bae82 100644 --- a/tests/testthat/test-principalcomponentanalysis.R +++ b/tests/testthat/test-principalcomponentanalysis.R @@ -329,16 +329,16 @@ options$variables <- list("contcor1", "contcor2", "facFifty", "facFive","contNor options("mc.cores" = 1L) set.seed(1) -results <- runAnalysis("principalComponentAnalysis", "test.csv", options) +results <- runAnalysis("principalComponentAnalysis", "test.csv", options, makeTests = F) test_that("Parallel Analysis table results match", { table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_parallelTable"]][["data"]] jaspTools::expect_equal_tables(table, - list("Component 1*", 1.7795916550878, 1.3666469872842, "Component 2*", 1.28644706023115, - 1.16634731028432, "Component 3*", 1.08333785331839, 1.04662919278838, - "Component 4", 0.848949206589453, 0.937115883176427, "Component 5", - 0.696170865182367, 0.806896345892467, "Component 6", 0.305503359590833, - 0.676364280574212)) + list("Component 1*", 1.7795916550878, 1.33053625507377, "Component 2*", + 1.28644706023115, 1.17402737320915, "Component 3*", 1.08333785331839, + 1.0367445878489, "Component 4", 0.848949206589453, 0.923477592629848, + "Component 5", 0.696170865182367, 0.837720518530386, "Component 6", + 0.305503359590833, 0.697493672707948)) })