From 795f339af5dac3425d5307184de6c1b529e007d6 Mon Sep 17 00:00:00 2001 From: Julius Pfadt Date: Wed, 16 Oct 2024 10:01:39 +0200 Subject: [PATCH] fix conflicts during rebase --- .Rprofile | 1 + R/confirmatoryfactoranalysis.R | 190 +- R/exploratoryfactoranalysis.R | 33 +- R/principalcomponentanalysis.R | 74 +- inst/qml/ConfirmatoryFactorAnalysis.qml | 16 + inst/qml/ExploratoryFactorAnalysis.qml | 18 +- inst/qml/PrincipalComponentAnalysis.qml | 18 +- renv.lock | 1997 +++++++++++++++-- renv/.gitignore | 7 + renv/activate.R | 1307 +++++++++++ .../test-confirmatoryfactoranalysis.R | 38 +- .../testthat/test-exploratoryfactoranalysis.R | 66 + .../test-principalcomponentanalysis.R | 64 + 13 files changed, 3568 insertions(+), 261 deletions(-) create mode 100644 .Rprofile create mode 100644 renv/.gitignore create mode 100644 renv/activate.R diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 00000000..81b960f5 --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/R/confirmatoryfactoranalysis.R b/R/confirmatoryfactoranalysis.R index 8161c2c7..630ad07f 100644 --- a/R/confirmatoryfactoranalysis.R +++ b/R/confirmatoryfactoranalysis.R @@ -15,7 +15,6 @@ # - confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ...) { jaspResults$addCitation("Rosseel, Y. (2012). lavaan: An R Package for Structural Equation Modeling. Journal of Statistical Software, 48(2), 1-36. URL http://www.jstatsoft.org/v48/i02/") @@ -29,23 +28,27 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. # Error checking errors <- .cfaCheckErrors(dataset, options) + # covariance matrix + dataset <- .cfaDataCovariance(dataset, options) + # Main table / model cfaResult <- .cfaComputeResults(jaspResults, dataset, options, errors) # Output tables - .cfaContainerMain( jaspResults, options, cfaResult) # Main table container - .cfaTableMain( jaspResults, options, cfaResult) # Main table with fit info - .cfaTableFitMeasures(jaspResults, options, cfaResult) # Additional fit indices - .cfaTableKMO( jaspResults, options, cfaResult) # Kaiser-Meyer-Olkin test. - .cfaTableBartlett( jaspResults, options, cfaResult) # Bartlett's test of sphericity - .cfaTableRsquared( jaspResults, options, cfaResult) # R-squared of indicators - .cfaTableParEst( jaspResults, options, cfaResult) # Parameter estimates tables - .cfaTableModIndices( jaspResults, options, cfaResult) # Modification Indices - .cfaTableImpliedCov( jaspResults, options, cfaResult) # Implied Covariance matrix - .cfaTableResCov( jaspResults, options, cfaResult) # Residual Covariance Matrix - .cfaTableAve( jaspResults, options, cfaResult) # Average variance explained table - .cfaTableHtmt( jaspResults, options, cfaResult) # Heterotrait monotrait - .cfaTableReliability(jaspResults, options, cfaResult) # Reliability + .cfaContainerMain( jaspResults, options, cfaResult ) # Main table container + .cfaTableMain( jaspResults, options, cfaResult ) # Main table with fit info + .cfaTableFitMeasures(jaspResults, options, cfaResult ) # Additional fit indices + .cfaTableKMO( jaspResults, options, cfaResult ) # Kaiser-Meyer-Olkin test. + .cfaTableBartlett( jaspResults, options, cfaResult ) # Bartlett's test of sphericity + .cfaTableRsquared( jaspResults, options, cfaResult ) # R-squared of indicators + .cfaTableParEst( jaspResults, options, cfaResult ) # Parameter estimates tables + .cfaTableModIndices( jaspResults, options, cfaResult ) # Modification Indices + .cfaTableImpliedCov( jaspResults, options, cfaResult ) # Implied Covariance matrix + .cfaTableResCov( jaspResults, options, cfaResult ) # Residual Covariance Matrix + .cfaTableAve( jaspResults, options, cfaResult ) # Average variance explained table + .cfaTableHtmt( jaspResults, options, cfaResult, dataset ) # Heterotrait monotrait + # weirdly enough I cannot find the exact sample cov matrix in the lavaan output + .cfaTableReliability(jaspResults, options, cfaResult ) # Reliability # Output plots @@ -61,29 +64,32 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. # Preprocessing functions ---- .cfaReadData <- function(dataset, options) { + if (!is.null(dataset)) return(dataset) # NOTE: The GUI does not yet allow for putting the same variable in different factors. # if the same variable is used twice but with a different type then this would # crash the R code. However, since this is not possible yet, this should be okay for now vars <- unlist(lapply(options[["factors"]], `[[`, "indicators"), use.names = FALSE) - types <- unlist(lapply(options[["factors"]], `[[`, "types"), use.names = FALSE) if (length(vars) == 0) return(data.frame()) duplicateVars <- duplicated(vars) vars <- vars[!duplicateVars] - types <- types[!duplicateVars] - splitVars <- split(vars, types) - groupVar <- if (options[["group"]] == "") NULL else options[["group"]] + if (options[["dataType"]] == "raw") { + # make sure on the qml side that groupVar is indeed a nominal variable + groupVar <- if (options[["group"]] == "") NULL else options[["group"]] + dataset <- .readDataSetToEnd(columns = c(vars, groupVar)) - return(.readDataSetToEnd( - columns.as.numeric = splitVars[["scale"]], - columns.as.ordinal = splitVars[["ordinal"]], - columns.as.factor = groupVar - )) + } else { + + dataset <- .readDataSetToEnd(all.columns = TRUE) + } + + + return(dataset) } @@ -100,9 +106,8 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. return(options) } -.cfaCheckErrors <- function(dataset, options) { - # TODO (vankesteren) content error checks, e.g., posdef covmat +.cfaCheckErrors <- function(dataset, options) { # Number of variables in the factors nVarsPerFactor <- unlist(lapply(options$factors, function(x) setNames(length(x$indicators), x$title))) @@ -117,26 +122,35 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. vars <- unique(unlist(lapply(options$factors, function(x) x$indicators))) - if (options$group == "") { + if (options[["dataType"]] == "raw") { - .hasErrors(dataset[, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, - varCovData.corFun = stats::cov) + # possible cov matrix: + if (ncol(dataset) > 0 && !nrow(dataset) > ncol(dataset)) { + .quitAnalysis(gettext("Not more cases than number of variables. Is your data a variance-covariance matrix?")) + } - } else { + if (options$group == "") { + + + .hasErrors(dataset[, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, + varCovData.corFun = stats::cov) - .hasErrors(dataset, type = "factorLevels", factorLevels.target = options$group, - factorLevels.amount = '< 2', exitAnalysisIfErrors = TRUE) + } else { + + .hasErrors(dataset, type = "factorLevels", factorLevels.target = options$group, + factorLevels.amount = '< 2', exitAnalysisIfErrors = TRUE) - for (group in levels(dataset[[options$group]])) { + for (group in levels(dataset[[options$group]])) { - idx <- dataset[[options$group]] == group + idx <- dataset[[options$group]] == group - if (any(sapply(dataset[, vars], is.ordered))) { - .hasErrors(dataset[idx, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, - varCovData.corFun = lavaan::lavCor) - } else { - .hasErrors(dataset[idx, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, - varCovData.corFun = stats::cov) + if (any(sapply(dataset[, vars], is.ordered))) { + .hasErrors(dataset[idx, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, + varCovData.corFun = lavaan::lavCor) + } else { + .hasErrors(dataset[idx, vars], type = 'varCovData', exitAnalysisIfErrors = TRUE, + varCovData.corFun = stats::cov) + } } } } @@ -144,6 +158,43 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. return(NULL) } +.cfaDataCovariance <- function(dataset, options) { + + if (options[["dataType"]] == "raw") { + return(dataset) + } + + vars <- unlist(lapply(options[["factors"]], `[[`, "indicators"), use.names = FALSE) + + if (length(vars) == 0) + return(data.frame()) + + duplicateVars <- duplicated(vars) + usedvars <- vars[!duplicateVars] + var_idx <- match(usedvars, colnames(dataset)) + mat <- try(as.matrix(dataset[var_idx, var_idx])) + if (inherits(mat, "try-error") || any(is.na(mat))) + .quitAnalysis("Input data does not seem to be a covariance matrix! Please check the format of the input data. + All cells must be numeric, and the number of rows must equal the number of columns.") + + if (options[["group"]] != "") .quitAnalysis("Grouping variable not supported for covariance matrix input") + + if (options[["meanStructure"]]) .quitAnalysis("Mean structure not supported for covariance matrix input") + + .hasErrors(mat, type = "varCovMatrix", message='default', exitAnalysisIfErrors = TRUE) + + colnames(mat) <- rownames(mat) <- colnames(dataset)[var_idx] + if (anyNA(mat)) { + inds <- which(is.na(mat)) + mat <- mat[-inds, -inds] + if (ncol(mat) < 3) { + .quitAnalysis("Not enough valid columns to run this analysis") + } + } + return(mat) +} + + .translateFactorNames <- function(factor_name, options, back = FALSE) { # make dictionary fac_names <- vapply(options$factors, function(x) x$name, "name") @@ -200,9 +251,30 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. naAction <- "listwise" } + # define estimator from options + estimator = switch(options[["estimator"]], + "default" = "default", + "maximumLikelihood" = "ML", + "generalizedLeastSquares" = "GLS", + "weightedLeastSquares" = "WLS", + "unweightedLeastSquares" = "ULS", + "diagonallyWeightedLeastSquares" = "DWLS" + ) + + if (options[["dataType"]] == "raw") { + dt <- dataset + sampCov <- NULL + sampCovN <- NULL + } else { + dt <- NULL + sampCov <- dataset + sampCovN <- options[["sampleSize"]] + } cfaResult[["lav"]] <- try(lavaan::lavaan( model = mod, - data = dataset, + data = dt, + sample.cov = sampCov, + sample.nobs = sampCovN, group = grp, group.equal = geq, meanstructure = options$meanStructure, @@ -273,11 +345,12 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. "all" = "std.all", "latentVariables" = "std.lv", "noExogenousCovariates" = "std.nox") - # change this once jaspSem is merged - cfaResult[["lav"]] <- lavBootstrap(cfaResult[["lav"]], options$bootstrapSamples, + + if (options[["dataType"]] == "varianceCovariance") { + .quitAnalysis(gettext("Bootstrapping is not available for variance-covariance matrix input.")) + } + cfaResult[["lav"]] <- jaspSem::lavBootstrap(cfaResult[["lav"]], options$bootstrapSamples, standard = options[["standardized"]] != "none", typeStd = type) - # cfaResult[["lav"]] <- jaspSem::lavBootstrap(cfaResult[["lav"]], options$bootstrapSamples, - # standard = options[["standardized"]] != "none", typeStd = type) } # Save cfaResult as state so it's available even when opts don't change @@ -285,8 +358,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. jaspResults[["stateCFAResult"]]$dependOn(c( "factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", - "group", "invarianceTesting", "interceptsFixedToZero", "standardized" - + "group", "invarianceTesting", "interceptsFixedToZero", "standardized", "dataType", "sampleSize" )) return(cfaResult) @@ -314,6 +386,9 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. spec$bootstrap <- TRUE } else { if (options$seType == "robust") { + if (options[["dataType"]] == "varianceCovariance") { + .quitAnalysis(gettext("Robust standard errors are not available for variance-covariance matrix input.")) + } spec$se <- "robust.sem" } else { spec$se <- options$seType @@ -422,7 +497,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. jaspResults[["maincontainer"]]$dependOn(c( "factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", - "group", "invarianceTesting", "interceptsFixedToZero" + "group", "invarianceTesting", "interceptsFixedToZero", "dataType", "sampleSize" )) } @@ -1369,7 +1444,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. } -.cfaTableHtmt <- function(jaspResults, options, cfaResult) { +.cfaTableHtmt <- function(jaspResults, options, cfaResult, dataset) { #### this has an ordering argument that still needs to be implemented once the categorical data stuff is done if (is.null(cfaResult) || !options[["htmt"]] || !is.null(jaspResults[["resHtmtTable"]])) return() @@ -1406,14 +1481,22 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. htmtTable$setData(tmp_dat) } else { - # get the dataset - dataset <- as.data.frame(lavaan::inspect(cfaResult[["lav"]], what = "data")) - colnames(dataset) <- cfaResult[["lav"]]@Data@ov.names[[1]] + if (options[["dataType"]] == "raw") { + # get the dataset + dataset <- as.data.frame(lavaan::inspect(cfaResult[["lav"]], what = "data")) + colnames(dataset) <- cfaResult[["lav"]]@Data@ov.names[[1]] + sampCov <- NULL + } else { + sampCov <- dataset + colnames(sampCov) <- rownames(sampCov) <- cfaResult[["lav"]]@Data@ov.names[[1]] + dataset <- NULL + } + if (is.null(cfaResult[["spec"]][["soIndics"]])) { - htmt_result <- semTools::htmt(model = cfaResult[["model"]], data = dataset, + htmt_result <- semTools::htmt(model = cfaResult[["model"]], data = dataset, sample.cov = sampCov, missing = cfaResult[["lav"]]@Options[["missing"]]) } else { # the htmt does not allow a second order factor, so we take the model syntax without the seco - htmt_result <- semTools::htmt(model = cfaResult[["model_simple"]], data = dataset, + htmt_result <- semTools::htmt(model = cfaResult[["model_simple"]], data = dataset, sample.cov = sampCov, missing = cfaResult[["lav"]]@Options[["missing"]]) } @@ -1425,6 +1508,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. } jaspResults[["resHtmtTable"]] <- htmtTable + return() } diff --git a/R/exploratoryfactoranalysis.R b/R/exploratoryfactoranalysis.R index 0bf418ef..1bf84bc8 100644 --- a/R/exploratoryfactoranalysis.R +++ b/R/exploratoryfactoranalysis.R @@ -19,8 +19,9 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... jaspResults$addCitation("Revelle, W. (2018) psych: Procedures for Personality and Psychological Research, Northwestern University, Evanston, Illinois, USA, https://CRAN.R-project.org/package=psych Version = 1.8.12.") # Read dataset - dataset <- .efaReadData(dataset, options) + dataset <- .pcaAndEfaReadData(dataset, options) ready <- length(options$variables) > 1 + dataset <- .pcaAndEfaDataCovariance(dataset, options) if (ready) .efaCheckErrors(dataset, options) @@ -49,16 +50,6 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... } -.efaReadData <- function(dataset, options) { - if (!is.null(dataset)) return(dataset) - - if (options[["naAction"]] == "listwise") { - return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables), exclude.na.listwise = unlist(options$variables))) - } else { - return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables))) - } -} - .efaCheckErrors <- function(dataset, options) { customChecksEFA <- list( function() { @@ -101,10 +92,20 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (all(S == 1)) { return(gettext("Data not valid: all variables are collinear")) } + }, + function() { + if (ncol(dataset) > 0 && !nrow(dataset) > ncol(dataset)) { + return(gettext("Not more cases than number of variables. Is your data a variance-covariance matrix?")) + } } ) - error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksEFA, - exitAnalysisIfErrors = TRUE) + + if (options[["dataType"]] == "raw") { + error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksEFA, + exitAnalysisIfErrors = TRUE) + } + + return() } @@ -115,7 +116,7 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... modelContainer <- createJaspContainer() modelContainer$dependOn(c("rotationMethod", "orthogonalSelector", "obliqueSelector", "variables", "factorCountMethod", "eigenValuesAbove", "manualNumberOfFactors", "naAction", "analysisBasedOn", "factoringMethod", - "parallelAnalysisMethod")) + "parallelAnalysisMethod", "dataType", "sampleSize")) jaspResults[["modelContainer"]] <- modelContainer } @@ -143,7 +144,6 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... "minimumChiSquare" = "minchi", "minimumRank" = "minrank" ) - efaResult <- try( psych::fa( r = dataset, @@ -152,7 +152,8 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... scores = TRUE, covar = options$analysisBasedOn == "covarianceMatrix", cor = corMethod, - fm = factoringMethod + fm = factoringMethod, + n.obs = ifelse(options[["dataType"]] == "raw", NULL, options[["sampleSize"]]) ) ) diff --git a/R/principalcomponentanalysis.R b/R/principalcomponentanalysis.R index 44efc55c..f172378e 100644 --- a/R/principalcomponentanalysis.R +++ b/R/principalcomponentanalysis.R @@ -20,12 +20,15 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. jaspResults$addCitation("Revelle, W. (2018) psych: Procedures for Personality and Psychological Research, Northwestern University, Evanston, Illinois, USA, https://CRAN.R-project.org/package=psych Version = 1.8.12.") # Read dataset - dataset <- .pcaReadData(dataset, options) + dataset <- .pcaAndEfaReadData(dataset, options) ready <- length(options$variables) > 1 + dataset <- .pcaAndEfaDataCovariance(dataset, options) + if (ready) .pcaCheckErrors(dataset, options) + modelContainer <- .pcaModelContainer(jaspResults) # output functions @@ -47,17 +50,53 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. } # Preprocessing functions ---- -.pcaReadData <- function(dataset, options) { +.pcaAndEfaReadData <- function(dataset, options) { + + # browser() if (!is.null(dataset)) return(dataset) - if (options[["naAction"]] == "listwise") { - return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables), exclude.na.listwise = unlist(options$variables))) - } else { - return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables))) + if (options[["dataType"]] == "raw") { + if (options[["naAction"]] == "listwise") { + return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables), exclude.na.listwise = unlist(options$variables))) + } else { + + return(.readDataSetToEnd(columns.as.numeric = unlist(options$variables))) + } + } else { # if variance covariance matrix as input + return(.readDataSetToEnd(all.columns = TRUE)) + } + +} + + +.pcaAndEfaDataCovariance <- function(dataset, options) { + + if (options[["dataType"]] == "raw") { + return(dataset) + } + usedvars <- unlist(options[["variables"]]) + var_idx <- match(usedvars, colnames(dataset)) + mat <- try(as.matrix(dataset[var_idx, var_idx])) + if (inherits(mat, "try-error") || any(is.na(mat))) + .quitAnalysis("Input data does not seem to be a covariance matrix! Please check the format of the input data. + All cells must be numeric, and the number of rows must equal the number of columns.") + .hasErrors(mat, type = "varCovMatrix", message='default', exitAnalysisIfErrors = TRUE) + + colnames(mat) <- rownames(mat) <- colnames(dataset)[var_idx] + + if (anyNA(mat)) { + inds <- which(is.na(mat)) + mat <- mat[-inds, -inds] + if (ncol(mat) < 3) { + .quitAnalysis("Not enough valid columns to run this analysis") + } } + return(mat) } + .pcaCheckErrors <- function(dataset, options) { + customChecksPCAEFA <- list( function() { if (length(options$variables) > 0 && options$componentCountMethod == "manual" && @@ -99,10 +138,19 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. if (all(S == 1)) { return(gettext("Data not valid: all variables are collinear")) } + }, + function() { + if (ncol(dataset) > 0 && !nrow(dataset) > ncol(dataset)) { + return(gettext("Not more cases than number of variables. Is your data a variance-covariance matrix?")) + } } ) - error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksPCAEFA, - exitAnalysisIfErrors = TRUE) + + if (options[["dataType"]] == "raw") { + error <- .hasErrors(dataset = dataset, type = c("infinity", "variance"), custom = customChecksPCAEFA, + exitAnalysisIfErrors = TRUE) + } + return() } @@ -113,7 +161,7 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. modelContainer <- createJaspContainer() modelContainer$dependOn(c("rotationMethod", "orthogonalSelector", "obliqueSelector", "variables", "componentCountMethod", "eigenValuesAbove", "manualNumberOfComponents", "naAction", "analysisBasedOn", - "parallelAnalysisMethod")) + "parallelAnalysisMethod", "dataType", "sampleSize")) jaspResults[["modelContainer"]] <- modelContainer } @@ -148,7 +196,6 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. "correlationMatrix" = "cor", "covarianceMatrix" = "cov", "polyTetrachoricCorrelationMatrix" = "mixed") - pcaResult <- try( psych::principal( r = dataset, @@ -156,7 +203,8 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. rotate = rotate, scores = TRUE, covar = options$analysisBasedOn == "covarianceMatrix", - cor = corMethod + cor = corMethod, + n.obs = ifelse(options[["dataType"]] == "raw", NULL, options[["sampleSize"]]) )) if (isTryError(pcaResult)) { @@ -237,12 +285,13 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. pcaResults <- .pcaComputeResults(modelContainer, dataset, options) if (modelContainer$getError()) return() - goodnessOfFitTable[["model"]] <- "Model" + goodnessOfFitTable[["chisq"]] <- pcaResults$STATISTIC goodnessOfFitTable[["df"]] <- pcaResults$dof goodnessOfFitTable[["p"]] <- pcaResults$PVAL + if (pcaResults$dof < 0) goodnessOfFitTable$addFootnote(message = gettext("Degrees of freedom below 0, model is unidentified."), symbol = gettext("Warning:")) } @@ -630,3 +679,4 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. } + diff --git a/inst/qml/ConfirmatoryFactorAnalysis.qml b/inst/qml/ConfirmatoryFactorAnalysis.qml index 2757c35f..fd11c80d 100644 --- a/inst/qml/ConfirmatoryFactorAnalysis.qml +++ b/inst/qml/ConfirmatoryFactorAnalysis.qml @@ -30,6 +30,22 @@ Form allowedColumns: ["ordinal", "scale"] allowTypeChange: true } + Group + { + // columns: 4 + title: qsTr("Data") + RadioButtonGroup + { + name: "dataType" + columns: 2 + RadioButton { value: "raw"; label: qsTr("Raw"); checked: true } + RadioButton + { + value: "varianceCovariance"; label: qsTr("Variance-covariance matrix") + IntegerField { name: "sampleSize"; label: qsTr("Sample size"); defaultValue: 200 } + } + } + } Section { diff --git a/inst/qml/ExploratoryFactorAnalysis.qml b/inst/qml/ExploratoryFactorAnalysis.qml index 78eebab0..e055a04f 100644 --- a/inst/qml/ExploratoryFactorAnalysis.qml +++ b/inst/qml/ExploratoryFactorAnalysis.qml @@ -24,7 +24,7 @@ Form VariablesForm { - preferredHeight: jaspTheme.smallDefaultVariablesFormHeight + // preferredHeight: jaspTheme.smallDefaultVariablesFormHeight AvailableVariablesList { name: "allVariablesList" } AssignedVariablesList { @@ -33,6 +33,22 @@ Form title: qsTr("Variables") allowedColumns: ["scale"] } + Group + { + // columns: 4 + title: qsTr("Data") + RadioButtonGroup + { + name: "dataType" + columns: 2 + RadioButton { value: "raw"; label: qsTr("Raw"); checked: true } + RadioButton + { + value: "varianceCovariance"; label: qsTr("Variance-covariance matrix") + IntegerField { name: "sampleSize"; label: qsTr("Sample size"); defaultValue: 200 } + } + } + } } Group diff --git a/inst/qml/PrincipalComponentAnalysis.qml b/inst/qml/PrincipalComponentAnalysis.qml index 3288e8ab..88456bbf 100644 --- a/inst/qml/PrincipalComponentAnalysis.qml +++ b/inst/qml/PrincipalComponentAnalysis.qml @@ -24,7 +24,7 @@ Form { VariablesForm { - 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+++ b/renv/activate.R @@ -0,0 +1,1307 @@ + +local({ + + # the requested version of renv + version <- "1.0.10" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # 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 (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/tests/testthat/test-confirmatoryfactoranalysis.R b/tests/testthat/test-confirmatoryfactoranalysis.R index 88406a8b..493ff95f 100644 --- a/tests/testthat/test-confirmatoryfactoranalysis.R +++ b/tests/testthat/test-confirmatoryfactoranalysis.R @@ -20,7 +20,7 @@ options$bartlettTest <- TRUE set.seed(1) -results <- jaspTools::runAnalysis("confirmatoryFactorAnalysis", "holzingerswineford.csv", options) +results <- jaspTools::runAnalysis("confirmatoryFactorAnalysis", testthat::test_path("holzingerswineford.csv"), options) test_that("[CFA 3-Factor] Factor Covariances table results match", { @@ -714,3 +714,39 @@ test_that("Intercepts table results match", { "x9", 0.0190291696997005, 0.600891884514286, -2.34495904524032 )) }) + + +# covariance matrix input +# 3-factor run + +options <- jaspTools::analysisOptions("confirmatoryFactorAnalysis") +options$group <- "" +options$invarianceTesting <- "configural" +options$packageMimiced <- "lavaan" +options$seType <- "standard" +options$estimator <- "default" +options$standardized <- "none" +options$factors <- list( + list(indicators = list("x1", "x2", "x3"), name = "Factor1", title = "Factor 1", types = rep("scale", 3)), + list(indicators = list("x4", "x5", "x6"), name = "Factor2", title = "Factor 2", types = rep("scale", 3)), + list(indicators = list("x7", "x8", "x9"), name = "Factor3", title = "Factor 3", types = rep("scale", 3)) +) +options$modelIdentification <- "factorVariance" +options$naAction <- "listwise" +options$dataType <- "varianceCovariance" +options$sampleSize <- 300 + +dt <- read.csv(testthat::test_path("holzingerswineford.csv")) +covMatrix <- cov(dt[, c("x1", "x2", "x3", "x4", "x5", "x6", "x7", "x8", "x9")]) +covMatrix <- as.data.frame(covMatrix) + +set.seed(1) +results <- jaspTools::runAnalysis("confirmatoryFactorAnalysis", covMatrix , options, makeTests = F) + + +test_that("Chi-square test table results match", { + table <- results[["results"]][["maincontainer"]][["collection"]][["maincontainer_cfatab"]][["data"]] + jaspTools::expect_equal_tables(table, + list(915.798926205035, 36, "Baseline model", "", 85.0221147234242, + 24, "Factor model", 9.45493439097334e-09)) +}) diff --git a/tests/testthat/test-exploratoryfactoranalysis.R b/tests/testthat/test-exploratoryfactoranalysis.R index f7424fd9..8d197d35 100644 --- a/tests/testthat/test-exploratoryfactoranalysis.R +++ b/tests/testthat/test-exploratoryfactoranalysis.R @@ -310,3 +310,69 @@ test_that("Parallel Analysis table results match", { 0.676364280574212)) }) + +# variance covariance matrix input +dt <- read.csv(testthat::test_path("holzingerswineford.csv")) +cdt <- as.data.frame(cov(dt[, 7:15])) +options <- list( + addScores = FALSE, + addedScoresPrefix = "FA", + analysisBasedOn = "correlationMatrix", + bartlettTest = FALSE, + dataType = "varianceCovariance", + eigenValuesAbove = 1, + factorCorrelations = FALSE, + factorCountMethod = "manual", + factorLoadingsOrder = "sortByVariables", + factorStructure = FALSE, + factoringMethod = "minimumResidual", + fitIndices = FALSE, + kaiserMeyerOlkinTest = FALSE, + loadingsDisplayLimit = 0.1, + manualNumberOfFactors = 1, + mardiaTest = FALSE, + naAction = "pairwise", + obliqueSelector = "promax", + orthogonalSelector = "none", + parallelAnalysisMethod = "principalComponentBased", + parallelAnalysisSeed = 1234, + parallelAnalysisTable = FALSE, + parallelAnalysisTableMethod = "principalComponentBased", + pathDiagram = FALSE, + plotHeight = 320, + plotWidth = 480, + residualMatrix = FALSE, + rotationMethod = "orthogonal", + sampleSize = 200, + screePlot = FALSE, + screePlotParallelAnalysisResults = TRUE, + variables = c("x1", "x2", "x3", "x4", "x5", "x6", "x7", "x8", "x9") +) + +set.seed(1) +results <- runAnalysis("exploratoryFactorAnalysis", cdt, options, makeTests = F) + +test_that("Factor Characteristics table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_eigenTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list("Factor 1", 0.292468690109419, 3.21634418143771, 0.292468690109419, + 2.63221821098477)) +}) + +test_that("Chi-squared Test table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_goodnessOfFitTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list(235.832782509408, 27, "Model", 3.1571356942318e-35)) +}) + +test_that("Factor Loadings table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_loadingsTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list(0.558950485489651, 0.687574354770883, "x1", 0.30045377286727, + 0.909727530369823, "x2", 0.365159382803395, 0.866658625150644, + "x3", 0.761746187230209, 0.41974274624024, "x4", 0.723809404128654, + 0.476099946494923, "x5", 0.768996689601407, 0.408644091382077, + "x6", 0.25910333096785, 0.932865463881365, "x7", 0.339140545375525, + 0.884983690482392, "x8", 0.467453266437421, 0.781487443696986, + "x9")) +}) diff --git a/tests/testthat/test-principalcomponentanalysis.R b/tests/testthat/test-principalcomponentanalysis.R index c1f6878e..e46ab0f3 100644 --- a/tests/testthat/test-principalcomponentanalysis.R +++ b/tests/testthat/test-principalcomponentanalysis.R @@ -340,3 +340,67 @@ test_that("Parallel Analysis table results match", { 0.696170865182367, 0.806896345892467, "Component 6", 0.305503359590833, 0.676364280574212)) }) + + +# variance covariance matrix input +dt <- read.csv(testthat::test_path("holzingerswineford.csv")) +cdt <- as.data.frame(cov(dt[, 7:15])) +options <- list( + addScores = FALSE, + addedScoresPrefix = "PC", + analysisBasedOn = "correlationMatrix", + bartlettTest = FALSE, + componentCorrelations = FALSE, + componentCountMethod = "manual", + componentLoadingsOrder = "sortByVariables", + dataType = "varianceCovariance", + eigenValuesAbove = 1, + kaiserMeyerOlkinTest = FALSE, + loadingsDisplayLimit = 0.1, + manualNumberOfComponents = 1, + mardiaTest = FALSE, + naAction = "pairwise", + obliqueSelector = "promax", + orthogonalSelector = "none", + parallelAnalysisMethod = "principalComponentBased", + parallelAnalysisSeed = 1234, + parallelAnalysisTable = FALSE, + parallelAnalysisTableMethod = "principalComponentBased", + pathDiagram = FALSE, + plotHeight = 320, + plotWidth = 480, + residualMatrix = FALSE, + rotationMethod = "orthogonal", + sampleSize = 200, + screePlot = FALSE, + screePlotParallelAnalysisResults = TRUE, + variables = c("x1", "x2", "x3", "x4", "x5", "x6", "x7", "x8", "x9") +) + +set.seed(1) +results <- runAnalysis("principalComponentAnalysis", cdt, options, makeTests = F) + +test_that("Component Characteristics table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_eigenTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list("Component 1", 0.357371575715301, 3.2163441814377, 0.357371575715301 + )) +}) + +test_that("Chi-squared Test table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_goodnessOfFitTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list(268.944880177337, 27, "Model", 1.0379031932901e-41)) +}) + +test_that("Component Loadings table results match", { + table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_loadingsTable"]][["data"]] + jaspTools::expect_equal_tables(table, + list(0.658301970425138, 0.566638515734381, "x1", 0.389685299082607, + 0.848145367678899, "x2", 0.477040613001908, 0.772432253546763, + "x3", 0.765811755326015, 0.413532355404489, "x4", 0.737544154070493, + 0.456028620796441, "x5", 0.772162747894139, 0.403764690764573, + "x6", 0.348796474669525, 0.878341019258111, "x7", 0.454247183933516, + 0.793659495888471, "x8", 0.590666149791766, 0.651113499490171, + "x9")) +})