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Fix indentation
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@maltelueken
maltelueken committed Sep 20, 2023
1 parent 57dd5c6 commit 5a37ef8
Showing 1 changed file with 26 additions and 26 deletions.
52 changes: 26 additions & 26 deletions R/classicProcess.R
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
# Which mediator index?
medIdx <- stringr::str_extract(vars[isMed], "[0-9]")
medIdx <- as.integer(medIdx[!is.na(medIdx)])

if (length(medIdx) > 0 && length(mediators) > 0) {
for (i in 1:length(medIdx)) {
if (length(mediators) >= medIdx[i]) {
Expand Down Expand Up @@ -264,7 +264,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {

# Replace dummy variables in dependent variables
names(regList) <- encodeColNames(.procReplaceDummyVars(names(regList), modelOptions, globalDependent))

return(regList)
}

Expand Down Expand Up @@ -312,7 +312,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {

modProbes <- lapply(names(modVars), function(nms) {
matchFac <- sapply(options[["factors"]], grepl, x = nms)

if (length(matchFac) > 0 && any(matchFac)) {
whichFac <- options[["factors"]][matchFac]
conMat <- contrasts[[whichFac]]
Expand All @@ -324,7 +324,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
})

names(modProbes) <- names(modVars)

return(modProbes)
}

Expand Down Expand Up @@ -387,7 +387,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
for (i in 1:length(regListA)) {
if (length(regListA[[i]][["vars"]]) != length(regListB[[i]][["vars"]]))
return(FALSE)

if (regListA[[i]][["dep"]] != regListB[[i]][["dep"]])
return(FALSE)
}
Expand All @@ -400,7 +400,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
pathList <- lapply(1:length(regList),
function(i) sapply(regList[[i]]$vars,
function(v) c(v, names(regList)[i])))

# Convert path list to matrix
paths <- matrix(unlist(pathList), ncol = 2, byrow = TRUE)

Expand Down Expand Up @@ -484,7 +484,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
for (i in 1:length(options[["processModels"]])) {
modelOptions <- options[["processModels"]][[i]]
modelName <- modelOptions[["name"]]

if (is.null(modelsContainer[[modelName]][["syntax"]])) {
regList <- .procAddLavModParNamesSingleModel(modelsContainer[[modelName]][["regList"]]$object)
modelsContainer[[modelName]][["regList"]]$object <- regList
Expand Down Expand Up @@ -609,7 +609,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
regList <- .procAddLavModVar(regList, independent, processVariable)
}
}

return(regList)
}

Expand Down Expand Up @@ -684,7 +684,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {

# Get simple paths
medPaths <- igraph::all_simple_paths(graph, from = exoVar, to = depVar, mode = "out")

# Get par names of simple paths
medEffectsList <- lapply(medPaths, .procMedEffectFromPath, regList = regList, modProbes = modProbes, contrasts = contrasts)

Expand Down Expand Up @@ -733,23 +733,23 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
totEffect <- .pasteExpandGrid(medEffectsListCombined, collapse = " + ")

totEffectNames <- .pasteExpandGrid(Filter(function(x) length(x) > 0, medEffectNamesListCombined), collapse = ".")

# Get total indirect effect of X on Y
totIndEffect <- .pasteExpandGrid(.doCallPaste(medEffectsListCombined[-1], sep = " + "), collapse = " + ")

indEffectNames <- .pasteExpandGrid(Filter(function(x) length(x) > 0, medEffectNamesListCombined[-1]), collapse = ".")

# Only select total effect if there are no indirect effects
if (length(totEffectNames) == 0) {
totLabels <- "tot"
} else {
totLabels <- .pasteDot(rep("tot", length(totEffect)), totEffectNames)
}
}
if (length(indEffectNames) == 0) {
indLabels <- "totInd"
} else {
indLabels <- .pasteDot(rep("totInd", length(totIndEffect)), indEffectNames)
}
}

totalEffectsSyntax <- paste(
c(totLabels, indLabels),
Expand Down Expand Up @@ -876,7 +876,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
# Replace dummy-coded variables in regList
regList[[i]][["vars"]] <- colnames(pathDummyMat)[-1]
}

modelsContainer[[modelName]][["contrasts"]] <- createJaspState(contrastList)
modelsContainer[[modelName]][["regList"]]$object <- regList
}
Expand Down Expand Up @@ -929,7 +929,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
if (options$errorCalculationMethod == "bootstrap") {
medResult <- jaspSem:::lavBootstrap(fittedModel, options$bootstrapSamples) # FIXME
}

return(fittedModel)
}

Expand Down Expand Up @@ -991,7 +991,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
regLists <- lapply(options[["processModels"]], function(mod) modelsContainer[[mod[["name"]]]][["regList"]]$object)
if (length(regLists) == 0) return()
modelNumbers <- sapply(regLists, .procRecognizeModelNumber)

modelNumberTable <- createJaspTable(title = gettext("Model numbers"))
modelNumberTable$dependOn(c(.procGetDependencies(), "processModels"))
modelNumberTable$position <- 0
Expand Down Expand Up @@ -1295,7 +1295,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {

.procEffectsTablesGetConditionalLabels <- function(paths, mods) {
modProbes <- list()

for (path in paths) {
pathMods <- sapply(path[-1], function(row) row[1])

Expand Down Expand Up @@ -1591,7 +1591,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
parTable <- lavaan::parTable(procResults)
# Only include free parameters in DAG
parTable <- parTable[parTable$op != ":=" & parTable$free > 0 & !grepl(":|__", parTable$rhs) & !grepl(":|__", parTable$lhs),]

arrows <- apply(parTable, 1, function(row) {
op <- switch(row[["op"]],
"~" = " <- ",
Expand All @@ -1610,8 +1610,8 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
conf.level = options$ciLevel,
R = nReps
)
if (nrow(localTestResult) > 0) {

if (nrow(localTestResult) > 0) {
implicationSplit <- strsplit(row.names(localTestResult), "\\s+(\\|+|_+\\|+_+)\\s+")
localTestTable[["lhs"]] <- sapply(implicationSplit, function(row) names(parNamesAbbr)[parNamesAbbr == row[1]])
localTestTable[["op1"]] <- rep("\u2AEB", length(implicationSplit))
Expand Down Expand Up @@ -1871,7 +1871,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
# Create path matrix where first col is "from" and second col is "to", third col is estimate
labelField <- ifelse(estimates, "est", "label")
paths <- matrix(c(parTbl$rhs, parTbl$lhs, parTbl[[labelField]])[parTbl$op == "~"], ncol = 3)

if (type == "conceptual") {
# Remove nodes for factor levels and replace them by factor name, removing levels (e.g., factorLevel1 -> factor)
paths[,1:2] <- apply(paths[, 1:2], 2, function(col) {
Expand All @@ -1887,7 +1887,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
for (j in 1:length(v_split)) {
# Check if variable name is a factor
matchFac <- sapply(options[["factors"]], grepl, x = v_split[j])

# If it is replace by factor name otherwise keep original variable name
if (length(matchFac) > 0 && any(matchFac)) {
v_out[j] <- options[["factors"]][matchFac]
Expand Down Expand Up @@ -1963,7 +1963,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
layout <- .procModGraphLayoutStatistical(intPathsSplitPruned, layout)
}
}

# Create edge list from paths
graph <- igraph::graph_from_edgelist(mainPaths[, 1:2, drop = FALSE])

Expand Down Expand Up @@ -2035,7 +2035,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {

# Scale x-axis to 4/3 (x/y) ratio of y-axis to make plot wider
layout[, 1] <- (layout[, 1]) * (max(layout[, 2]) - min(layout[, 2])) / (max(layout[, 1]) - min(layout[, 1]))

p <- ggraph::ggraph(
graph,
layout = layout
Expand Down Expand Up @@ -2067,7 +2067,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
# Make helper nodes transparent and hide color from legend
ggplot2::scale_color_manual(values = c("black", "transparent"), guide = NULL) +
ggplot2::scale_fill_manual(values = colorPalette, guide = NULL)

if (options[["pathPlotsLegend"]]) {
nodeLabelUnique <- unique(nodeLabels)
nodeLabelUniqueSorted <- sort(nodeLabelUnique, index.return = TRUE)
Expand All @@ -2083,7 +2083,7 @@ ClassicProcess <- function(jaspResults, dataset = NULL, options) {
)
)
}

p <- p +
ggplot2::coord_fixed() +
jaspGraphs::getEmptyTheme() +
Expand Down

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