Fixes for length > 1 tests for EFA and latent class counts in R 4.3+

michaelhallquist · Jul 15, 2023 · ec0c959 · ec0c959
1 parent af7e60a
commit ec0c959
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/NEWS b/NEWS
@@ -1,5 +1,6 @@
 Version 1.1.1
  - patch:       multi-class columns are now treated as their first class in prepareMplusData()
+ - patch:       extract alternative parameterizations of categorical latent variables (thanks to sam-crawley for the pull request)
 
 Version 1.1.0
  - bugfix:      fixed a bug in handling multiply imputed data introduced in 1.0.0 

diff --git a/R/extractModIndices.R b/R/extractModIndices.R
@@ -26,10 +26,10 @@ extractModIndices_1chunk <- function(chunk, columnNames, filename) {
     #in the on/by section, the on comes first with a trailing / and no data, followed by the by line with the MI data
     #check for this and propagate data from subsequent row to this row
     if (length(thisLine) < numCols && length(thisLine) >= 4 &&
-        thisLine[4] == "/" &&
+        thisLine[4L] == "/" &&
         length(nextLine) > 4 &&
-        nextLine[1] == thisLine[3] && #var1 of ON line corresponds to var2 of BY line
-        nextLine[3] == thisLine[1] #var2 of ON line corresponds to var1 of BY line
+        nextLine[1L] == thisLine[3L] && #var1 of ON line corresponds to var2 of BY line
+        nextLine[3L] == thisLine[1L] #var2 of ON line corresponds to var1 of BY line
         ) {
       splitParams[[line]][4:length(nextLine)] <- nextLine[4:length(nextLine)]
     } else if (length(thisLine) < numCols && substr(thisLine[1], 1, 1) == "[") {

diff --git a/R/parseOutput.R b/R/parseOutput.R
@@ -947,9 +947,9 @@ extractSummaries_1file <- function(outfiletext, filename, input)
 
   #calculate adjusted AIC per Burnham & Anderson(2004), which is better than AIC for non-nested model selection
   #handle AICC calculation, requires AIC, Parameters, and observations
-  if (!is.null(arglist$Parameters) && !is.na(arglist$Parameters) &&
-    !is.null(arglist$AIC) && !is.na(arglist$AIC) &&
-    !is.null(arglist$Observations) && !is.na(arglist$Observations)) {
+  if (!is.null(arglist$Parameters) && !all(is.na(arglist$Parameters)) &&
+    !is.null(arglist$AIC) && !all(is.na(arglist$AIC)) &&
+    !is.null(arglist$Observations) && !all(is.na(arglist$Observations))) {
     arglist$AICC <- arglist$AIC + (2*arglist$Parameters*(arglist$Parameters+1))/(arglist$Observations-arglist$Parameters-1)
   } else {
     arglist$AICC <- NA_real_
@@ -2060,10 +2060,10 @@ extractClassCounts <- function(outfiletext, filename, summaries) {
 
   countlist <- list()
 
-  if (is.null(summaries) || missing(summaries) || summaries$NCategoricalLatentVars==1 || is.na(summaries$NCategoricalLatentVars)) {
+  if (is.null(summaries) || missing(summaries) || isTRUE(summaries$NCategoricalLatentVars[1L]==1) || all(is.na(summaries$NCategoricalLatentVars))) {
     #Starting in Mplus v7.3 and above, formatting of the class counts appears to have changed...
     #Capture the alternatives here
-    if (is.null(summaries) || missing(summaries) || is.null(summaries$Mplus.version) || as.numeric(summaries$Mplus.version) < 7.3) {
+    if (is.null(summaries) || missing(summaries) || is.null(summaries$Mplus.version) || as.numeric(summaries$Mplus.version[1L]) < 7.3) {
       modelCounts <- getSection("^FINAL CLASS COUNTS AND PROPORTIONS FOR THE LATENT CLASSES$", outfiletext)
       ppCounts <- getSection("^FINAL CLASS COUNTS AND PROPORTIONS FOR THE LATENT CLASS PATTERNS$", outfiletext)
       mostLikelyCounts <- getSection("^CLASSIFICATION OF INDIVIDUALS BASED ON THEIR MOST LIKELY LATENT CLASS MEMBERSHIP$", outfiletext)