fix encoded names display in total effects table

Author: juliuspfadt

R/sem.R

@@ -20,6 +20,9 @@
 SEMInternal <- 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/")
 
+  # sink(file="~/Downloads/log.txt")
+  # on.exit(sink(NULL))
+
   # Read dataset
   options <- .semPrepOpts(options)
 
@@ -624,10 +627,10 @@ checkLavaanModel <- function(model, availableVars) {
     }
 
     total_effects <- c()
-    for (pred in unique(c(pred,regressions[[group]][["rhs"]]))) {
+    for (pred in unique(c(pred, regressions[[group]][["rhs"]]))) {
       for (out in unique(c(out, regressions[[group]][["lhs"]]))) {
         total_effect <- NULL
-        total_effect_name <- paste0("total_", groups[group], "_", pred, "_", out)
+        total_effect_name <- paste0("total_", groups[group], "__", pred, "__", out)
         indirect_effect_idx <- unlist(lapply(names(indirect_effects), function(x) {
           startsWith(x, pred) && endsWith(x, out)
         }))
@@ -1195,10 +1198,6 @@ checkLavaanModel <- function(model, availableVars) {
 
   }
 
-  # TODO: bootstrap standardized CI:
-  #' Do we want the standardization to happen for the fit of each bootstrap sample and then save the std coeffs?
-  #' Or do we want to save all the unstd coeffs from the bootstrap, and after summarizing them with mean
-  #' and se and such standardize them?
 
   if (options[["group"]] != "")  {
     pe[pe[["op"]] != ":=", "groupname"] <- lavaan::lavInspect(fit, "group.label")[pe[["group"]]]
@@ -1382,8 +1381,22 @@ checkLavaanModel <- function(model, availableVars) {
 
     path <- list()
     for (idx in 1:nrow(pe_toteff)) {
-      path[[idx]] <- gsub("_", " \u2192 ", pe_toteff[idx, "lhs"])
-      path[[idx]] <- gsub("total \u2192", "", path[[idx]])
+      # path[[idx]] <- gsub("_", " \u2192 ", pe_toteff[idx, "lhs"])
+      # path[[idx]] <- gsub("total \u2192", "", path[[idx]])
+
+      # Step 1: Remove the "total_X__" prefix (X can be a number or word)
+      path[[idx]] <- gsub("^total_[^_]+__", "", pe_toteff[idx, "lhs"])
+
+      # Step 2: Decode any "JaspColumn_X_Encoded" variable names
+      matches <- regmatches(path[[idx]], gregexpr("JaspColumn_[0-9]+_Encoded", path[[idx]]))
+      if (length(matches[[1]]) > 0) {
+        decoded_matches <- sapply(matches[[1]], jaspBase::decodeColNames) # Decode each match
+        regmatches(path[[idx]], gregexpr("JaspColumn_[0-9]+_Encoded", path[[idx]])) <- list(decoded_matches)
+      }
+
+      # Step 3: Replace double underscores "__" with " → "
+      path[[idx]] <- gsub("__", " \u2192 ", path[[idx]])
+
       for (group in groups)
         path[[idx]] <- gsub(paste0(" ", group, " \u2192"), "", path[[idx]])
 

jaspSem.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: d2e2ff5f-0cf8-4e57-82f3-e5f5382b33f9
 
 RestoreWorkspace: No
 SaveWorkspace: No

renv.lock

@@ -502,7 +502,7 @@
     },
     "cluster": {
       "Package": "cluster",
-      "Version": "2.1.6",
+      "Version": "2.1.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -512,7 +512,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "0aaa05204035dc43ea0004b9c76611dd"
+      "Hash": "b361779da7f8b129a1859b6cf243ba58"
     },
     "coda": {
       "Package": "coda",
@@ -1531,15 +1531,15 @@
     },
     "nnet": {
       "Package": "nnet",
-      "Version": "7.3-19",
+      "Version": "7.3-20",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "stats",
         "utils"
       ],
-      "Hash": "2c797b46eea7fb58ede195bc0b1f1138"
+      "Hash": "c955edf99ff24a32e96bd0a22645af60"
     },
     "numDeriv": {
       "Package": "numDeriv",

tests/testthat/test-sem.R

@@ -82,7 +82,7 @@ options$modelTest         <- "standard"
 options$reliability       <- TRUE
 options$ave               <- TRUE
 options$htmt              <- TRUE
-results <- jaspTools::runAnalysis("SEM", "poldem_grouped.csv", options)
+results <- jaspTools::runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options)
 
 
 container   <- results[["results"]][["modelContainer"]][["collection"]]
@@ -175,7 +175,7 @@ options$models = list(
   list(name = "more constrained", syntax = modelMoreConstrained)
 )
 
-results <- jaspTools::runAnalysis("SEM", "poldem_grouped.csv", options)
+results <- jaspTools::runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options)
 
 
 test_that("Model fit table results match", {
@@ -603,7 +603,7 @@ options$bootstrapCiType   <- "percentile"
 options$bootstrapSamples  <- 100
 
 set.seed(1)
-results <- jaspTools::runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options, makeTests = T)
+results <- jaspTools::runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options, makeTests = F)
 
 # Model fit table results match
 test_that("Bootstrapping model fit table works", {
@@ -830,7 +830,7 @@ options$models = list(
   list(name = "default", syntax = modelDefault)
 )
 
-results <- jaspTools::runAnalysis("SEM", "poldem_grouped.csv", options)
+results <- jaspTools::runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options)
 
 
 test_that("Residual covariances table results match", {
@@ -1023,7 +1023,7 @@ options$models <- list(list(name = "Model1",
                             syntax = list(model=model,
                                           columns = c("x1", "x2", "x3", "y1", "y2", "y3", "y4", "y5", "y6", "y7", "y8"))))
 set.seed(1)
-results <- runAnalysis("SEM", "poldem_grouped.csv", options)
+results <- runAnalysis("SEM", testthat::test_path("poldem_grouped.csv"), options)
 
 test_that("Sensitivity parameters that led to a change in significance table results match", {
   table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_sensitivity"]][["collection"]][["modelContainer_sensitivity_senpar"]][["data"]]