0.3.2.1: Update to better detect manifest and latent variables

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,8 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          # Temporarily disabled due to OpenMx's dependence on R 4.5.0
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'release', nosuggests: true, special: "No Suggests"}
 
     env:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: semptools
 Title: Customizing Structural Equation Modelling Plots
-Version: 0.3.2
+Version: 0.3.2.1
 Authors@R: c(
     person(given = "Shu Fai",
            family = "Cheung",

NEWS.md

@@ -1,3 +1,12 @@
+# semptools 0.3.2.1
+
+## Improvement
+
+- Updated to treat rectangles as
+  manifest variables and ellipses as
+  latent variables
+  (0.3.2.1)
+
 # semptools 0.3.2
 
 ## New Features

R/helpers.R

@@ -9,22 +9,22 @@ node_plot <- function(semPaths_plot) {
 
 man_plot <- function(semPaths_plot) {
     nodes <- semPaths_plot$graphAttributes$Nodes
-    nodes$names[nodes$shape == "square"]
+    nodes$names[nodes$shape == "square"] | nodes$names[nodes$shape == "rectangle"]
   }
 
 #' @noRd
 
 lat_plot <- function(semPaths_plot) {
     nodes <- semPaths_plot$graphAttributes$Nodes
-    nodes$names[nodes$shape == "circle"]
+    nodes$names[nodes$shape == "circle"] | nodes$names[nodes$shape == "ellipse"]
   }
 
 #' @noRd
 
 indicator_plot <- function(semPaths_plot) {
     nodes <- semPaths_plot$graphAttributes$Nodes
-    man_id <- which(nodes$shape == "square")
-    lat_id <- which(nodes$shape == "circle")
+    man_id <- which((nodes$shape == "square") | (nodes$shape == "rectangle"))
+    lat_id <- which((nodes$shape == "circle") | (nodes$shape == "ellipse"))
     edges <- as.data.frame(semPaths_plot$Edgelist)
     edges2 <- edges[edges$directed & !edges$bidirectional, ]
     id <- (edges2$from %in% lat_id) & (edges2$to %in% man_id)
@@ -39,8 +39,8 @@ loading_plot <- function(semPaths_plot,
     # Assume that:
     #   squares are manifest variables
     #   circles are latent variables
-    man_id <- which(nodes$shape == "square")
-    lat_id <- which(nodes$shape == "circle")
+    man_id <- which((nodes$shape == "square") | (nodes$shape == "rectangle"))
+    lat_id <- which((nodes$shape == "circle") | (nodes$shape == "ellipse"))
     edges <- as.data.frame(semPaths_plot$Edgelist)
     edges2 <- edges[edges$directed & !edges$bidirectional, ]
     id <- (edges2$from %in% lat_id) & (edges2$to %in% man_id)

R/set_sem_layout.R

@@ -280,10 +280,11 @@ set_sem_layout <- function(semPaths_plot,
       } else {
         Nodes_names2 <- NA
       }
-
-    if (!all(Nodes_names[semPaths_plot$graphAttributes$Nodes$shape == "square"] %in% indicator_order)) {
-        if (!all(Nodes_names2[semPaths_plot$graphAttributes$Nodes$shape == "square"] %in% indicator_order)) {
-            tmp1 <- Nodes_names2[semPaths_plot$graphAttributes$Nodes$shape == "square"]
+    tmp0 <- semPaths_plot$graphAttributes$Nodes$shape == "square" |
+            semPaths_plot$graphAttributes$Nodes$shape == "rectangle"
+    if (!all(Nodes_names[tmp0] %in% indicator_order)) {
+        if (!all(Nodes_names2[tmp0] %in% indicator_order)) {
+            tmp1 <- Nodes_names2[tmp0]
             tmp2 <- indicator_order
             msg_tmp <- setdiff(tmp1,
                                indicator_order)
@@ -299,8 +300,10 @@ set_sem_layout <- function(semPaths_plot,
             indicator_order <- tmp
           }
       }
-    if (!all(Nodes_names[semPaths_plot$graphAttributes$Nodes$shape == "circle"] %in% indicator_factor)) {
-        if (!all(Nodes_names2[semPaths_plot$graphAttributes$Nodes$shape == "circle"] %in% indicator_factor)) {
+    tmp0 <- (semPaths_plot$graphAttributes$Nodes$shape == "circle") |
+            (semPaths_plot$graphAttributes$Nodes$shape == "ellipse")
+    if (!all(Nodes_names[tmp0] %in% indicator_factor)) {
+        if (!all(Nodes_names2[tmp0] %in% indicator_factor)) {
             warning("One or more factors in the graph are not in indicator_factor. Unexpected results may occur.")
           } else {
             tmp <- sapply(indicator_factor, function(x) {
@@ -320,10 +323,12 @@ set_sem_layout <- function(semPaths_plot,
     # if (!all(Nodes_names[semPaths_plot$graphAttributes$Nodes$shape == "circle"] %in% indicator_factor)) {
     #     warning("One or more factors in the graph may not be in indicator_factor. Unexpected results may occur.")
     #   }
+    tmp0 <- (semPaths_plot$graphAttributes$Nodes$shape == "circle") |
+            (semPaths_plot$graphAttributes$Nodes$shape == "ellipse")
     if (!all(indicator_factor %in% factor_layout[!is.na(factor_layout)])) {
-        if (!all(Nodes_names2[semPaths_plot$graphAttributes$Nodes$shape == "circle"] %in%
+        if (!all(Nodes_names2[tmp0] %in%
                  factor_layout[!is.na(factor_layout)])) {
-            tmp <- Nodes_names2[semPaths_plot$graphAttributes$Nodes$shape == "circle"]
+            tmp <- Nodes_names2[tmp0]
             msg_tmp <- setdiff(tmp,
                                factor_layout[!is.na(factor_layout)])
             msg_tmp <- paste(unlist(msg_tmp),

README.md

@@ -9,7 +9,7 @@
 [![R-CMD-check](https://github.com/sfcheung/semptools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/semptools/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
-(Version 0.3.2, updated on 2025-07-12, [release history](https://sfcheung.github.io/semptools/news/index.html))
+(Version 0.3.2.1, updated on 2025-07-20, [release history](https://sfcheung.github.io/semptools/news/index.html))
 
 # semptools <img src="man/figures/logo.png" align="right" height="150" />