Improve vignette compatibility for missing OpenMx

Updated vignettes to gracefully handle cases where OpenMx or EasyMx are not installed, preventing errors on older R versions. Added conditional checks and informative messages in the vignette code. Updated cran-comments.md to document this enhancement.

Author: smasongarrison

cran-comments.md

@@ -1,7 +1,7 @@
 
 # Description
 
-This update includes minor enhancements and bug fixes related to how string ids are handled in various functions.
+This update includes minor enhancements and bug fixes related to how string ids are handled in various functions. It also now allows certain vignettes to not throw an error if openmx is not installed for older R versions.
 
 # Test Environments
 

vignettes/v1_modelingvariancecomponents.Rmd

@@ -24,8 +24,18 @@ This vignette provides a detailed guide to specific functions within the `BGmisc
 
 ```{r setup, include=FALSE}
 library(BGmisc)
-require(EasyMx)
-require(OpenMx)
+if (!requireNamespace("EasyMx", quietly = TRUE)) {
+ message("Please install OpenMx to run the model fitting examples.")
+} else {
+  require(EasyMx)
+}
+if (!requireNamespace("OpenMx", quietly = TRUE)) {
+message("Please install OpenMx to run the model fitting examples.")
+} else {
+  require(OpenMx)
+}
+
+
 ```
 
 Ensure that the `BGmisc` package is installed and loaded.
@@ -37,7 +47,7 @@ Ensure that the following dependencies are installed before proceeding as they p
 - `OpenMx`
 
 
-```{r}
+```r
 library(BGmisc)
 library(EasyMx)
 library(OpenMx)
@@ -88,11 +98,54 @@ identifyComponentModel(
 
 As you can see the model is identified, now that we've added another group. Let us confirm by fitting a model. First we prepare the data.
 
-```{r}
+```{r, include=FALSE}
+if (!requireNamespace("OpenMx", quietly = TRUE)) {
+  # if OpenMx isn't available
+  n_subjects <- 500
+
+  df_summary_data <- data.frame(
+    age_mean = 34.45,
+    age_sd = 10.12345,
+    ht1_mean = 1.662,
+    ht1_sd = 0.0896277,
+    ht2_mean = 1.694,
+    ht2_sd = 0.09903498
+  )
+  set.seed(12345)
+  twinData <- data.frame(
+    ht1 = rnorm(n_subjects, mean = df_summary_data$ht1_mean, sd = df_summary_data$ht1_sd),
+    zyg = rep(c(1, 3), each = n_subjects / 2)
+  )
+  twinData$ht2 <- twinData$ht1 * ifelse(twinData$zyg == 1, 1, 0.5) +
+    rnorm(n_subjects, mean = 0, sd = df_summary_data$ht2_sd) + .1*rnorm(n_subjects, mean = df_summary_data$ht2_mean, sd = df_summary_data$ht2_sd)
+twinData$ht2[twinData$zyg == 3] <- twinData$ht2[twinData$zyg == 3] + .5*rnorm(sum(twinData$zyg == 3), mean = df_summary_data$ht2_mean, sd = df_summary_data$ht2_sd)
+
+} else {
+data(twinData, package = "OpenMx")
+
 require(dplyr)
 # require(purrr)
 
+selVars <- c("ht1", "ht2")
+
+mzdzData <- subset(
+  twinData, zyg %in% c(1, 3),
+  c(selVars, "zyg")
+)
+
+mzdzData$RCoef <- c(1, NA, .5)[mzdzData$zyg]
+
+
+mzData <- mzdzData %>% filter(zyg == 1)
+}
+```
+
+
+```r
+require(dplyr)
+
 data(twinData, package = "OpenMx")
+
 selVars <- c("ht1", "ht2")
 
 mzdzData <- subset(
@@ -109,6 +162,9 @@ mzData <- mzdzData %>% filter(zyg == 1)
 Let us fit the data with MZ twins by themselves. 
 
 ```{r}
+if (!requireNamespace("EasyMx", quietly = TRUE)) {
+ print("Please install EasyMx to run the model fitting examples.")
+} else {
 run1 <- emxTwinModel(
   model = "Cholesky",
   relatedness = "RCoef",
@@ -118,11 +174,15 @@ run1 <- emxTwinModel(
 )
 
 summary(run1)
+}
 ```
 
 As you can see the model was unsuccessful because it was not identified. But when we add another group, so that the model is identified, the model now fits.
 
 ```{r}
+if (!requireNamespace("EasyMx", quietly = TRUE)) {
+ print("Please install EasyMx to run the model fitting examples.")
+} else {
 run2 <- emxTwinModel(
   model = "Cholesky",
   relatedness = "RCoef",
@@ -132,4 +192,5 @@ run2 <- emxTwinModel(
 )
 
 summary(run2)
+}
 ```