Improve vignette compatibility for missing OpenMx #108
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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.
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Pull request overview
This PR aims to improve vignette compatibility by adding conditional checks to handle cases where OpenMx or EasyMx packages are not installed, particularly for older R versions. The changes add graceful fallbacks with informative messages and synthetic data generation.
Key Changes:
- Added conditional package loading with
requireNamespace()checks for EasyMx and OpenMx in the vignette setup - Wrapped model fitting code blocks with conditionals to prevent errors when EasyMx is unavailable
- Added synthetic data generation as a fallback when OpenMx is not installed
- Updated cran-comments.md to document this enhancement
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| vignettes/v1_modelingvariancecomponents.Rmd | Added conditional checks for OpenMx/EasyMx availability, synthetic data fallback, and wrapped model fitting examples in conditionals |
| vignettes/v1_modelingvariancecomponents.html | Regenerated HTML output reflecting the Rmd changes with updated timestamps and removed warning messages |
| cran-comments.md | Updated description to document vignette compatibility improvements for systems without OpenMx |
| ```{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) | ||
| } |
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The data preparation logic in the include=FALSE chunk only defines selVars, mzdzData, and mzData when OpenMx IS available (inside the else block at lines 123-140). When OpenMx is NOT available, only twinData is created but selVars, mzdzData, and mzData are never defined. This will cause errors in subsequent code chunks that reference these variables (lines 164-177 and 182-195). The data preparation steps should be moved outside the conditional or duplicated in both branches.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Streamlined and clarified the data preparation steps for the twin modeling example in v1_modelingvariancecomponents.Rmd. Moved and consolidated code blocks for loading and filtering data, and ensured consistent use of dplyr. Updated the corresponding HTML output.
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.