Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: smasongarrison

R/buildComponent.R

@@ -235,12 +235,12 @@ ped2com <- function(ped, component,
         verbose_message = "Subsetting adjacency matrix to %d target individuals\n"
       ) # also need to drop columns here because the adjacency matrix is used in the path tracing and we want to make sure the paths are correct for the target individuals.  We will keep all columns for the path tracing but subset to the target rows so that the relatedness values are correct for the target individuals.
 
-      if (length(rownames(isPar) > 1)) {
-        isPar <- isPar[, rownames(isPar), drop = FALSE]
-      } # else {
-      #      isPar <- isPar[rownames(isPar)]
-      #    }
-      #  isPar <- isPar[, rownames(isPar)] #
+    if (length(rownames(isPar)) > 1) {
+      isPar <- isPar[, rownames(isPar), drop = FALSE]
+    } # else {
+    #      isPar <- isPar[rownames(isPar)]
+    #    }
+    #  isPar <- isPar[, rownames(isPar)] #
     }
     if (config$sparse == FALSE) {
       isPar <- as.matrix(isPar)

R/trimPedigree.R

@@ -230,10 +230,14 @@ trimPedigree <- function(ped,
 
   # Nullify dangling parent references introduced by removals
   if (momID %in% names(ped)) {
-    ped[[momID]][!as.character(ped[[momID]]) %in% as.character(ped[[personID]])] <- NA
+    mom_vec <- ped[[momID]]
+    mom_idx <- !is.na(mom_vec) & !as.character(mom_vec) %in% as.character(ped[[personID]])
+    ped[[momID]][mom_idx] <- NA
   }
   if (dadID %in% names(ped)) {
-    ped[[dadID]][!as.character(ped[[dadID]]) %in% as.character(ped[[personID]])] <- NA
+    dad_vec <- ped[[dadID]]
+    dad_idx <- !is.na(dad_vec) & !as.character(dad_vec) %in% as.character(ped[[personID]])
+    ped[[dadID]][dad_idx] <- NA
   }
 
   return(ped)

vignettes/articles/v61_pedigree_model_fitting.Rmd

@@ -30,14 +30,16 @@ if (has_openmx) {
   )
 }
 
-run_models <- has_openmx && interactive() && !isTRUE(Sys.getenv("BGMISC_TESTING", unset = FALSE))
+bgmisc_testing_env <- Sys.getenv("BGMISC_TESTING", unset = "")
+bgmisc_testing <- tolower(bgmisc_testing_env) %in% c("1", "true", "yes")
+run_models <- has_openmx && interactive() && !bgmisc_testing
 rds_dir <- file.path( "inst/extdata/")
 rds_file <- file.path(rds_dir, "fitted_multi.rds")
 ```
 
 # Introduction
 
-This vignette extends the example from `vignette("v60_pedigree_model_fitting.Rmd", package = "BGmisc")` to show how to fit models to multiple families simultaneously. The key functions are `buildOneFamilyGroup()` and `buildPedigreeMx()`, which translate pedigree data into OpenMx model specifications.
+This vignette extends the example from `vignette("v60_pedigree_model_fitting", package = "BGmisc")` to show how to fit models to multiple families simultaneously. The key functions are `buildOneFamilyGroup()` and `buildPedigreeMx()`, which translate pedigree data into OpenMx model specifications.
 
 # Scaling Up to Many Families
 
@@ -113,9 +115,9 @@ for (i in seq_len(n_families)) {
     dimnames = list(NULL, obs_ids_i)
   )
 
-  rownames(A_i) <- colnames(A_i) <- id_order_i
-  rownames(Cn_i) <- colnames(Cn_i) <- id_order_i
-  rownames(Mt_i) <- colnames(Mt_i) <- id_order_i
+  rownames(A_i) <- colnames(A_i) <- obs_ids_i
+  rownames(Cn_i) <- colnames(Cn_i) <- obs_ids_i
+  rownames(Mt_i) <- colnames(Mt_i) <- obs_ids_i
   add_list[[i]] <- A_i
   cn_list[[i]] <- Cn_i
   mt_list[[i]] <- Mt_i

vignettes/v60_pedigree_model_fitting.Rmd

@@ -26,7 +26,7 @@ The `BGmisc` package provides a complete pipeline for pedigree-based variance co
 3. **Build** OpenMx group models with `buildOneFamilyGroup()`
 4. **Fit** the combined model with `buildPedigreeMx()` and `mxRun()` (or the wrapper `fitPedigreeModel()`)
 
-This vignette builds up in three parts: a single-family model, a two-family multi-group model, and a scaled-up simulation study. An extension vignette  `vignette("v61_pedigree_model_fitting.Rmd", package = "BGmisc")` covers more complex models using squirel data from the Kluane Red Squirrel Project.
+This vignette builds up in three parts: a single-family model, a two-family multi-group model, and a scaled-up simulation study. An extension vignette  `vignette("v61_pedigree_model_fitting", package = "BGmisc")` covers more complex models using squirrel data from the Kluane Red Squirrel Project.
 
 ## Prerequisites
 

vignettes/v7_trimPedigree.Xmd

@@ -168,9 +168,9 @@ ggpedigree(
   ),
   config = list(
     overlay_include   = TRUE,
-    status_include    = T,
+    status_include    = TRUE,
     code_male         = 0,
-    sex_color_include = T,
+    sex_color_include = TRUE,
     overlay_mode    = "shape"
   )
 )