Prefix OpenMx calls and remove library()

Remove direct library(OpenMx) usage and rely on requireNamespace checks, replacing unqualified OpenMx function calls with explicit OpenMx:: qualifiers across the file. Also make a small call-site clarity change by using named arguments when building the pedigree model. This avoids attaching the OpenMx namespace globally and prevents potential symbol conflicts or side effects from loading the package.

Author: smasongarrison

R/buildmxPedigrees.R

@@ -35,8 +35,6 @@ buildPedigreeModelCovariance <- function(
 ) {
   if (!requireNamespace("OpenMx", quietly = TRUE)) {
     stop("OpenMx package is required for buildPedigreeModelCovariance function. Please install it.")
-  } else {
-    library(OpenMx)
   }
 
   # Coerce to list so both c() vectors and list() inputs work with [[ ]]
@@ -45,49 +43,49 @@ buildPedigreeModelCovariance <- function(
   # Build the list of mxMatrix components conditionally
   mat_list <- list()
   if (Vad) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["ad2"]], labels = "vad", name = "Vad", lbound = 1e-10
     )))
   }
   if (Vdd) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["dd2"]], labels = "vdd", name = "Vdd", lbound = 1e-10
     )))
   }
   if (Vcn) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["cn2"]], labels = "vcn", name = "Vcn", lbound = 1e-10
     )))
   }
   if (Vce) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["ce2"]], labels = "vce", name = "Vce", lbound = 1e-10
     )))
   }
   if (Vmt) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["mt2"]], labels = "vmt", name = "Vmt", lbound = 1e-10
     )))
   }
   if (Vam) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["am2"]], labels = "vam", name = "Vam", lbound = 1e-10
     )))
   }
   if (Ver) {
-    mat_list <- c(mat_list, list(mxMatrix(
+    mat_list <- c(mat_list, list(OpenMx::mxMatrix(
       type = "Full", nrow = 1, ncol = 1, free = TRUE,
       values = vars[["ee2"]], labels = "ver", name = "Ver", lbound = 1e-10
     )))
   }
 
-  do.call(mxModel, c(list("ModelOne"), mat_list))
+  do.call(OpenMx::mxModel, c(list("ModelOne"), mat_list))
 }
 
 #' Build one family group model
@@ -124,8 +122,6 @@ buildOneFamilyGroup <- function(
 ) {
   if (!requireNamespace("OpenMx", quietly = TRUE)) {
     stop("OpenMx package is required for buildOneFamilyGroup function. Please install it.")
-  } else {
-    library(OpenMx)
   }
 
   # Determine family size from first available matrix
@@ -143,15 +139,15 @@ buildOneFamilyGroup <- function(
   # so we never reference a matrix or variance component that doesn't exist.
   # ------------------------------------------------------------------
   mat_list <- list(
-    mxMatrix("Iden", nrow = fsize, ncol = fsize, name = "I"),
-    mxMatrix("Unit", nrow = fsize, ncol = fsize, name = "U")
+    OpenMx::mxMatrix("Iden", nrow = fsize, ncol = fsize, name = "I"),
+    OpenMx::mxMatrix("Unit", nrow = fsize, ncol = fsize, name = "U")
   )
 
   algebra_terms <- character(0)
 
   if (!is.null(Addmat)) {
     mat_list <- c(mat_list, list(
-      mxMatrix("Symm",
+      OpenMx::mxMatrix("Symm",
         nrow = fsize, ncol = fsize,
         values = as.matrix(Addmat), name = "A"
       )
@@ -160,7 +156,7 @@ buildOneFamilyGroup <- function(
   }
   if (!is.null(Dmgmat)) {
     mat_list <- c(mat_list, list(
-      mxMatrix("Symm",
+      OpenMx::mxMatrix("Symm",
         nrow = fsize, ncol = fsize,
         values = as.matrix(Dmgmat), name = "D"
       )
@@ -169,7 +165,7 @@ buildOneFamilyGroup <- function(
   }
   if (!is.null(Nucmat)) {
     mat_list <- c(mat_list, list(
-      mxMatrix("Symm",
+      OpenMx::mxMatrix("Symm",
         nrow = fsize, ncol = fsize,
         values = as.matrix(Nucmat), name = "Cn"
       )
@@ -182,7 +178,7 @@ buildOneFamilyGroup <- function(
   }
   if (!is.null(Amimat)) {
     mat_list <- c(mat_list, list(
-      mxMatrix("Symm",
+      OpenMx::mxMatrix("Symm",
         nrow = fsize, ncol = fsize,
         values = as.matrix(Amimat), name = "Am"
       )
@@ -191,7 +187,7 @@ buildOneFamilyGroup <- function(
   }
   if (!is.null(Mtdmat)) {
     mat_list <- c(mat_list, list(
-      mxMatrix("Symm",
+      OpenMx::mxMatrix("Symm",
         nrow = fsize, ncol = fsize,
         values = as.matrix(Mtdmat), name = "Mt"
       )
@@ -209,20 +205,20 @@ buildOneFamilyGroup <- function(
     list(name = group_name),
     mat_list,
     list(
-      mxData(observed = full_df_row, type = "raw", sort = FALSE),
-      mxMatrix("Full",
+      OpenMx::mxData(observed = full_df_row, type = "raw", sort = FALSE),
+      OpenMx::mxMatrix("Full",
         nrow = 1, ncol = fsize, name = "M", free = TRUE,
         labels = "meanLI", dimnames = list(NULL, ytemp)
       ),
-      mxAlgebraFromString(algebra_str,
+      OpenMx::mxAlgebraFromString(algebra_str,
         name = "V", dimnames = list(ytemp, ytemp)
       ),
-      mxExpectationNormal(covariance = "V", means = "M"),
-      mxFitFunctionML()
+      OpenMx::mxExpectationNormal(covariance = "V", means = "M"),
+      OpenMx::mxFitFunctionML()
     )
   )
 
-  do.call(mxModel, model_args)
+  do.call(OpenMx::mxModel, model_args)
 }
 
 #' Build family group models
@@ -253,9 +249,7 @@ buildFamilyGroups <- function(
   prefix = "fam"
 ) {
   if (!requireNamespace("OpenMx", quietly = TRUE)) {
-    stop("OpenMx package is required for fitPedigreeModel function. Please install it.")
-  } else {
-    library(OpenMx)
+    stop("OpenMx package is required for buildFamilyGroups function. Please install it.")
   }
 
   numfam <- nrow(dat)
@@ -295,8 +289,6 @@ buildFamilyGroups <- function(
 buildPedigreeMx <- function(model_name, vars, group_models) {
   if (!requireNamespace("OpenMx", quietly = TRUE)) {
     stop("OpenMx package is required for buildPedigreeMx function. Please install it.")
-  } else {
-    library(OpenMx)
   }
 
   group_names <- vapply(group_models, function(m) m$name, character(1))
@@ -326,7 +318,7 @@ buildPedigreeMx <- function(model_name, vars, group_models) {
 
   flags <- lapply(vc_map, function(pat) grepl(pat, all_formulas, fixed = TRUE))
 
-  mxModel(
+  OpenMx::mxModel(
     model_name,
     buildPedigreeModelCovariance(
       vars,
@@ -339,7 +331,7 @@ buildPedigreeMx <- function(model_name, vars, group_models) {
       Ver = isTRUE(flags$Ver)
     ),
     group_models,
-    mxFitFunctionMultigroup(group_names)
+    OpenMx::mxFitFunctionMultigroup(group_names)
   )
 }
 
@@ -388,8 +380,6 @@ fitPedigreeModel <- function(
 ) {
   if (!requireNamespace("OpenMx", quietly = TRUE)) {
     stop("OpenMx package is required for fitPedigreeModel function. Please install it.")
-  } else {
-    library(OpenMx)
   }
 
   if (is.null(group_models)) {
@@ -410,11 +400,15 @@ fitPedigreeModel <- function(
     )
   }
 
-  pedigree_model <- buildPedigreeMx(model_name, vars, group_models)
+  pedigree_model <- buildPedigreeMx(
+    model_name = model_name,
+    vars = vars,
+    group_models = group_models
+  )
   if (tryhard) {
-    fitted_model <- mxTryHard(pedigree_model, silent = TRUE, extraTries = 10, intervals = TRUE)
+    fitted_model <- OpenMx::mxTryHard(pedigree_model, silent = TRUE, extraTries = 10, intervals = TRUE)
   } else {
-    fitted_model <- mxRun(pedigree_model)
+    fitted_model <- OpenMx::mxRun(pedigree_model)
   }
   fitted_model
 }