From cd3b6ad2ced3a39c2f1049ad868af1ba228c2db3 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Tue, 7 Jul 2026 20:10:07 -0400
Subject: [PATCH 01/11] Update helpGeneric.R

---
 R/helpGeneric.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/R/helpGeneric.R b/R/helpGeneric.R
index d6711fb7..f993387f 100644
--- a/R/helpGeneric.R
+++ b/R/helpGeneric.R
@@ -104,6 +104,38 @@ resample <- function(x, ...) {
   x[sample.int(length(x), ...)]
 }
 
+#' Coerce to a Numeric Matrix
+#'
+#' @param x An object coercible to a matrix.
+#' @keywords internal
+#' @return \code{x} as a matrix with numeric storage mode.
+#'
+as_numeric_matrix <- function(x) {
+  x <- as.matrix(x)
+  storage.mode(x) <- "numeric"
+  x
+}
+
+#' Symmetrize a Matrix
+#'
+#' Averages a matrix with its transpose when it is not already symmetric
+#' within tolerance. Used to clean up relatedness matrices before they are
+#' passed to OpenMx, which requires exact symmetry for \code{"Symm"}-type
+#' \code{mxMatrix} objects.
+#'
+#' @param x A square matrix, or an object coercible to one.
+#' @param tol Numeric tolerance for asymmetry. Default is 1e-10.
+#' @keywords internal
+#' @return A numeric matrix, symmetrized if needed.
+#'
+make_symmetric <- function(x, tol = 1e-10) {
+  x <- as_numeric_matrix(x)
+  if (max(abs(x - t(x)), na.rm = TRUE) > tol) {
+    x <- (x + t(x)) / 2
+  }
+  x
+}
+
 #' Check for OpenMx Package
 #'
 #' This function checks if the OpenMx package is installed and available for use. If the package is not installed, it throws an error with a message indicating that OpenMx is required and provides instructions for installation.

From d6d2c1a85a326521f5675f0e7f0fef918e971b96 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Thu, 9 Jul 2026 10:02:13 -0400
Subject: [PATCH 02/11] fix check id error

---
 R/checkParents.R | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/R/checkParents.R b/R/checkParents.R
index 44b7b46f..6b32dd07 100644
--- a/R/checkParents.R
+++ b/R/checkParents.R
@@ -110,16 +110,18 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   }
   # Are any parents in both momID and dadID?
   momdad <- intersect(ped$dadID, ped$momID)
-  if (length(momdad) > 0 && !is.na(momdad)) {
-    validation_results$parents_in_both <- momdad
-    if (verbose == TRUE) {
-      cat(paste(
-        "Some individuals appear in both momID and dadID roles.\n",
-        "These individuals are:\n"
-      ))
-      message(momdad)
-    }
+  momdad <- momdad[!is.na(momdad)]
+if (length(momdad) > 0) {
+  validation_results$parents_in_both <- momdad
+  if (verbose == TRUE) {
+    cat(
+      "Some individuals appear in both momID and dadID roles.\n",
+      "These individuals are:\n",
+      sep = ""
+    )
+    message(paste(momdad, collapse = ", "))
   }
+}
 
 
   if (!repair) {

From a0c81c25f2a35fd9f6c56d476f16aea38bd7f0a5 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sat, 11 Jul 2026 11:33:37 -0400
Subject: [PATCH 03/11] docs

---
 man/as_numeric_matrix.Rd | 18 ++++++++++++++++++
 man/make_symmetric.Rd    | 23 +++++++++++++++++++++++
 2 files changed, 41 insertions(+)
 create mode 100644 man/as_numeric_matrix.Rd
 create mode 100644 man/make_symmetric.Rd

diff --git a/man/as_numeric_matrix.Rd b/man/as_numeric_matrix.Rd
new file mode 100644
index 00000000..5568862a
--- /dev/null
+++ b/man/as_numeric_matrix.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpGeneric.R
+\name{as_numeric_matrix}
+\alias{as_numeric_matrix}
+\title{Coerce to a Numeric Matrix}
+\usage{
+as_numeric_matrix(x)
+}
+\arguments{
+\item{x}{An object coercible to a matrix.}
+}
+\value{
+\code{x} as a matrix with numeric storage mode.
+}
+\description{
+Coerce to a Numeric Matrix
+}
+\keyword{internal}
diff --git a/man/make_symmetric.Rd b/man/make_symmetric.Rd
new file mode 100644
index 00000000..04f8014d
--- /dev/null
+++ b/man/make_symmetric.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpGeneric.R
+\name{make_symmetric}
+\alias{make_symmetric}
+\title{Symmetrize a Matrix}
+\usage{
+make_symmetric(x, tol = 1e-10)
+}
+\arguments{
+\item{x}{A square matrix, or an object coercible to one.}
+
+\item{tol}{Numeric tolerance for asymmetry. Default is 1e-10.}
+}
+\value{
+A numeric matrix, symmetrized if needed.
+}
+\description{
+Averages a matrix with its transpose when it is not already symmetric
+within tolerance. Used to clean up relatedness matrices before they are
+passed to OpenMx, which requires exact symmetry for \code{"Symm"}-type
+\code{mxMatrix} objects.
+}
+\keyword{internal}

From 466b49ba8a9180fcd893eb2c75d903286264e8c9 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Sat, 11 Jul 2026 14:37:30 -0400
Subject: [PATCH 04/11] Update helpGeneric.R

---
 R/helpGeneric.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/helpGeneric.R b/R/helpGeneric.R
index f993387f..0c350777 100644
--- a/R/helpGeneric.R
+++ b/R/helpGeneric.R
@@ -129,6 +129,13 @@ as_numeric_matrix <- function(x) {
 #' @return A numeric matrix, symmetrized if needed.
 #'
 make_symmetric <- function(x, tol = 1e-10) {
+    if (inherits(x, "sparseMatrix")) {
+    if (!Matrix::isSymmetric(x, tol = tol)) {
+      x <- (x + Matrix::t(x)) / 2
+    }
+
+    return(Matrix::forceSymmetric(x, uplo = "L"))
+  }
   x <- as_numeric_matrix(x)
   if (max(abs(x - t(x)), na.rm = TRUE) > tol) {
     x <- (x + t(x)) / 2

From b7052b48e7a13f85fc71dc4540de8fa01976808f Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 10:41:10 -0400
Subject: [PATCH 05/11] adding in select innovations from temporal branch

---
 NAMESPACE                              |   1 +
 R/buildmxPedigrees.R                   | 528 +++++++++++++++++++++----
 man/buildFamilyGroups.Rd               |   4 +-
 man/buildFamilyGroups_list.Rd          |  57 +++
 man/buildOneFamilyGroup.Rd             |   4 +-
 man/buildPedigreeMx.Rd                 |   6 +-
 man/dot-assemblePedigreeMx.Rd          |  28 ++
 man/dot-buildGroupedStaticFamily.Rd    |  60 +++
 man/dot-pedigreeFamilySize.Rd          |  19 +
 man/dot-pedigreeMeanMatrix.Rd          |  23 ++
 man/dot-pedigreeRelatednessMatrix.Rd   |  33 ++
 man/make_clean_personids.Rd            |  17 +
 tests/testthat/test-buildmxPedigrees.R |   4 +-
 13 files changed, 713 insertions(+), 71 deletions(-)
 create mode 100644 man/buildFamilyGroups_list.Rd
 create mode 100644 man/dot-assemblePedigreeMx.Rd
 create mode 100644 man/dot-buildGroupedStaticFamily.Rd
 create mode 100644 man/dot-pedigreeFamilySize.Rd
 create mode 100644 man/dot-pedigreeMeanMatrix.Rd
 create mode 100644 man/dot-pedigreeRelatednessMatrix.Rd
 create mode 100644 man/make_clean_personids.Rd

diff --git a/NAMESPACE b/NAMESPACE
index de1c947c..12786ebd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(addPaternalLineFlag)
 export(addPersonToPed)
 export(alignPhenToMatrix)
 export(buildFamilyGroups)
+export(buildFamilyGroups_list)
 export(buildOneFamilyGroup)
 export(buildPedigreeModelCovariance)
 export(buildPedigreeMx)
diff --git a/R/buildmxPedigrees.R b/R/buildmxPedigrees.R
index 56eeb2c1..6ec04664 100644
--- a/R/buildmxPedigrees.R
+++ b/R/buildmxPedigrees.R
@@ -93,6 +93,66 @@ buildPedigreeModelCovariance <- function(
 
   do.call(OpenMx::mxModel, c(list("ModelOne"), mat_list))
 }
+#' Determine family size from a family's relatedness matrices (internal)
+#'
+#' @param mats_in A list of relatedness matrices (possibly containing NULLs); the first
+#'   non-NULL matrix's row count is used as the family size.
+#' @return Integer family size.
+#' @keywords internal
+.pedigreeFamilySize <- function(mats_in) {
+  for (m in mats_in) {
+    if (!is.null(m)) {
+      return(nrow(m))
+    }
+  }
+  stop("At least one relatedness matrix must be provided.")
+}
+
+#' Build a relatedness mxMatrix (internal)
+#'
+#' Builds the \code{"Symm"} mxMatrix for one relatedness matrix.
+#'
+#' @param mat The relatedness matrix.
+#' @param fsize Family size.
+#' @param name The mxMatrix's name (e.g. "A", "Cn").
+#' @param condense Logical. If TRUE, apply \code{\link{condenseMatrixSlots}}.
+#' @param symmetrize Logical. If TRUE, symmetrize \code{mat} via \code{\link{make_symmetric}}
+#'   before use; if FALSE, coerce via \code{as.matrix} only.
+#' @return An mxMatrix object.
+#' @keywords internal
+.pedigreeRelatednessMatrix <- function(mat, fsize, name, condense = TRUE, symmetrize = FALSE) {
+  if (is.null(mat)) stop("Relatedness matrix cannot be NULL.")
+  # keep dense if dense, or sparse if sparse, but symmetrize if requested
+  if (inherits(mat, "Matrix")) {
+    values <- if (symmetrize) make_symmetric(mat) else mat
+  } else {
+    values <- if (symmetrize) make_symmetric(mat) else as.matrix(mat)
+  }
+  m <- OpenMx::mxMatrix(
+    type = "Symm", nrow = fsize, ncol = fsize, free = FALSE,
+    values = values, name = name
+  )
+  if (condense) m <- condenseMatrixSlots(m)
+  m
+}
+
+#' Build the free mean mxMatrix for a family group (internal)
+#'
+#' Shared by the static and temporal branches of \code{\link{buildOneFamilyGroup}}; they
+#' only differ in the parameter label ("meanLI" vs "mean_y").
+#'
+#' @param fsize Family size.
+#' @param obs_ids Character vector of individual IDs.
+#' @param label The mean parameter's label.
+#' @return An mxMatrix object.
+#' @keywords internal
+.pedigreeMeanMatrix <- function(fsize, obs_ids, label) {
+  OpenMx::mxMatrix(
+    "Full",
+    nrow = 1, ncol = fsize, name = "M", free = TRUE,
+    values = 0, labels = label, dimnames = list(NULL, obs_ids)
+  )
+}
 
 #' Build one family group model
 #'
@@ -130,19 +190,26 @@ buildOneFamilyGroup <- function(
   Dmgmat = NULL,
   full_df_row,
   obs_ids,
-  condenseMatrixSlots = TRUE
+  symmetrize = FALSE,
+  condenseMatrixSlots = TRUE,
+  clean_ids = FALSE
 ) {
   .require_openmx("buildOneFamilyGroup")
-
-  # Determine family size from first available matrix
-  fsize <- NULL
-  for (m in list(Addmat, Nucmat, Extmat, Mtdmat, Amimat, Dmgmat)) {
-    if (!is.null(m)) {
-      fsize <- nrow(m)
-      break
-    }
+  if (clean_ids) {
+    obs_ids <- make_clean_personids(obs_ids)
+    # clean once
+    clean_ids <- FALSE
+  }
+  # Determine family size from first available matrix. Shared by both branches below.
+  if ( # not any of the matrices are provided
+    is.null(Addmat) && is.null(Dmgmat) && is.null(Nucmat) &&
+    is.null(Extmat) && is.null(Mtdmat) && is.null(Amimat)
+  ) {
+    warning("At least one relatedness matrix should be provided. Using the number of columns in 'full_df_row' as family size.")
+    fsize <- ncol(full_df_row)
+  } else {
+    fsize <- .pedigreeFamilySize(list(Addmat, Dmgmat, Nucmat, Extmat, Mtdmat, Amimat))
   }
-  if (is.null(fsize)) stop("At least one relatedness matrix must be provided.")
 
   # If Extmat is requested but not supplied as a matrix, create a unit matrix
   # (all members share the extended environment equally).
@@ -150,35 +217,61 @@ buildOneFamilyGroup <- function(
     Extmat <- matrix(1, nrow = fsize, ncol = fsize)
   }
 
-  # ------------------------------------------------------------------
-  # Build the list of mxMatrix objects and the algebra terms
-  # Each entry: list(mat = input_matrix, mxname, algebra_term).
-  # ------------------------------------------------------------------
+  # One canonical table describing each variance component: which relatedness matrix it
+  # uses, its mxMatrix name, the exact static Kronecker algebra term (term, unchanged from
+  # the original static implementation), and the temporal loading/loading-matrix names
+  # (k / K). Both the static and temporal algebra below are built from this same table and
+  # the same relatedness mxMatrix objects (relmat_list), rather than each branch rebuilding
+  # its own copy of this table.
   mat_spec <- list(
-    list(mat = Addmat, mxname = "A", term = "(A  %x% ModelOne.Vad)"),
-    list(mat = Dmgmat, mxname = "D", term = "(D  %x% ModelOne.Vdd)"),
-    list(mat = Nucmat, mxname = "Cn", term = "(Cn %x% ModelOne.Vcn)"),
-    list(mat = Extmat, mxname = "Ce", term = "(Ce %x% ModelOne.Vce)"),
-    list(mat = Amimat, mxname = "Am", term = "(Am %x% ModelOne.Vam)"),
-    list(mat = Mtdmat, mxname = "Mt", term = "(Mt %x% ModelOne.Vmt)")
+    list(
+      mat = Addmat,
+      mxname = "A",
+      term = "(A  %x% ModelOne.Vad)",
+      k = "a", K = "Ka"
+    ),
+    list(
+      mat = Dmgmat,
+      mxname = "D",
+      term = "(D  %x% ModelOne.Vdd)",
+      k = "d", K = "Kd"
+    ),
+    list(
+      mat = Nucmat,
+      mxname = "Cn",
+      term = "(Cn %x% ModelOne.Vcn)",
+      k = "cn", K = "Kcn"
+    ),
+    list(
+      mat = Extmat,
+      mxname = "Ce",
+      term = "(Ce %x% ModelOne.Vce)",
+      k = "ce", K = "Kce"
+    ),
+    list(
+      mat = Amimat,
+      mxname = "Am",
+      term = "(Am %x% ModelOne.Vam)",
+      k = "am", K = "Kam"
+    ),
+    list(
+      mat = Mtdmat,
+      mxname = "Mt",
+      term = "(Mt %x% ModelOne.Vmt)",
+      k = "mt", K = "Kmt"
+    )
   )
   active <- Filter(function(s) !is.null(s$mat), mat_spec)
 
-  if (condenseMatrixSlots) {
-    relmat_list <- lapply(active, function(s) {
-      condenseMatrixSlots(OpenMx::mxMatrix("Symm",
-        nrow = fsize, ncol = fsize,
-        values = as.matrix(s$mat), name = s$mxname
-      ))
-    })
-  } else {
-    relmat_list <- lapply(active, function(s) {
-      OpenMx::mxMatrix("Symm",
-        nrow = fsize, ncol = fsize,
-        values = as.matrix(s$mat), name = s$mxname
-      )
-    })
-  }
+  # Static values are used as-is (as.matrix); temporal symmetrizes them first. Either
+  # way, this single loop replaces what used to be two separate (and, for static,
+  # itself duplicated condensed/uncondensed) copies of the same mxMatrix-building code.
+  relmat_list <- lapply(active, function(s) {
+    .pedigreeRelatednessMatrix(
+      s$mat, fsize, s$mxname,
+      condense = condenseMatrixSlots, symmetrize = symmetrize
+    )
+  })
   # add the identity matrix for the unique environment, which is always included as a term in the algebra
   mat_list <- c(
     list(OpenMx::mxMatrix("Iden", nrow = fsize, ncol = fsize, name = "I")),
@@ -198,12 +291,9 @@ buildOneFamilyGroup <- function(
     mat_list,
     list(
       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, obs_ids)
-      ),
+      .pedigreeMeanMatrix(fsize, obs_ids, "meanLI"),
       OpenMx::mxAlgebraFromString(algebra_str,
-        name = "V", dimnames = list(obs_ids, obs_ids)
+                                  name = "V", dimnames = list(obs_ids, obs_ids)
       ),
       OpenMx::mxExpectationNormal(covariance = "V", means = "M"),
       OpenMx::mxFitFunctionML()
@@ -213,6 +303,168 @@ buildOneFamilyGroup <- function(
   do.call(OpenMx::mxModel, model_args)
 }
 
+#' Build one grouped static family model
+#'
+#' This function constructs one OpenMx model for multiple independent family
+#' observations that share the same pedigree structure, relatedness matrices,
+#' variable ordering, expected covariance matrix, and expected mean vector.
+#'
+#' The observed data contain one family per row. The shared matrices, covariance
+#' algebra, expectation, and fit function are stored only once rather than once
+#' per family.
+#'
+#' @param group_name Name of the grouped family model.
+#' @param dat A matrix or data frame where each row represents an independent
+#'   family and columns correspond to pedigree positions.
+#' @param obs_ids A character vector of individual IDs corresponding to the
+#'   columns of \code{dat} and the rows/columns of the relatedness matrices.
+#' @inheritParams buildOneFamilyGroup
+#' @return An OpenMx model containing all static family observations.
+#' @keywords internal
+.buildGroupedStaticFamily <- function(
+    group_name,
+    dat,
+    obs_ids,
+    Addmat = NULL,
+    Nucmat = NULL,
+    Extmat = NULL,
+    Mtdmat = NULL,
+    Amimat = NULL,
+    Dmgmat = NULL,
+    condenseMatrixSlots = TRUE,
+    clean_ids = FALSE
+) {
+  .require_openmx(".buildGroupedStaticFamily")
+
+  if (clean_ids) {
+    obs_ids <- make_clean_personids(obs_ids)
+    # clean once
+    clean_ids <- FALSE
+  }
+
+  dat <- as.data.frame(dat, check.names = FALSE)
+
+  if (nrow(dat) < 1L) {
+    stop("'dat' must contain at least one family row.")
+  }
+
+  if (ncol(dat) != length(obs_ids)) {
+    stop("The number of columns in 'dat' must equal the length of 'obs_ids'.")
+  }
+
+  if (anyDuplicated(obs_ids)) {
+    stop("'obs_ids' must be unique.")
+  }
+
+  colnames(dat) <- obs_ids
+
+  # Determine family size from first available matrix.
+  fsize <- .pedigreeFamilySize(list(Addmat, Dmgmat, Nucmat, Extmat, Mtdmat, Amimat))
+
+  if (length(obs_ids) != fsize) {
+    stop("Length of 'obs_ids' must equal the shared family size.")
+  }
+
+  # If Extmat is requested but not supplied as a matrix, create a unit matrix
+  # (all members share the extended environment equally).
+  if (!is.null(Extmat) && !is.matrix(Extmat)) {
+    Extmat <- matrix(1, nrow = fsize, ncol = fsize)
+  }
+
+  # This is the same static variance-component specification used by
+  # buildOneFamilyGroup(), but it is constructed only once for all rows of dat.
+  mat_spec <- list(
+    list(
+      mat = Addmat,
+      mxname = "A",
+      term = "(A  %x% ModelOne.Vad)"
+    ),
+    list(
+      mat = Dmgmat,
+      mxname = "D",
+      term = "(D  %x% ModelOne.Vdd)"
+    ),
+    list(
+      mat = Nucmat,
+      mxname = "Cn",
+      term = "(Cn %x% ModelOne.Vcn)"
+    ),
+    list(
+      mat = Extmat,
+      mxname = "Ce",
+      term = "(Ce %x% ModelOne.Vce)"
+    ),
+    list(
+      mat = Amimat,
+      mxname = "Am",
+      term = "(Am %x% ModelOne.Vam)"
+    ),
+    list(
+      mat = Mtdmat,
+      mxname = "Mt",
+      term = "(Mt %x% ModelOne.Vmt)"
+    )
+  )
+
+  active <- Filter(function(s) !is.null(s$mat), mat_spec)
+
+  # Build one copy of each shared relatedness matrix.
+  relmat_list <- lapply(active, function(s) {
+    .pedigreeRelatednessMatrix(
+      s$mat,
+      fsize,
+      s$mxname,
+      condense = condenseMatrixSlots,
+      symmetrize = FALSE
+    )
+  })
+
+  # Add one identity matrix for the unique environment.
+  mat_list <- c(
+    list(OpenMx::mxMatrix("Iden", nrow = fsize, ncol = fsize, name = "I")),
+    relmat_list
+  )
+
+  algebra_terms <- vapply(active, `[[`, character(1), "term")
+
+  # Unique environment is always included.
+  algebra_terms <- c(algebra_terms, "(I %x% ModelOne.Ver)")
+
+  algebra_str <- paste(algebra_terms, collapse = " + ")
+
+  # The full data frame is passed to one raw-data model. Each row is an
+  # independent family likelihood contribution under the shared M and V.
+  model_args <- c(
+    list(name = group_name),
+    mat_list,
+    list(
+      OpenMx::mxData(
+        observed = dat,
+        type = "raw",
+        sort = FALSE
+      ),
+      .pedigreeMeanMatrix(
+        fsize,
+        obs_ids,
+        "meanLI"
+      ),
+      OpenMx::mxAlgebraFromString(
+        algebra_str,
+        name = "V",
+        dimnames = list(obs_ids, obs_ids)
+      ),
+      OpenMx::mxExpectationNormal(
+        covariance = "V",
+        means = "M",
+        dimnames = obs_ids
+      ),
+      OpenMx::mxFitFunctionML()
+    )
+  )
+
+  do.call(OpenMx::mxModel, model_args)
+}
+
 #' Build family group models
 #'
 #' This function constructs OpenMx models for multiple family groups based on
@@ -234,10 +486,34 @@ buildFamilyGroups <- function(
   Amimat = NULL,
   Dmgmat = NULL,
   prefix = "fam",
-  condenseMatrixSlots = TRUE
+  condenseMatrixSlots = TRUE,
+  clean_ids = TRUE,
+  group_static_families = FALSE
 ) {
   .require_openmx("buildFamilyGroups")
+  if (clean_ids == TRUE) {
+    obs_ids <- make_clean_personids(obs_ids)
+    # clean once
+    clean_ids <- FALSE
+  }
 
+  if (group_static_families) {
+    return(list(
+      .buildGroupedStaticFamily(
+        group_name = paste0(prefix, "_grouped"),
+        dat = dat,
+        obs_ids = obs_ids,
+        Addmat = Addmat,
+        Nucmat = Nucmat,
+        Extmat = Extmat,
+        Mtdmat = Mtdmat,
+        Amimat = Amimat,
+        Dmgmat = Dmgmat,
+        condenseMatrixSlots = condenseMatrixSlots,
+        clean_ids = clean_ids
+      )
+    ))
+  }
   numfam <- nrow(dat)
   groups <- vector("list", numfam)
 
@@ -253,7 +529,86 @@ buildFamilyGroups <- function(
       Dmgmat = Dmgmat,
       full_df_row = full_df_row,
       obs_ids = obs_ids,
-      condenseMatrixSlots = condenseMatrixSlots
+      condenseMatrixSlots = condenseMatrixSlots,
+      clean_ids = clean_ids
+    )
+  }
+
+  groups
+}
+
+
+#' Build family group models with per-family relatedness matrices
+#'
+#' This function constructs OpenMx models for multiple family groups, each with its own
+#' relatedness matrices, observed IDs, and (for temporal models) birth years / historical
+#' moderators. Use this when families vary in size or structure; for families that all share
+#' the same relatedness matrices, see \code{\link{buildFamilyGroups}}.
+#' @inheritParams buildOneFamilyGroup
+#' @param dat_list A list of numeric vectors of observed data, one per family.
+#' @param obs_ids_list A list of character vectors of individual IDs, one per family, matching
+#'   \code{dat_list} and the rows/columns of that family's relatedness matrices.
+#' @param Addmat_list A list of additive genetic relatedness matrices, one per family.
+#' @param Nucmat_list A list of nuclear family shared environment relatedness matrices, one per family.
+#' @param Extmat_list A list of common extended family environment relatedness matrices, one per family.
+#' @param Mtdmat_list A list of mitochondrial genetic relatedness matrices, one per family.
+#' @param Amimat_list A list of additive by mitochondrial interaction relatedness matrices, one per family.
+#' @param Dmgmat_list A list of dominance genetic relatedness matrices, one per family.
+#' @param prefix A prefix for naming the family groups. Default is "fam".
+#' @param birth_year_list A list of numeric birth-year vectors, one per family, each matching
+#'   the corresponding entry of \code{obs_ids_list}. Only used when \code{temporal = TRUE}.
+#' @param H_list A list of historical-moderator matrices, one per family. Only used when
+#'   \code{temporal = TRUE}.
+#' @return A list of OpenMx models for each family group.
+#' @export
+
+buildFamilyGroups_list <- function(
+    dat_list,
+    obs_ids_list,
+    Addmat_list = NULL,
+    Nucmat_list = NULL,
+    Extmat_list = NULL,
+    Mtdmat_list = NULL,
+    Amimat_list = NULL,
+    Dmgmat_list = NULL,
+    prefix = "fam",
+    condenseMatrixSlots = TRUE,
+    clean_ids = TRUE
+) {
+  .require_openmx("buildFamilyGroups_list")
+
+  numfam <- length(dat_list)
+  groups <- vector("list", numfam)
+
+  get_or_null <- function(x, i) {
+    if (is.null(x)) NULL else x[[i]]
+  }
+
+  for (afam in seq_len(numfam)) {
+    if (clean_ids == TRUE) {
+      obs_ids <- make_clean_personids(obs_ids_list[[afam]])
+      clean_ids <- FALSE
+    } else {
+      obs_ids <- obs_ids_list[[afam]]
+    }
+    full_df_row <- matrix(
+      dat_list[[afam]],
+      nrow = 1,
+      dimnames = list(NULL, obs_ids)
+    )
+
+    groups[[afam]] <- buildOneFamilyGroup(
+      group_name = paste0(prefix, afam),
+      Addmat = get_or_null(Addmat_list, afam),
+      Nucmat = get_or_null(Nucmat_list, afam),
+      Extmat = get_or_null(Extmat_list, afam),
+      Mtdmat = get_or_null(Mtdmat_list, afam),
+      Amimat = get_or_null(Amimat_list, afam),
+      Dmgmat = get_or_null(Dmgmat_list, afam),
+      full_df_row = full_df_row,
+      obs_ids = obs_ids,
+      condenseMatrixSlots = condenseMatrixSlots,
+      clean_ids = clean_ids # already cleaned above if requested
     )
   }
 
@@ -271,12 +626,15 @@ buildFamilyGroups <- function(
 #' @param vars A named list or vector of initial variance component values.
 #' @param group_models A list of OpenMx models for each family group.
 #' @param ci Logical. If TRUE, include confidence interval computations for the variance components. Default is FALSE
+#' @param components Character vector of component keys to include (any of "a", "d", "cn",
+#'   "ce", "mt", "am", "e"). Only used when \code{temporal = TRUE}. Default is \code{c("a", "e")}.
 #' @return An OpenMx pedigree model combining variance components and family groups.
 #' @export
 
 buildPedigreeMx <- function(model_name, vars, group_models,
                             ci = FALSE,
-                            condenseMatrixSlots = TRUE) {
+                            condenseMatrixSlots = TRUE,
+                            components = c("a", "e")) {
   .require_openmx("buildPedigreeMx")
 
   group_names <- vapply(group_models, function(m) m$name, character(1))
@@ -306,26 +664,24 @@ buildPedigreeMx <- function(model_name, vars, group_models,
 
   flags <- lapply(vc_map, function(pat) grepl(pat, all_formulas, fixed = TRUE))
 
-  OpenMx::mxModel(
-    model_name,
-    buildPedigreeModelCovariance(
-      vars,
-      Vad = isTRUE(flags$Vad),
-      Vdd = isTRUE(flags$Vdd),
-      Vcn = isTRUE(flags$Vcn),
-      Vce = isTRUE(flags$Vce),
-      Vmt = isTRUE(flags$Vmt),
-      Vam = isTRUE(flags$Vam),
-      Ver = isTRUE(flags$Ver)
-    ),
-    group_models,
-    OpenMx::mxFitFunctionMultigroup(group_names),
-    ci = if (ci & any(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)) {
-      OpenMx::mxCI(c("vad", "vdd", "vcn", "vce", "vmt", "vam", "ver")[c(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)])
-    } else {
-      NULL
-    }
+  model_one <- buildPedigreeModelCovariance(
+    vars,
+    Vad = isTRUE(flags$Vad),
+    Vdd = isTRUE(flags$Vdd),
+    Vcn = isTRUE(flags$Vcn),
+    Vce = isTRUE(flags$Vce),
+    Vmt = isTRUE(flags$Vmt),
+    Vam = isTRUE(flags$Vam),
+    Ver = isTRUE(flags$Ver)
   )
+
+  ci_obj <- if (ci & any(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)) {
+    OpenMx::mxCI(c("vad", "vdd", "vcn", "vce", "vmt", "vam", "ver")[c(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)])
+  } else {
+    NULL
+  }
+
+  .assemblePedigreeMx(model_name, model_one, group_models, ci_obj)
 }
 
 #' Fit an OpenMx pedigree model to observed data
@@ -406,18 +762,46 @@ fitPedigreeModel <- function(
   )
   if (runmodel == TRUE) {
     if (tryhard == TRUE) {
-      fitted_model <- OpenMx::mxTryHard(pedigree_model, silent = TRUE, extraTries = extraTries, intervals = intervals)
+      return_model <- OpenMx::mxTryHard(pedigree_model, silent = TRUE, extraTries = extraTries, intervals = intervals)
     } else {
-      fitted_model <- OpenMx::mxRun(pedigree_model, intervals = intervals)
+      return_model <- OpenMx::mxRun(pedigree_model, intervals = intervals)
     }
   } else {
-    fitted_model <- pedigree_model
+    return_model <- pedigree_model
   }
 
-  fitted_model
+  return_model
 }
 
 
+#' Assemble the top-level pedigree mxModel (internal)
+#'
+#' Combines the covariance sub-model (named \code{"ModelOne"}), the family-group models,
+#' the multigroup fit function, and (optionally) a confidence-interval specification into
+#' one mxModel. Shared by both the static and temporal branches of
+#' \code{\link{buildPedigreeMx}}, which otherwise only differ in how \code{model_one}
+#' and \code{ci_obj} are built.
+#'
+#' @param model_name Name of the overall pedigree model.
+#' @param model_one The covariance sub-model (from \code{\link{buildPedigreeModelCovariance}}).
+#' @param group_models A list of OpenMx models for each family group.
+#' @param ci_obj An \code{mxCI} object to include, or NULL to omit confidence intervals.
+#' @return An OpenMx pedigree model.
+#' @keywords internal
+.assemblePedigreeMx <- function(model_name, model_one, group_models, ci_obj = NULL) {
+  group_names <- vapply(group_models, function(m) m$name, character(1))
+
+  model_parts <- c(
+    list(model_name),
+    list(model_one),
+    group_models,
+    list(OpenMx::mxFitFunctionMultigroup(group_names))
+  )
+  if (!is.null(ci_obj)) model_parts[[length(model_parts) + 1]] <- ci_obj
+
+  do.call(OpenMx::mxModel, model_parts)
+}
+
 #' Align Phenotype Vector to Matrix Format for OpenMx
 #'
 #' This function takes a pedigree data frame, a specified phenotype column, and a vector of IDs to keep, and returns a matrix formatted for use in OpenMx models. The resulting matrix has one row and columns corresponding to the specified IDs, with values taken from the phenotype column of the pedigree.
@@ -455,3 +839,15 @@ condenseMatrixSlots <- function(model) {
   # }
   OpenMx::imxConDecMatrixSlots(model)
 }
+
+#' Make Clean IDs for OpenMx
+#'
+#' This function takes a vector of IDs and returns a cleaned version suitable for use in OpenMx models. It replaces any illegal characters (such as '.') with underscores and ensures that the IDs are valid R variable names. This is important because OpenMx does not allow certain characters in matrix or variable names, which can lead to errors when building models.
+#' @param ids A vector of IDs to be cleaned.
+#' @return A vector of cleaned IDs suitable for use in OpenMx models.
+#'
+make_clean_personids <- function(ids) {
+  .require_openmx("make_clean_personids")
+  OpenMx::mxMakeNames(as.character(ids))
+}
+
diff --git a/man/buildFamilyGroups.Rd b/man/buildFamilyGroups.Rd
index fd5a4f3a..bf67c351 100644
--- a/man/buildFamilyGroups.Rd
+++ b/man/buildFamilyGroups.Rd
@@ -14,7 +14,9 @@ buildFamilyGroups(
   Amimat = NULL,
   Dmgmat = NULL,
   prefix = "fam",
-  condenseMatrixSlots = TRUE
+  condenseMatrixSlots = TRUE,
+  clean_ids = TRUE,
+  group_static_families = FALSE
 )
 }
 \arguments{
diff --git a/man/buildFamilyGroups_list.Rd b/man/buildFamilyGroups_list.Rd
new file mode 100644
index 00000000..1dd236c5
--- /dev/null
+++ b/man/buildFamilyGroups_list.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{buildFamilyGroups_list}
+\alias{buildFamilyGroups_list}
+\title{Build family group models with per-family relatedness matrices}
+\usage{
+buildFamilyGroups_list(
+  dat_list,
+  obs_ids_list,
+  Addmat_list = NULL,
+  Nucmat_list = NULL,
+  Extmat_list = NULL,
+  Mtdmat_list = NULL,
+  Amimat_list = NULL,
+  Dmgmat_list = NULL,
+  prefix = "fam",
+  condenseMatrixSlots = TRUE,
+  clean_ids = TRUE
+)
+}
+\arguments{
+\item{dat_list}{A list of numeric vectors of observed data, one per family.}
+
+\item{obs_ids_list}{A list of character vectors of individual IDs, one per family, matching
+\code{dat_list} and the rows/columns of that family's relatedness matrices.}
+
+\item{Addmat_list}{A list of additive genetic relatedness matrices, one per family.}
+
+\item{Nucmat_list}{A list of nuclear family shared environment relatedness matrices, one per family.}
+
+\item{Extmat_list}{A list of common extended family environment relatedness matrices, one per family.}
+
+\item{Mtdmat_list}{A list of mitochondrial genetic relatedness matrices, one per family.}
+
+\item{Amimat_list}{A list of additive by mitochondrial interaction relatedness matrices, one per family.}
+
+\item{Dmgmat_list}{A list of dominance genetic relatedness matrices, one per family.}
+
+\item{prefix}{A prefix for naming the family groups. Default is "fam".}
+
+\item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+
+\item{birth_year_list}{A list of numeric birth-year vectors, one per family, each matching
+the corresponding entry of \code{obs_ids_list}. Only used when \code{temporal = TRUE}.}
+
+\item{H_list}{A list of historical-moderator matrices, one per family. Only used when
+\code{temporal = TRUE}.}
+}
+\value{
+A list of OpenMx models for each family group.
+}
+\description{
+This function constructs OpenMx models for multiple family groups, each with its own
+relatedness matrices, observed IDs, and (for temporal models) birth years / historical
+moderators. Use this when families vary in size or structure; for families that all share
+the same relatedness matrices, see \code{\link{buildFamilyGroups}}.
+}
diff --git a/man/buildOneFamilyGroup.Rd b/man/buildOneFamilyGroup.Rd
index d9cf6b02..1cf09e62 100644
--- a/man/buildOneFamilyGroup.Rd
+++ b/man/buildOneFamilyGroup.Rd
@@ -14,7 +14,9 @@ buildOneFamilyGroup(
   Dmgmat = NULL,
   full_df_row,
   obs_ids,
-  condenseMatrixSlots = TRUE
+  symmetrize = FALSE,
+  condenseMatrixSlots = TRUE,
+  clean_ids = FALSE
 )
 }
 \arguments{
diff --git a/man/buildPedigreeMx.Rd b/man/buildPedigreeMx.Rd
index 69f07ee1..f01a66b0 100644
--- a/man/buildPedigreeMx.Rd
+++ b/man/buildPedigreeMx.Rd
@@ -9,7 +9,8 @@ buildPedigreeMx(
   vars,
   group_models,
   ci = FALSE,
-  condenseMatrixSlots = TRUE
+  condenseMatrixSlots = TRUE,
+  components = c("a", "e")
 )
 }
 \arguments{
@@ -22,6 +23,9 @@ buildPedigreeMx(
 \item{ci}{Logical. If TRUE, include confidence interval computations for the variance components. Default is FALSE}
 
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+
+\item{components}{Character vector of component keys to include (any of "a", "d", "cn",
+"ce", "mt", "am", "e"). Only used when \code{temporal = TRUE}. Default is \code{c("a", "e")}.}
 }
 \value{
 An OpenMx pedigree model combining variance components and family groups.
diff --git a/man/dot-assemblePedigreeMx.Rd b/man/dot-assemblePedigreeMx.Rd
new file mode 100644
index 00000000..cdb88cdf
--- /dev/null
+++ b/man/dot-assemblePedigreeMx.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{.assemblePedigreeMx}
+\alias{.assemblePedigreeMx}
+\title{Assemble the top-level pedigree mxModel (internal)}
+\usage{
+.assemblePedigreeMx(model_name, model_one, group_models, ci_obj = NULL)
+}
+\arguments{
+\item{model_name}{Name of the overall pedigree model.}
+
+\item{model_one}{The covariance sub-model (from \code{\link{buildPedigreeModelCovariance}}).}
+
+\item{group_models}{A list of OpenMx models for each family group.}
+
+\item{ci_obj}{An \code{mxCI} object to include, or NULL to omit confidence intervals.}
+}
+\value{
+An OpenMx pedigree model.
+}
+\description{
+Combines the covariance sub-model (named \code{"ModelOne"}), the family-group models,
+the multigroup fit function, and (optionally) a confidence-interval specification into
+one mxModel. Shared by both the static and temporal branches of
+\code{\link{buildPedigreeMx}}, which otherwise only differ in how \code{model_one}
+and \code{ci_obj} are built.
+}
+\keyword{internal}
diff --git a/man/dot-buildGroupedStaticFamily.Rd b/man/dot-buildGroupedStaticFamily.Rd
new file mode 100644
index 00000000..87a23e50
--- /dev/null
+++ b/man/dot-buildGroupedStaticFamily.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{.buildGroupedStaticFamily}
+\alias{.buildGroupedStaticFamily}
+\title{Build one grouped static family model}
+\usage{
+.buildGroupedStaticFamily(
+  group_name,
+  dat,
+  obs_ids,
+  Addmat = NULL,
+  Nucmat = NULL,
+  Extmat = NULL,
+  Mtdmat = NULL,
+  Amimat = NULL,
+  Dmgmat = NULL,
+  condenseMatrixSlots = TRUE,
+  clean_ids = FALSE
+)
+}
+\arguments{
+\item{group_name}{Name of the grouped family model.}
+
+\item{dat}{A matrix or data frame where each row represents an independent
+family and columns correspond to pedigree positions.}
+
+\item{obs_ids}{A character vector of individual IDs corresponding to the
+columns of \code{dat} and the rows/columns of the relatedness matrices.}
+
+\item{Addmat}{Additive genetic relatedness matrix (from \code{\link{ped2add}}).}
+
+\item{Nucmat}{Nuclear family shared environment relatedness matrix (from \code{\link{ped2cn}}).}
+
+\item{Extmat}{Common extended family environment relatedness matrix. When non-NULL,
+a Vce term scaled by this matrix is added to the covariance. If a non-matrix
+value (e.g. \code{TRUE}) is supplied, a unit matrix (all members share equally)
+is created automatically.}
+
+\item{Mtdmat}{Mitochondrial genetic relatedness matrix (from \code{\link{ped2mit}}).}
+
+\item{Amimat}{Additive by mitochondrial interaction relatedness matrix.}
+
+\item{Dmgmat}{Dominance genetic relatedness matrix.}
+
+\item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+}
+\value{
+An OpenMx model containing all static family observations.
+}
+\description{
+This function constructs one OpenMx model for multiple independent family
+observations that share the same pedigree structure, relatedness matrices,
+variable ordering, expected covariance matrix, and expected mean vector.
+}
+\details{
+The observed data contain one family per row. The shared matrices, covariance
+algebra, expectation, and fit function are stored only once rather than once
+per family.
+}
+\keyword{internal}
diff --git a/man/dot-pedigreeFamilySize.Rd b/man/dot-pedigreeFamilySize.Rd
new file mode 100644
index 00000000..6287c600
--- /dev/null
+++ b/man/dot-pedigreeFamilySize.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{.pedigreeFamilySize}
+\alias{.pedigreeFamilySize}
+\title{Determine family size from a family's relatedness matrices (internal)}
+\usage{
+.pedigreeFamilySize(mats_in)
+}
+\arguments{
+\item{mats_in}{A list of relatedness matrices (possibly containing NULLs); the first
+non-NULL matrix's row count is used as the family size.}
+}
+\value{
+Integer family size.
+}
+\description{
+Determine family size from a family's relatedness matrices (internal)
+}
+\keyword{internal}
diff --git a/man/dot-pedigreeMeanMatrix.Rd b/man/dot-pedigreeMeanMatrix.Rd
new file mode 100644
index 00000000..0fd9ceb7
--- /dev/null
+++ b/man/dot-pedigreeMeanMatrix.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{.pedigreeMeanMatrix}
+\alias{.pedigreeMeanMatrix}
+\title{Build the free mean mxMatrix for a family group (internal)}
+\usage{
+.pedigreeMeanMatrix(fsize, obs_ids, label)
+}
+\arguments{
+\item{fsize}{Family size.}
+
+\item{obs_ids}{Character vector of individual IDs.}
+
+\item{label}{The mean parameter's label.}
+}
+\value{
+An mxMatrix object.
+}
+\description{
+Shared by the static and temporal branches of \code{\link{buildOneFamilyGroup}}; they
+only differ in the parameter label ("meanLI" vs "mean_y").
+}
+\keyword{internal}
diff --git a/man/dot-pedigreeRelatednessMatrix.Rd b/man/dot-pedigreeRelatednessMatrix.Rd
new file mode 100644
index 00000000..dd4d3c48
--- /dev/null
+++ b/man/dot-pedigreeRelatednessMatrix.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{.pedigreeRelatednessMatrix}
+\alias{.pedigreeRelatednessMatrix}
+\title{Build a relatedness mxMatrix (internal)}
+\usage{
+.pedigreeRelatednessMatrix(
+  mat,
+  fsize,
+  name,
+  condense = TRUE,
+  symmetrize = FALSE
+)
+}
+\arguments{
+\item{mat}{The relatedness matrix.}
+
+\item{fsize}{Family size.}
+
+\item{name}{The mxMatrix's name (e.g. "A", "Cn").}
+
+\item{condense}{Logical. If TRUE, apply \code{\link{condenseMatrixSlots}}.}
+
+\item{symmetrize}{Logical. If TRUE, symmetrize \code{mat} via \code{\link{make_symmetric}}
+before use; if FALSE, coerce via \code{as.matrix} only.}
+}
+\value{
+An mxMatrix object.
+}
+\description{
+Builds the \code{"Symm"} mxMatrix for one relatedness matrix.
+}
+\keyword{internal}
diff --git a/man/make_clean_personids.Rd b/man/make_clean_personids.Rd
new file mode 100644
index 00000000..5b96e50d
--- /dev/null
+++ b/man/make_clean_personids.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildmxPedigrees.R
+\name{make_clean_personids}
+\alias{make_clean_personids}
+\title{Make Clean IDs for OpenMx}
+\usage{
+make_clean_personids(ids)
+}
+\arguments{
+\item{ids}{A vector of IDs to be cleaned.}
+}
+\value{
+A vector of cleaned IDs suitable for use in OpenMx models.
+}
+\description{
+This function takes a vector of IDs and returns a cleaned version suitable for use in OpenMx models. It replaces any illegal characters (such as '.') with underscores and ensures that the IDs are valid R variable names. This is important because OpenMx does not allow certain characters in matrix or variable names, which can lead to errors when building models.
+}
diff --git a/tests/testthat/test-buildmxPedigrees.R b/tests/testthat/test-buildmxPedigrees.R
index f97227f4..1c6d0200 100644
--- a/tests/testthat/test-buildmxPedigrees.R
+++ b/tests/testthat/test-buildmxPedigrees.R
@@ -96,7 +96,7 @@ test_that("buildPedigreeModelCovariance works with minimal components (Vad + Ver
 test_that("buildOneFamilyGroup errors when no relatedness matrix is provided", {
   skip_if_not_installed("OpenMx")
   dat <- make_dat2()
-  expect_error(
+  expect_warning(
     buildOneFamilyGroup(
       group_name = "fam1",
       Addmat = NULL, Nucmat = NULL, Extmat = NULL,
@@ -104,7 +104,7 @@ test_that("buildOneFamilyGroup errors when no relatedness matrix is provided", {
       full_df_row = dat,
       obs_ids = c("y1", "y2")
     ),
-    regexp = "At least one relatedness matrix must be provided"
+    regexp = "At least one relatedness matrix should be provided"
   )
 })
 

From 1e9dbdd09913e6f28293c7e33497270651f48449 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 10:43:31 -0400
Subject: [PATCH 06/11] Update addParentalChain.R

---
 R/addParentalChain.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/addParentalChain.R b/R/addParentalChain.R
index c0cad13b..7a468250 100644
--- a/R/addParentalChain.R
+++ b/R/addParentalChain.R
@@ -197,12 +197,11 @@ addParentalChain <- function(
     }
 
     # Find all nodes reachable from this person by following paternal edges.
-    reachable_ids <- igraph::subcomponent(
+    reachable_ids <- names(igraph::subcomponent(
       graph = parental_graph,
       v = id_chr,
       mode = traversal_direction
-    ) |>
-      names()
+    ))
 
     # Remove the person themselves from their paternal ancestor list.
     reachable_ids <- setdiff(reachable_ids, id_chr)

From 28b376d8b8f9caec7075d50c15b36b5d110230fa Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 10:47:24 -0400
Subject: [PATCH 07/11] documentation

---
 R/buildmxPedigrees.R                | 53 +++++++++++++++--------------
 R/checkParents.R                    | 20 +++++------
 R/helpGeneric.R                     |  2 +-
 data-raw/benchmark_rowlessParents.R |  2 +-
 man/buildFamilyGroups.Rd            |  2 ++
 man/buildFamilyGroups_list.Rd       |  2 ++
 man/buildOneFamilyGroup.Rd          |  4 +++
 man/dot-buildGroupedStaticFamily.Rd |  2 ++
 8 files changed, 49 insertions(+), 38 deletions(-)

diff --git a/R/buildmxPedigrees.R b/R/buildmxPedigrees.R
index 6ec04664..76fc5306 100644
--- a/R/buildmxPedigrees.R
+++ b/R/buildmxPedigrees.R
@@ -177,6 +177,8 @@ buildPedigreeModelCovariance <- function(
 #'   \code{full_df_row} and the rows/columns of the relatedness matrices. Must be in the
 #'   same order as the relatedness matrix rows.
 #' @param condenseMatrixSlots Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.
+#' @param clean_ids Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.
+#' @param symmetrize Logical. If TRUE, symmetrize the relatedness matrices before use. Default is FALSE.
 #' @return An OpenMx model for the specified family group.
 #' @export
 
@@ -203,7 +205,7 @@ buildOneFamilyGroup <- function(
   # Determine family size from first available matrix. Shared by both branches below.
   if ( # not any of the matrices are provided
     is.null(Addmat) && is.null(Dmgmat) && is.null(Nucmat) &&
-    is.null(Extmat) && is.null(Mtdmat) && is.null(Amimat)
+      is.null(Extmat) && is.null(Mtdmat) && is.null(Amimat)
   ) {
     warning("At least one relatedness matrix should be provided. Using the number of columns in 'full_df_row' as family size.")
     fsize <- ncol(full_df_row)
@@ -293,7 +295,7 @@ buildOneFamilyGroup <- function(
       OpenMx::mxData(observed = full_df_row, type = "raw", sort = FALSE),
       .pedigreeMeanMatrix(fsize, obs_ids, "meanLI"),
       OpenMx::mxAlgebraFromString(algebra_str,
-                                  name = "V", dimnames = list(obs_ids, obs_ids)
+        name = "V", dimnames = list(obs_ids, obs_ids)
       ),
       OpenMx::mxExpectationNormal(covariance = "V", means = "M"),
       OpenMx::mxFitFunctionML()
@@ -322,17 +324,17 @@ buildOneFamilyGroup <- function(
 #' @return An OpenMx model containing all static family observations.
 #' @keywords internal
 .buildGroupedStaticFamily <- function(
-    group_name,
-    dat,
-    obs_ids,
-    Addmat = NULL,
-    Nucmat = NULL,
-    Extmat = NULL,
-    Mtdmat = NULL,
-    Amimat = NULL,
-    Dmgmat = NULL,
-    condenseMatrixSlots = TRUE,
-    clean_ids = FALSE
+  group_name,
+  dat,
+  obs_ids,
+  Addmat = NULL,
+  Nucmat = NULL,
+  Extmat = NULL,
+  Mtdmat = NULL,
+  Amimat = NULL,
+  Dmgmat = NULL,
+  condenseMatrixSlots = TRUE,
+  clean_ids = FALSE
 ) {
   .require_openmx(".buildGroupedStaticFamily")
 
@@ -563,17 +565,17 @@ buildFamilyGroups <- function(
 #' @export
 
 buildFamilyGroups_list <- function(
-    dat_list,
-    obs_ids_list,
-    Addmat_list = NULL,
-    Nucmat_list = NULL,
-    Extmat_list = NULL,
-    Mtdmat_list = NULL,
-    Amimat_list = NULL,
-    Dmgmat_list = NULL,
-    prefix = "fam",
-    condenseMatrixSlots = TRUE,
-    clean_ids = TRUE
+  dat_list,
+  obs_ids_list,
+  Addmat_list = NULL,
+  Nucmat_list = NULL,
+  Extmat_list = NULL,
+  Mtdmat_list = NULL,
+  Amimat_list = NULL,
+  Dmgmat_list = NULL,
+  prefix = "fam",
+  condenseMatrixSlots = TRUE,
+  clean_ids = TRUE
 ) {
   .require_openmx("buildFamilyGroups_list")
 
@@ -675,7 +677,7 @@ buildPedigreeMx <- function(model_name, vars, group_models,
     Ver = isTRUE(flags$Ver)
   )
 
-  ci_obj <- if (ci & any(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)) {
+  ci_obj <- if (ci && any(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)) {
     OpenMx::mxCI(c("vad", "vdd", "vcn", "vce", "vmt", "vam", "ver")[c(flags$Vad, flags$Vdd, flags$Vcn, flags$Vce, flags$Vmt, flags$Vam, flags$Ver)])
   } else {
     NULL
@@ -850,4 +852,3 @@ make_clean_personids <- function(ids) {
   .require_openmx("make_clean_personids")
   OpenMx::mxMakeNames(as.character(ids))
 }
-
diff --git a/R/checkParents.R b/R/checkParents.R
index 6b32dd07..c720fdcb 100644
--- a/R/checkParents.R
+++ b/R/checkParents.R
@@ -111,17 +111,17 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   # Are any parents in both momID and dadID?
   momdad <- intersect(ped$dadID, ped$momID)
   momdad <- momdad[!is.na(momdad)]
-if (length(momdad) > 0) {
-  validation_results$parents_in_both <- momdad
-  if (verbose == TRUE) {
-    cat(
-      "Some individuals appear in both momID and dadID roles.\n",
-      "These individuals are:\n",
-      sep = ""
-    )
-    message(paste(momdad, collapse = ", "))
+  if (length(momdad) > 0) {
+    validation_results$parents_in_both <- momdad
+    if (verbose == TRUE) {
+      cat(
+        "Some individuals appear in both momID and dadID roles.\n",
+        "These individuals are:\n",
+        sep = ""
+      )
+      message(paste(momdad, collapse = ", "))
+    }
   }
-}
 
 
   if (!repair) {
diff --git a/R/helpGeneric.R b/R/helpGeneric.R
index 0c350777..2bb0c4e6 100644
--- a/R/helpGeneric.R
+++ b/R/helpGeneric.R
@@ -129,7 +129,7 @@ as_numeric_matrix <- function(x) {
 #' @return A numeric matrix, symmetrized if needed.
 #'
 make_symmetric <- function(x, tol = 1e-10) {
-    if (inherits(x, "sparseMatrix")) {
+  if (inherits(x, "sparseMatrix")) {
     if (!Matrix::isSymmetric(x, tol = tol)) {
       x <- (x + Matrix::t(x)) / 2
     }
diff --git a/data-raw/benchmark_rowlessParents.R b/data-raw/benchmark_rowlessParents.R
index 3928f040..e4f09331 100644
--- a/data-raw/benchmark_rowlessParents.R
+++ b/data-raw/benchmark_rowlessParents.R
@@ -130,7 +130,7 @@ df_plot <- benchmark_results %>% mutate(
     ) ~ "big"
   ),
   method = case_when(
-       expr %in% c("base_small", "base_big") ~ "base",
+    expr %in% c("base_small", "base_big") ~ "base",
     expr %in% c("rows_small", "rows_big") ~ "rows",
     expr %in% c("schur_small", "schur_big") ~ "schur"
   ) # make base the reference level for the linear model, so that the intercept is the mean of the base method
diff --git a/man/buildFamilyGroups.Rd b/man/buildFamilyGroups.Rd
index bf67c351..7242ee48 100644
--- a/man/buildFamilyGroups.Rd
+++ b/man/buildFamilyGroups.Rd
@@ -43,6 +43,8 @@ is created automatically.}
 \item{prefix}{A prefix for naming the family groups. Default is "fam".}
 
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+
+\item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
 }
 \value{
 A list of OpenMx models for each family group.
diff --git a/man/buildFamilyGroups_list.Rd b/man/buildFamilyGroups_list.Rd
index 1dd236c5..f27ac18e 100644
--- a/man/buildFamilyGroups_list.Rd
+++ b/man/buildFamilyGroups_list.Rd
@@ -40,6 +40,8 @@ buildFamilyGroups_list(
 
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
 
+\item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
+
 \item{birth_year_list}{A list of numeric birth-year vectors, one per family, each matching
 the corresponding entry of \code{obs_ids_list}. Only used when \code{temporal = TRUE}.}
 
diff --git a/man/buildOneFamilyGroup.Rd b/man/buildOneFamilyGroup.Rd
index 1cf09e62..2800d569 100644
--- a/man/buildOneFamilyGroup.Rd
+++ b/man/buildOneFamilyGroup.Rd
@@ -43,7 +43,11 @@ is created automatically.}
 \code{full_df_row} and the rows/columns of the relatedness matrices. Must be in the
 same order as the relatedness matrix rows.}
 
+\item{symmetrize}{Logical. If TRUE, symmetrize the relatedness matrices before use. Default is FALSE.}
+
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+
+\item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
 }
 \value{
 An OpenMx model for the specified family group.
diff --git a/man/dot-buildGroupedStaticFamily.Rd b/man/dot-buildGroupedStaticFamily.Rd
index 87a23e50..daada573 100644
--- a/man/dot-buildGroupedStaticFamily.Rd
+++ b/man/dot-buildGroupedStaticFamily.Rd
@@ -43,6 +43,8 @@ is created automatically.}
 \item{Dmgmat}{Dominance genetic relatedness matrix.}
 
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
+
+\item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
 }
 \value{
 An OpenMx model containing all static family observations.

From 8d609b2a157a027057899adfa2a26db661a65f19 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 11:19:29 -0400
Subject: [PATCH 08/11] missed documentation

---
 R/buildmxPedigrees.R     | 7 ++++++-
 man/buildFamilyGroups.Rd | 2 ++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/buildmxPedigrees.R b/R/buildmxPedigrees.R
index 76fc5306..a412c0f3 100644
--- a/R/buildmxPedigrees.R
+++ b/R/buildmxPedigrees.R
@@ -476,6 +476,7 @@ buildOneFamilyGroup <- function(
 #' @param obs_ids A character vector of individual IDs corresponding to the columns of \code{dat}
 #'   and the rows/columns of the relatedness matrices.
 #' @param prefix A prefix for naming the family groups. Default is "fam".
+#' @param group_static_families Logical. If TRUE, build one grouped static family model instead of separate models for each family. Default is FALSE.
 #' @return A list of OpenMx models for each family group.
 #' @export
 
@@ -683,7 +684,11 @@ buildPedigreeMx <- function(model_name, vars, group_models,
     NULL
   }
 
-  .assemblePedigreeMx(model_name, model_one, group_models, ci_obj)
+  .assemblePedigreeMx(
+    model_name = model_name,
+    model_one = model_one,
+    group_models = group_models,
+    ci_obj  = ci_obj)
 }
 
 #' Fit an OpenMx pedigree model to observed data
diff --git a/man/buildFamilyGroups.Rd b/man/buildFamilyGroups.Rd
index 7242ee48..1a7e3d3d 100644
--- a/man/buildFamilyGroups.Rd
+++ b/man/buildFamilyGroups.Rd
@@ -45,6 +45,8 @@ is created automatically.}
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
 
 \item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
+
+\item{group_static_families}{Logical. If TRUE, build one grouped static family model instead of separate models for each family. Default is FALSE.}
 }
 \value{
 A list of OpenMx models for each family group.

From 461899e6e32ab84f69e1912ea19d1f1602bb818b Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 13:43:06 -0400
Subject: [PATCH 09/11] Refactor .pedigreeRelatednessMatrix for matrix handling

Updated the .pedigreeRelatednessMatrix function to ensure that the matrix is always coerced to a base dense matrix after symmetrization. Added error handling for matrix creation.
---
 R/buildmxPedigrees.R | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/R/buildmxPedigrees.R b/R/buildmxPedigrees.R
index a412c0f3..6b53312e 100644
--- a/R/buildmxPedigrees.R
+++ b/R/buildmxPedigrees.R
@@ -122,16 +122,21 @@ buildPedigreeModelCovariance <- function(
 #' @keywords internal
 .pedigreeRelatednessMatrix <- function(mat, fsize, name, condense = TRUE, symmetrize = FALSE) {
   if (is.null(mat)) stop("Relatedness matrix cannot be NULL.")
-  # keep dense if dense, or sparse if sparse, but symmetrize if requested
-  if (inherits(mat, "Matrix")) {
-    values <- if (symmetrize) make_symmetric(mat) else mat
-  } else {
-    values <- if (symmetrize) make_symmetric(mat) else as.matrix(mat)
-  }
-  m <- OpenMx::mxMatrix(
+ # Symmetrize if requested, then coerce to a base dense matrix. OpenMx::mxMatrix()
+  # accepts only a scalar, vector, or base R matrix for 'values'; a Matrix-package
+  # sparse object (e.g. the dsCMatrix returned by ped2add(sparse = TRUE)) is rejected
+  # by matrixCheckArgument(), so it must be densified here.
+  values <- if (symmetrize) make_symmetric(mat) else mat
+  values <- as.matrix(values)
+ #todo allow this to be sparse and use sparse algebra in OpenMx
+  m <-   tryCatch( OpenMx::mxMatrix(
     type = "Symm", nrow = fsize, ncol = fsize, free = FALSE,
     values = values, name = name
-  )
+  ), error = function(e) {
+    print(values)
+    stop("Error creating mxMatrix for ", name, ": ", e$message)
+  })
+
   if (condense) m <- condenseMatrixSlots(m)
   m
 }
@@ -575,6 +580,8 @@ buildFamilyGroups_list <- function(
   Amimat_list = NULL,
   Dmgmat_list = NULL,
   prefix = "fam",
+  birth_year_list = NULL,
+  H_list = NULL,
   condenseMatrixSlots = TRUE,
   clean_ids = TRUE
 ) {

From 0be0c1f63ec08809292bb3b4bb47af05baadc4a5 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 13:57:34 -0400
Subject: [PATCH 10/11] fix warning about paramets

---
 R/buildmxPedigrees.R                 | 8 ++------
 man/buildFamilyGroups_list.Rd        | 6 ------
 tests/testthat/test-rowlessParents.R | 2 +-
 3 files changed, 3 insertions(+), 13 deletions(-)

diff --git a/R/buildmxPedigrees.R b/R/buildmxPedigrees.R
index 6b53312e..704ca3a2 100644
--- a/R/buildmxPedigrees.R
+++ b/R/buildmxPedigrees.R
@@ -184,6 +184,7 @@ buildPedigreeModelCovariance <- function(
 #' @param condenseMatrixSlots Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.
 #' @param clean_ids Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.
 #' @param symmetrize Logical. If TRUE, symmetrize the relatedness matrices before use. Default is FALSE.
+
 #' @return An OpenMx model for the specified family group.
 #' @export
 
@@ -325,6 +326,7 @@ buildOneFamilyGroup <- function(
 #'   family and columns correspond to pedigree positions.
 #' @param obs_ids A character vector of individual IDs corresponding to the
 #'   columns of \code{dat} and the rows/columns of the relatedness matrices.
+#'
 #' @inheritParams buildOneFamilyGroup
 #' @return An OpenMx model containing all static family observations.
 #' @keywords internal
@@ -563,10 +565,6 @@ buildFamilyGroups <- function(
 #' @param Amimat_list A list of additive by mitochondrial interaction relatedness matrices, one per family.
 #' @param Dmgmat_list A list of dominance genetic relatedness matrices, one per family.
 #' @param prefix A prefix for naming the family groups. Default is "fam".
-#' @param birth_year_list A list of numeric birth-year vectors, one per family, each matching
-#'   the corresponding entry of \code{obs_ids_list}. Only used when \code{temporal = TRUE}.
-#' @param H_list A list of historical-moderator matrices, one per family. Only used when
-#'   \code{temporal = TRUE}.
 #' @return A list of OpenMx models for each family group.
 #' @export
 
@@ -580,8 +578,6 @@ buildFamilyGroups_list <- function(
   Amimat_list = NULL,
   Dmgmat_list = NULL,
   prefix = "fam",
-  birth_year_list = NULL,
-  H_list = NULL,
   condenseMatrixSlots = TRUE,
   clean_ids = TRUE
 ) {
diff --git a/man/buildFamilyGroups_list.Rd b/man/buildFamilyGroups_list.Rd
index f27ac18e..c708a66e 100644
--- a/man/buildFamilyGroups_list.Rd
+++ b/man/buildFamilyGroups_list.Rd
@@ -41,12 +41,6 @@ buildFamilyGroups_list(
 \item{condenseMatrixSlots}{Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.}
 
 \item{clean_ids}{Logical. If TRUE, clean the \code{obs_ids} using \code{\link{make_clean_personids}}. Default is FALSE.}
-
-\item{birth_year_list}{A list of numeric birth-year vectors, one per family, each matching
-the corresponding entry of \code{obs_ids_list}. Only used when \code{temporal = TRUE}.}
-
-\item{H_list}{A list of historical-moderator matrices, one per family. Only used when
-\code{temporal = TRUE}.}
 }
 \value{
 A list of OpenMx models for each family group.
diff --git a/tests/testthat/test-rowlessParents.R b/tests/testthat/test-rowlessParents.R
index 4a9dec5f..f467a6fc 100644
--- a/tests/testthat/test-rowlessParents.R
+++ b/tests/testthat/test-rowlessParents.R
@@ -19,7 +19,7 @@ test_that("ped2add warns when momID/dadID reference parents with no row", {
   expect_warning(
     ped2add(ped_rowless, sparse = FALSE),
     "no matching row"
-  )
+  ) |> suppressWarnings()  #
 })
 
 test_that("repair_rowless_parents = TRUE fixes diagonal and sibling relatedness without warning, and does not grow the returned matrix", {

From 9b7d43fb67a066bacd279e5620fb4ebb299d92ff Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Sun, 12 Jul 2026 17:51:52 -0400
Subject: [PATCH 11/11] Update test-helpGeneric.R

---
 tests/testthat/test-helpGeneric.R | 34 +++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/tests/testthat/test-helpGeneric.R b/tests/testthat/test-helpGeneric.R
index 20097167..e5e73da7 100644
--- a/tests/testthat/test-helpGeneric.R
+++ b/tests/testthat/test-helpGeneric.R
@@ -67,3 +67,37 @@ test_that("functions issue a deprecation warning", {
   expect_warning(related_coef(), "deprecated")
   expect_warning(relatedness(obsR = .5), "deprecated")
 })
+
+test_that("as_numeric_matrix coerces a data.frame to a numeric matrix", {
+  df <- data.frame(a = c(1L, 2L), b = c(3L, 4L))
+  result <- as_numeric_matrix(df)
+  expect_true(is.matrix(result))
+  expect_equal(storage.mode(result), "double")
+  expect_equal(unname(result[1, 1]), 1)
+})
+
+test_that("as_numeric_matrix passes through an already-numeric matrix", {
+  m <- matrix(c(1.5, 2.5, 3.5, 4.5), nrow = 2)
+  result <- as_numeric_matrix(m)
+  expect_equal(result, m)
+})
+
+test_that("make_symmetric leaves an already-symmetric matrix unchanged", {
+  m <- matrix(c(1, 0.5, 0.5, 1), nrow = 2)
+  expect_equal(make_symmetric(m), m)
+})
+
+test_that("make_symmetric averages a matrix with its transpose when asymmetric", {
+  m <- matrix(c(1, 0.4, 0.6, 1), nrow = 2)
+  result <- make_symmetric(m)
+  expect_equal(result[1, 2], 0.5)
+  expect_equal(result[2, 1], 0.5)
+  expect_true(isSymmetric(result))
+})
+
+test_that("make_symmetric treats differences within tol as already symmetric", {
+  m <- matrix(c(1, 0.5, 0.5 + 1e-12, 1), nrow = 2)
+  result <- make_symmetric(m)
+  # Below tolerance: returned as-is, not averaged
+  expect_equal(result[1, 2], m[1, 2])
+})