Build Pedigree mxModel

This function constructs an OpenMx pedigree model by combining variance component parameters and family group models. For static (temporal = FALSE) models, it auto-detects which variance components are referenced in the group algebras and creates only those parameters.

Usage

buildPedigreeMx(
  model_name,
  vars,
  group_models,
  ci = FALSE,
  condenseMatrixSlots = TRUE,
  temporal = FALSE,
  p_hist = 0,
  param_year = NULL,
  components = c("a", "e"),
  ci_names = NULL,
  time_point_max = NULL,
  start_beta0 = 0.5,
  start_beta_time = 0,
  start_gamma = 0,
  mean_degree = 0,
  start_mean = 0,
  mean_hist_free = FALSE,
  start_mean_hist = 0
)

Arguments

model_name

Name of the overall pedigree model.

vars

A named list or vector of initial variance component values. Only used when temporal = FALSE.

group_models

A list of OpenMx models for each family group.

ci

Logical. If TRUE, include confidence interval computations for the variance components. Default is FALSE

condenseMatrixSlots

Logical. If TRUE, use the mxCondenseMatrixSlots wrapper to optimize memory usage for large matrices. Default is TRUE.

temporal

Logical. If TRUE, build a time-varying family-group model where each component's weight is a function of param_year (and, optionally, H) instead of a fixed scalar. Default is FALSE.

p_hist

Integer. Number of historical moderator columns. Only used when temporal = TRUE. Default is 0.

param_year

Numeric vector of birth years (or another time index), one per member of the family, in the same order as obs_ids. Only used when temporal = TRUE.

components

Character vector of component keys to include (any of "a", "d", "cn", "ce", "mt", "am", "e"). Only used when temporal = TRUE. Default is c("a", "e").

ci_names

A vector of parameters for confidence intervals. If not provided, it is derived from components

time_point_max

Integer degree of the polynomial birth-year basis. Only used when temporal = TRUE. Default is 3.

start_beta0

Numeric. Starting value for each component's intercept loading. Only used when temporal = TRUE. Default is 0.5.

start_beta_time

Numeric. Starting value for each component's time-slope loadings. Only used when temporal = TRUE. Default is 0.

start_gamma

Numeric. Starting value for historical-moderator loadings. Only used when temporal = TRUE. Default is 0.

mean_degree

Integer. Degree of the polynomial temporal mean. The default, 0, estimates a constant mean. Must not exceed time_point_max.

start_mean

Numeric. Starting value for the mean's intercept. Set this near the observed phenotype mean.

mean_hist_free

Logical, length 1 or p_hist. Whether historical moderators can shift the phenotypic mean. Defaults to FALSE, fixing those shifts at zero.

start_mean_hist

Numeric. Starting value for the free elements of G_mean.

Value

An OpenMx pedigree model combining variance components and family groups.