Fit an OpenMx pedigree model to observed data

This function constructs and fits an OpenMx model for a pedigree using specified variance components and family group models.

Usage

fitPedigreeModel(
  model_name = "PedigreeModel",
  vars = list(ad2 = 0.5, dd2 = 0.3, cn2 = 0.2, ce2 = 0.4, mt2 = 0.1, am2 = 0.25, ee2 =
    0.6),
  data = NULL,
  group_models = NULL,
  Addmat = NULL,
  Nucmat = NULL,
  Extmat = NULL,
  Mtdmat = NULL,
  Amimat = NULL,
  Dmgmat = NULL,
  tryhard = TRUE,
  intervals = TRUE,
  extraTries = 10,
  condenseMatrixSlots = TRUE
)

Arguments

model_name

Character. Name for the overall OpenMx model. Default is "PedigreeModel".

vars

A named list or vector of initial variance component values.

data

A matrix or data frame of observed data, where each row is a family and columns correspond to individuals. Only used when group_models is NULL.

group_models

Optional list of pre-built OpenMx family group models (from buildOneFamilyGroup). If NULL, they are generated from data using the provided relatedness matrices.

Addmat

Additive genetic relatedness matrix (from ped2add).

Nucmat

Nuclear family shared environment relatedness matrix (from ped2cn).

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. TRUE) is supplied, a unit matrix (all members share equally) is created automatically.

Mtdmat

Mitochondrial genetic relatedness matrix (from ped2mit).

Amimat

Additive by mitochondrial interaction relatedness matrix.

Dmgmat

Dominance genetic relatedness matrix.

tryhard

Logical. If TRUE (default), use mxTryHard for robust optimization; if FALSE, use mxRun.

intervals

Logical. If TRUE (default), compute confidence intervals for the parameters using mxSE and mxCI.

extraTries

Numeric. The number of extra optimization attempts to make when tryhard is TRUE. Default is 10.

condenseMatrixSlots

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

Value

A fitted OpenMx model.