Fit a Temporal OpenMx Pedigree Model to Observed Data

Wrapper around fitPedigreeModel with temporal = TRUE, exposing only the temporal-relevant arguments.

Usage

fitTemporalPedigreeModel(
  model_name = "TemporalPedigreeModel",
  group_models = NULL,
  dat_list = NULL,
  obs_ids_list = NULL,
  param_year_list = NULL,
  H_list = NULL,
  Addmat_list = NULL,
  Nucmat_list = NULL,
  Extmat_list = NULL,
  Mtdmat_list = NULL,
  Amimat_list = NULL,
  Dmgmat_list = NULL,
  p_hist = NULL,
  components = c("a", "d", "cn", "ce", "mt", "e"),
  use_exp_loadings = FALSE,
  tryhard = TRUE,
  intervals = TRUE,
  extraTries = 10,
  runmodel = TRUE,
  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,
  clean_ids = FALSE
)

Arguments

model_name

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

group_models

Optional list of pre-built OpenMx family group models (from buildOneFamilyGroup). If NULL, they are generated from data (or, when temporal = TRUE, from dat_list and friends) using the provided relatedness matrices.

dat_list

A list of numeric vectors of observed data, one per family. Only used when temporal = TRUE and group_models is NULL.

obs_ids_list

A list of character vectors of individual IDs, one per family. Only used when temporal = TRUE and group_models is NULL.

param_year_list

A list of numeric birth-year vectors, one per family. Only used when temporal = TRUE and group_models is NULL.

H_list

A list of historical-moderator matrices, one per family. Only used when temporal = TRUE.

Addmat_list

A list of additive genetic relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

Nucmat_list

A list of nuclear family shared environment relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

Extmat_list

A list of common extended family environment relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

Mtdmat_list

A list of mitochondrial genetic relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

Amimat_list

A list of additive by mitochondrial interaction relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

Dmgmat_list

A list of dominance genetic relatedness matrices, one per family. Only used when temporal = TRUE and group_models is NULL.

p_hist

Integer. Number of historical moderator columns. Only used when temporal = TRUE. If NULL, inferred from H_list.

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").

use_exp_loadings

Logical. If TRUE (default), each component's loading is exponentiated so its implied variance stays positive. Only used when temporal = TRUE.

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.

runmodel

Logical. If TRUE (default), the model is fitted; if FALSE, the model is returned without fitting.

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.

clean_ids

Logical. If TRUE, clean the obs_ids to be syntactically valid R names using make.names. Default is FALSE.

Value

A fitted OpenMx model.