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Build Temporal Family Group Models with Per-Family Relatedness Matrices

Source: R/buildTemporalPedigreeModel.R
buildTemporalFamilyGroups_list.Rd

Wrapper around buildFamilyGroups_list with temporal = TRUE. Use this when families vary in size or structure.

Usage

buildTemporalFamilyGroups_list(
  dat_list,
  obs_ids_list,
  param_year_list,
  H_list,
  Addmat_list = NULL,
  Nucmat_list = NULL,
  Extmat_list = NULL,
  Mtdmat_list = NULL,
  Amimat_list = NULL,
  Dmgmat_list = NULL,
  prefix = "fam",
  use_exp_loadings = FALSE,
  condenseMatrixSlots = TRUE,
  time_point_max = NULL,
  clean_ids = FALSE
)

Arguments

dat_list

A list of numeric vectors of observed data, one per family.

obs_ids_list

A list of character vectors of individual IDs, one per family, matching dat_list and the rows/columns of that family's relatedness matrices.

param_year_list

A list of numeric birth-year vectors, one per family, each matching the corresponding entry of obs_ids_list. Only used when temporal = TRUE.

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.

Nucmat_list

A list of nuclear family shared environment relatedness matrices, one per family.

Extmat_list

A list of common extended family environment relatedness matrices, one per family.

Mtdmat_list

A list of mitochondrial genetic relatedness matrices, one per family.

Amimat_list

A list of additive by mitochondrial interaction relatedness matrices, one per family.

Dmgmat_list

A list of dominance genetic relatedness matrices, one per family.

prefix

A prefix for naming the family groups. Default is "fam".

use_exp_loadings

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

condenseMatrixSlots

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

time_point_max

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

clean_ids

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

Value

A list of OpenMx models for each family group.