Concordance Probability from Twostage Model — p11_binomial_twostage

Computes concordance probability (joint probability of both subjects experiencing the event) given dependence parameters and random-effect variance structures from a twostage model.

Computes concordance probabilities for twin ACE/ADE models from a binomial twostage object.

Functions for constructing random-effects design matrices for twin and family models. These designs specify the genetic (A), dominance (D), common environment (C), and unique environment (E) variance components.

Usage

p11_binomial_twostage_RV(
  theta,
  rv1,
  rv2,
  p1,
  p2,
  pardes,
  ags = NULL,
  link = 0,
  i = 1,
  j = 1
)

concordanceTwostage(
  theta,
  p,
  rv1,
  rv2,
  theta.des,
  additive.gamma.sum = NULL,
  link = 0,
  var.par = 0,
  ...
)

concordanceTwinACE(
  object,
  rv1 = NULL,
  rv2 = NULL,
  xmarg = NULL,
  type = "ace",
  ...
)

kendall_ClaytonOakes_twin_ace(parg, parc, K = 10000, test = 0)

kendall.ClaytonOakes.twin.ace(x, y, ...)

kendall_normal_twin_ace(parg, parc, K = 10000)

ascertained_pairs(pairs, data, cr.models, bin = FALSE)

twin.polygen.design(x, ...)

ace_family_design(
  data,
  id = "id",
  member = "type",
  mother = "mother",
  father = "father",
  child = "child",
  child1 = "child",
  type = "ace",
  ...
)

make_pairwise_design(pairs, kinship, type = "ace")

Arguments

theta: dependence parameter vector.
rv1: random-effects design for subject 1.
rv2: random-effects design for subject 2.
p1: marginal probability for subject 1.
p2: marginal probability for subject 2.
pardes: parameter design matrix.
ags: additive gamma sum matrix (optional).
link: link function indicator (0 = identity, 1 = log).
i: index for subject 1.
j: index for subject 2.
p: matrix of marginal probabilities (n x 2).
theta.des: parameter design matrix linking theta to lambda parameters.
additive.gamma.sum: optional matrix for additive gamma sums.
var.par: if 1, parameters are rescaled by sum squared.
...: additional arguments.
object: a binomial twostage model object.
xmarg: optional covariate values for marginal probabilities.
type: model type: "ace", "ade", "ae", "de", "dce", or "un".
parg: genetic variance parameter (gamma shape for genetic component).
parc: common environment variance parameter (gamma shape for environment).
K: number of simulated twin pairs (multiplied by 2 internally).
test: if 1, prints diagnostic correlations.
x: passed as parg (alias wrapper).
y: passed as parc (alias wrapper).
pairs: matrix of pair indices (n x 2).
data: a data.frame with twin/family data.
cr.models: formula specifying time and status variables.
bin: logical; if TRUE uses binary (prevalence) ordering rather than time ordering.
id: character name of the cluster (pair) identifier column.
member: character name of the family member type column.
mother: value identifying mothers in the member column.
father: value identifying fathers in the member column.
child: value identifying children in the member column.
child1: column name distinguishing first child from second.
kinship: vector of kinship coefficients for each pair.

Value

A list of concordance tables, one per pair, each containing pmat (2x2 probability matrix), casewise (casewise concordance), and marg (marginal probabilities).

A list of concordance tables per zygosity group.

A list with components:

pardes: parameter design matrix linking random effects to variance parameters.
des.rv: random-effects design matrix for subjects.

Details

twin_polygen_design creates a polygenic random-effects design for twin pairs, distinguishing MZ and DZ twins.

twin.polygen.design is an alias for twin_polygen_design.

ace_family_design creates designs for nuclear families (mother, father, children).

make_pairwise_design creates pairwise random-effects designs for arbitrary kinship structures.

concordanceTwostage computes concordance probabilities from a twostage model.

concordanceTwinACE computes concordance from a twin ACE model.

kendall_ClaytonOakes_twin_ace and kendall_normal_twin_ace compute Kendall's tau for Clayton-Oakes and normal-frailty twin ACE models respectively.

ascertained_pairs identifies ascertained (affected) pairs in clustered survival data.

p11_binomial_twostage_RV computes the joint probability P(T1<=t, T2<=t) for the additive gamma binary random effects model.

Author

Klaus K. Holst, Thomas Scheike