simulate_under_LTM_single {LTFHPlus}

Simulate under the liability threshold model (single phenotype).

Description

simulate_under_LTM_single simulates families and thresholds under the liability threshold model for a given family structure and a single phenotype. Please note that it is not possible to simulate different family structures.

Usage

simulate_under_LTM_single(
  fam_vec = c("m", "f", "s1", "mgm", "mgf", "pgm", "pgf"),
  n_fam = NULL,
  add_ind = TRUE,
  h2 = 0.5,
  n_sim = 1000,
  pop_prev = 0.1
)

Arguments

fam_vec

A vector of strings holding the different family members. All family members must be represented by strings from the following list:

• m (Mother)

• f (Father)

• c[0-9]*.[0-9]* (Children)

• mgm (Maternal grandmother)

• mgf (Maternal grandfather)

• pgm (Paternal grandmother)

• pgf (Paternal grandfather)

• s[0-9]* (Full siblings)

• mhs[0-9]* (Half-siblings - maternal side)

• phs[0-9]* (Half-siblings - paternal side)

• mau[0-9]* (Aunts/Uncles - maternal side)

• pau[0-9]* (Aunts/Uncles - paternal side). Defaults to c("m","f","s1","mgm","mgf","pgm","pgf").

n_fam

A named vector holding the desired number of family members. See setNames. All names must be picked from the list mentioned above. Defaults to NULL.

add_ind

A logical scalar indicating whether the genetic component of the full liability as well as the full liability for the underlying target individual should be included in the covariance matrix. Defaults to TRUE.

h2

A number representing the liability-scale heritability for a single phenotype. Must be non-negative. Note that under the liability threshold model, the heritability must also be at most 1. Defaults to 0.5.

n_sim

A positive number representing the number of simulations. Defaults to 1000.

pop_prev

A positive number representing the population prevalence, i.e. the overall prevalence in the population. Must be smaller than 1. Defaults to 0.1.

Value

If either fam_vec or n_fam is used as the argument, if it is of the required format, if the liability-scale heritability h2 is a number satisfying 0 \leq h^2, n_sim is a strictly positive number, and pop_prev is a positive number that is at most one, then the output will be a list holding two tibbles. The first tibble, sim_obs, holds the simulated liabilities, the disease status and the current age/age-of-onset for all family members in each of the n_sim families. The second tibble, thresholds, holds the family identifier, the personal identifier, the role (specified in fam_vec or n_fam) as well as the lower and upper thresholds for all individuals in all families. Note that this tibble has the format required in estimate_liability. In addition, note that if neither fam_vec nor n_fam are specified, the function returns the disease status, the current age/age-of-onset, the lower and upper thresholds, as well as the personal identifier for a single individual, namely the individual under consideration (called o). If both fam_vec and n_fam are defined, the user is asked to ' decide on which of the two vectors to use.

See Also

construct_covmat, simulate_under_LTM_multi, simulate_under_LTM

Examples

simulate_under_LTM_single()
simulate_under_LTM_single(fam_vec = NULL, n_fam = stats::setNames(c(1,1,1,2), 
c("m","mgm","mgf","mhs")))
simulate_under_LTM_single(fam_vec = c("m","f","s1"), n_fam = NULL, add_ind = FALSE, 
h2 = 0.5, n_sim = 500, pop_prev = .05)
simulate_under_LTM_single(fam_vec = c(), n_fam = NULL, add_ind = TRUE, h2 = 0.5, 
n_sim = 200, pop_prev = 0.05)