sashagusev

set.seed(42)
options(digits=3)

# --- Parameters
# sibling pairs
N = 100e3
# unadmixed individuals (for population estimate)
N_unadmixed = 10e3
# number of variants
M = 100

sashagusev

library("RColorBrewer")

# ---
# Parameters
# ---
# Samples
N = 2e3
# Epistatic heritability :
hsq_epistatic = 0.5
# Allele frequencies to use

sashagusev

clr = c("#d53e4f","#fc8d59","#99d594")
n=500e3
hsq = 0.5
seeds = 10

par(mfrow=c(1,4))
for ( maf in c(0,0.05,0.2,0.5) ) {
  plot(0,0,xaxt="n",las=1,type="n",pch=19,ylab="Phenotype",xlab="Genotype",ylim=c(-1,30),xlim=c(0,2),bty="n",main="")
  axis(side=1,at=c(0,1,2),labels = c("AA","Aa","aa"))
  hsq_add = rep(NA,seeds)

sashagusev

library(survival)

# ---
# Parameters
# ---
# number of individuals
n = 50e3
# desired hazard ratio
HR = 1.64
beta = log(HR)

sashagusev

# Fixed parameters
N = 10e6
AM_cor = 0.50

for ( Cultural_cor in c(sqrt(0.15),0.51) ) {
  cat("\nSimulating cultural transmission of" , Cultural_cor , '\n' )

  # Simulate two parental traits
  y_mother = rnorm(N,0,1)
  y_father = rnorm(N,0,1)

sashagusev

set.seed(42)

### --- REML
# Original code:
# https://github.com/sashagusev/SKK-REML-sim/blob/master/func_reml.R

library('msm')

# Utility function for calculating log of determinant
`logdet` <-

sashagusev

# Simulations and visualization of a heritable liability threshold model across generations and in families
# ---
# Liability functions (from Baselmans et al.)
# See: https://github.com/BartBaselmans/CHARRGe

risk_from_liability = function( prev , h2 ) {
  # Threshold
  Tx = -qnorm(prev,0,1)
  z = dnorm(Tx)
  i = z/prev

sashagusev

set.seed(1)

# Library for GLMM computations
library(PQLseq2)
# Library for mixed model / Wald test
library("GMMAT")

# convenience function to suppress prints
quiet <- function(x) { 
  sink(tempfile()) 

sashagusev

set.seed(42)

# Library for GLMM computations
library(PQLseq2)
# Library for mixed model / Wald test
library("GMMAT")

# convenience function to suppress prints
quiet <- function(x) { 
  sink(tempfile()) 

sashagusev

set.seed(42)

# Library for GLMM computations
library(PQLseq2)

quiet <- function(x) { 
  sink(tempfile()) 
  on.exit(sink()) 
  invisible(force(x)) 
}