R/familyDesign_tvc.R

In FamEvent: Family Age-at-Onset Data Simulation and Penetrance Estimation

familyDesign_tvc <- function(n=1000, affectnum = 0,  m.carrier = 0, variation = "none", interaction = FALSE,
          add.x = FALSE, x.dist = NULL, x.parms = NULL, depend = 1, 
          add.tvc = FALSE, tvc.type = "PE", tvc.range = NULL, tvc.parms = 1,
	        base.dist = "Weibull", frailty.dist = "gamma", 
          base.parms = c(0.016, 3), vbeta = c(1, 1),  allelefreq = 0.02,
          dominant.m = TRUE, dominant.s = TRUE,  mrate = 0.1, probandage = c(45, 1.5), 
          agemin = 20, agemax = 100) 
{
data<-numeric()
cumind<-0
i<- 1
j<- 0

while (i <= n) {
  j <- j + 1
  dat<-try(familyStructure_tvc(i,cumind=cumind, m.carrier=m.carrier, variation=variation, interaction=interaction,
  		 add.x = add.x, x.dist = x.dist, x.parms = x.parms, depend=depend,  
  		 add.tvc = add.tvc, tvc.type = tvc.type, tvc.range = tvc.range, tvc.parms = tvc.parms,
  		 base.dist=base.dist, frailty.dist=frailty.dist, 
       base.parms=base.parms, vbeta=vbeta, allelefreq=allelefreq, dominant.m=dominant.m, dominant.s=dominant.s,
	     mrate=mrate, probandage=probandage, agemin=agemin, agemax=agemax))
	    
  if(is.null(attr(dat, "class"))){
	   # At least one parent in first gen and two sibs in the second gen should be affected
     #[,7]=generation, [,6]=proband, [,13]=status
	
	if(affectnum==3) until <- ifelse(sum(dat[dat[,7]==1,13]) > 0 & sum(dat[dat[,7]==2,13]) > 1, TRUE, FALSE)
	else if(affectnum==2) until <- ifelse(sum(dat[, 13]) >= affectnum, TRUE, FALSE)
	else if(affectnum==1) until <- ifelse(dat[dat[,6]==1,13] == 1, TRUE, FALSE)
	else if(affectnum==0) until <- TRUE
	else if(variation=="frailty") until <- ifelse( dat[dat[,6]==1,13] == 1, TRUE, FALSE) 
	else until <- TRUE
	
			if(!is.null(dim(dat))){
	      if(nrow(dat)>0 ){
	    	  if(until){
		   	    data<-rbind(data, dat)
        		cumind<-cumind+nrow(dat)
        		i<-i+1
	   		  }    
		    }
	    }
} # close "is.null(attr(dat, "class"))"
} # close while

data
}