R/ancom.R

In musto101/wilcox_R: What the package does (short line)

ancom <-
function(x1,y1,x2,y2,dchk=FALSE,plotit=TRUE,plotfun=rplot,nboot=500,
alpha=.05,SEED=TRUE,PARTEST=FALSE,tr=0,...){
#
# Omnibus ANCOVA
# tr=0 is recommended for general use. tr>0 might result in
#   poor control over the probability of a Type I error.
#  PARTEST=T will test the hypothesis of parallel regression lines.
#
# Setting plotfun=rplotsm will smooth the plots via bagging
#
# dchk=T, points in design space with a halfspace of zero are eliminated
#
# PARTEST=F tests hypothesis that regression surface is a horizontal
# plane through the origin
# PARTEST=T tests the hypothesis that the two regression surfaces
# are parallel.
#
flag1<-rep(T,length(y1))
flag2<-rep(T,length(y2))
if(dchk){
dep1<-fdepth(x2,x1) # depth of points in x1 relative to x2
dep2<-fdepth(x1,x2)
flag1<-(dep1>0)
flag2<-(dep2>0)
}
n1<-sum(flag1)
n2<-sum(flag2)
n<-n1+n2
y<-c(n2*y1[flag1]/n,0-n1*y2[flag2]/n)
x1<-as.matrix(x1)
x1<-x1[flag1,]
x2<-as.matrix(x2)
x2<-x2[flag2,]
x1<-as.matrix(x1)
x2<-as.matrix(x2)
x<-rbind(x1,x2)
if(plotit){
if(ncol(x)<=2)plotfun(x,y,...)
}
if(PARTEST)output<-indt(x,y,tr=tr,nboot=nboot,alpha=alpha,SEED=SEED)
if(!PARTEST)output<-indt0(x,y,nboot=nboot,alpha=alpha,SEED=SEED)
list(dstat=output$dstat,critd=output$critd)
}