Nothing
cpg.everything.matrix <-
function(x,i.p,levin,chip.id,...) {
p<-x
if(levin){
if(is.null(i.p)) {
ranmixed<-function(z) {
temp<-tryCatch(anova(lme(z~p,random=~1|factor(chip.id),na.action=na.omit)),
error = function(e) NULL)
if(is.null(temp)) {
info<-matrix(NA,3)}
else {
temp<-as.matrix(temp)
if(temp[nrow(temp),4]==0) {
info<-c(temp[nrow(temp),3],df(temp[nrow(temp),3],temp[nrow(temp),1],temp[nrow(temp),2]))
}
else {
info<-temp[nrow(temp),3:4]
}
info<-c(info,temp[nrow(temp),2])
}
info
}}
else {
ranmixed<-function(z) {
temp <- tryCatch(anova(lme(z~p+i.p,random=~1|factor(chip.id),na.action=na.omit)),
error = function(e) NULL)
if(is.null(temp)) {
info<-matrix(NA,3)}
else {
temp<-as.matrix(temp)
if(temp[nrow(temp),4]==0) {
info<-c(temp[nrow(temp),3],df(temp[nrow(temp),3],temp[nrow(temp),1],temp[nrow(temp),2]))
}
else {
info<-temp[nrow(temp),3:4]
}
info<-c(info,temp[nrow(temp),2])
}
info
} }}
else {
ranmixed<-function(z) {
temp <- tryCatch(summary(lme(z~p,random = ~1|factor(chip.id),na.action = na.omit))[["tTable"]],
error = function(e) NULL)
if(!is.null(temp)) {
info <- temp[2,c(4:5,3)]
if(is.null(ncol(p))) {
info<-c(info,temp[1:2,1])
}
else{
betas<-temp[-2,1]
altdesign<-as.matrix(p[!is.na(z),2:ncol(p)])
thecolmeans<-colMeans(altdesign)
thecolmeans<-thecolmeans[colSums(altdesign)!=0]
newint<-betas[1]+sum(thecolmeans*betas[2:length(betas)])
info<-c(info,newint,temp[2,1])
} }
else {
info<-matrix(NA,5)}
info
}}
return(ranmixed)}
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