Nothing
summary.simfam <- function(object, digits = max(3, getOption("digits") - 3), ...){
savedig <- options(digits = digits)
on.exit(options(savedig))
design <- attr(object, "design")
variation <- attr(object, "variation")
frailty.dist <- attr(object, "frailty.dist")
base.dist <- attr(object, "base.dist")
if(!is.null(design)){
design.name <- c("pop: population-based study with affected probands",
"pop+: population-based study with affected and mutation carrier probands",
"cli: clinic-based study with affected probands",
"cli+: clinic-based study with affected and mutation carrier probands",
"twostage: two-stage design")[match(design, c("pop","pop+","cli","cli+","twostage"))]
cat("Study design: ", design,"\n")
}
if(!is.null(base.dist)) cat("Baseline distribution: ", base.dist,"\n")
if(!is.null(variation)) {
if(variation == "frailty")
cat("Frailty distribution: ", attr(object,"frailty.dist"),"\n")
else if(variation=="secondgene")
cat("Residucal familial correlation indueced by a second gene variation \n")
}
if(is.null(object$weight)) object$weight <- 1
# k <- ifelse(design=="twostage",2,1)
k <- ifelse(is.null(design), 1, ifelse(design=="twostage",2,1))
for(i in 1:k){
if(is.null(design)) data <- object
else if(design=="twostage"){
if(i==1){
data <- object[object$weight==1,]
cat("\n ## High risk families", "\n")
}
else{
data <- object[object$weight!=1,]
cat("\n ## Low risk families", "\n")
}
}
else data <- object
numfam <- length(data$famID[data$proband==1])
avgnumaffec <- sum(data$status, na.rm=TRUE)/numfam
avgnumcarr <- sum(data$mgene,na.rm=TRUE)/numfam
if(!is.null(data$fsize)) avgfamsize <- mean(data$fsize[data$proband==1])
else avgfamsize <- mean(aggregate(data$indID, by=list(data$famID), length)[,2])
avgageonset <- mean(data$time[data$status==1], na.rm=TRUE)
wt <- unique(data$weight)
ans <- list(num.fam=numfam, avg.num.affected=avgnumaffec, avg.num.carriers=avgnumcarr, avg.family.size=avgfamsize,avgageonset=avgageonset)
if(i==1) ans.high <- ans
nn<-c(
"Number of families: ",
"Average number of affected per family: ",
"Average number of carriers per family: ",
"Average family size: ",
"Average age of onset for affected: ")
for(j in 1:5) cat(nn[j], ans[[j]], "\n")
cat("Sampling weights used: ", unique(data$weight))
cat("\n")
if(i==2) ans<-cbind(HighRisk=ans.high, LowRisk=ans)
}
attr(ans,"design") <- design
attr(ans,"base.dist") <- base.dist
if(is.null(variation)) attr(ans, "frailty.dist") <- NULL
else if(variation=="frailty") attr(ans,"frailty.dist") <- frailty.dist
else attr(ans,"frailty.dist") <- NA
attr(ans, "variation") <- variation
class(ans) <- "summary.simfam"
invisible(ans)
}
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