Nothing
perc.cis <- function(object, ncomp = object$ncomp, conf = .95,
type = c("coefficients",
"loadings", "weights")) {
if ((object$val.method == "none" | object$val.method == "loo")) {
stop("No bootstrapping was done for this model")
}
conf <- conf
Bootstraps <- do.call("rbind", object$validation[names(object$validation) == type][[1]])
Bootstraps <- as.matrix(Bootstraps[, ncomp])
Upper <- 1 - (((1 - conf)/2))
Lower <- 1 - Upper
Order <- as.factor(row.names(data.frame((object[names(object) == type])[[1]][, 1])))
if(length(ncomp) > 1) {
Bootstraps.boot.cis <- llply(ncomp, function(y) {
do.call("rbind", as.list(
by(Bootstraps[, y], list(row.names(Bootstraps)), function(x){
c(ncomp = y, boot.mean = mean(x), quantile(x, c(Lower, Upper), na.rm = T))
}
)))
})
} else {
Bootstraps.boot.cis <- llply(ncomp, function(y) {
do.call("rbind", as.list(
by(Bootstraps[, 1], list(row.names(Bootstraps)), function(x){
c(ncomp = y, boot.mean = mean(x), quantile(x, c(Lower, Upper), na.rm = T))
}
)))
})
}
llply(1:length(Bootstraps.boot.cis), function(x) {
Bootstraps.boot.cis2 <- as.data.frame(Bootstraps.boot.cis[[x]])
Bootstraps.boot.cis2$variables <- row.names(Bootstraps.boot.cis[[x]])
row.names(Bootstraps.boot.cis2) <- NULL
Out <- Bootstraps.boot.cis2[Order, ]
row.names(Out) <- NULL
Out[, c(1, 5, 2:4)]
})
}
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