Nothing
.vcovBSenv <- new.env()
vcovBS <- function(x, ...) {
UseMethod("vcovBS")
}
vcovBS.default <- function(x, cluster = NULL, R = 250, start = FALSE, type = "xy", ..., fix = FALSE, use = "pairwise.complete.obs", applyfun = NULL, cores = NULL, center = "mean")
{
## set up return value with correct dimension and names
cf0 <- coef(x)
k <- length(cf0)
n <- nobs0(x)
rval <- matrix(0, nrow = k, ncol = k, dimnames = list(names(cf0), names(cf0)))
## try to figure out environment for update()
env <- try(environment(terms(x)))
if(inherits(env, "try-error")) env <- NULL
## cluster can either be supplied explicitly or
## be an attribute of the model...FIXME: other specifications?
if (is.null(cluster)) cluster <- attr(x, "cluster")
## resort to cross-section if no clusters are supplied
if (is.null(cluster)) cluster <- 1L:n
## collect 'cluster' variables in a data frame
if(inherits(cluster, "formula")) {
cluster_tmp <- if("Formula" %in% loadedNamespaces()) { ## FIXME to suppress potential warnings due to | in Formula
suppressWarnings(expand.model.frame(x, cluster, na.expand = FALSE))
} else {
expand.model.frame(x, cluster, na.expand = FALSE)
}
cluster <- model.frame(cluster, cluster_tmp, na.action = na.pass)
} else {
cluster <- as.data.frame(cluster)
}
## handle omitted or excluded observations
if((n != NROW(cluster)) && !is.null(x$na.action) && (class(x$na.action) %in% c("exclude", "omit"))) {
cluster <- cluster[-x$na.action, , drop = FALSE]
}
if(NROW(cluster) != n) stop("number of observations in 'cluster' and 'nobs()' do not match")
## catch NAs in cluster -> need to be addressed in the model object by the user
if(anyNA(cluster)) stop("cannot handle NAs in 'cluster': either refit the model without the NA observations in 'cluster' or impute the NAs")
## for multi-way clustering: set up interaction patterns
p <- NCOL(cluster)
if (p > 1L) {
cl <- lapply(1L:p, function(i) combn(1L:p, i, simplify = FALSE))
cl <- unlist(cl, recursive = FALSE)
sign <- sapply(cl, function(i) (-1L)^(length(i) + 1L))
paste_ <- function(...) paste(..., sep = "_")
for (i in (p + 1L):length(cl)) {
cluster <- cbind(cluster, Reduce(paste_, unclass(cluster[, cl[[i]] ]))) ## faster than: interaction()
}
} else {
cl <- list(1)
sign <- 1
}
## apply infrastructure for refitting models
if(is.null(applyfun)) {
applyfun <- if(is.null(cores)) {
lapply
} else {
if(.Platform$OS.type == "windows") {
cl_cores <- parallel::makeCluster(cores)
on.exit(parallel::stopCluster(cl_cores))
function(X, FUN, ...) parallel::parLapply(cl = cl_cores, X, FUN, ...)
} else {
function(X, FUN, ...) parallel::mclapply(X, FUN, ..., mc.cores = cores)
}
}
}
## use starting values?
assign(".vcovBSstart", if(isTRUE(start)) coef(x) else NULL, envir = .vcovBSenv)
## xy bootstrap vs. jackknife
type <- match.arg(tolower(type), c("xy", "jackknife", "fractional"))
## bootstrap for each cluster dimension
for (i in 1L:length(cl)) {
## cluster structure
cli <- if(type != "fractional") {
split(seq_along(cluster[[i]]), cluster[[i]])
} else {
factor(cluster[[i]], levels = unique(cluster[[i]]))
}
## bootstrap fitting function via update()
bootfit <- function(j, ...) {
clj <- switch(type,
"xy" = {
unlist(cli[sample(names(cli), length(cli), replace = TRUE)])
},
"jackknife" = {
unlist(cli[-j])
},
"fractional" = {
fw <- rexp(nlevels(cli))
fw <- fw[cli]/mean(fw)
mw <- weights(x)
j <- if(is.null(mw)) fw else mw * fw
})
assign(".vcovBSsubset", clj, envir = .vcovBSenv)
up <- if(is.null(.vcovBSenv$.vcovBSstart)) {
if(type != "fractional") {
update(x, subset = .vcovBSenv$.vcovBSsubset, ..., evaluate = FALSE)
} else {
update(x, weights = .vcovBSenv$.vcovBSsubset, ..., evaluate = FALSE)
}
} else {
if(type != "fractional") {
update(x, subset = .vcovBSenv$.vcovBSsubset, start = .vcovBSenv$.vcovBSstart, ..., evaluate = FALSE)
} else {
update(x, weights = .vcovBSenv$.vcovBSsubset, start = .vcovBSenv$.vcovBSstart, ..., evaluate = FALSE)
}
}
up <- eval(up, envir = env, enclos = parent.frame())
coef(up)
}
## for jackknife the number of replications is always the number of "observations" (cluster units)
if(type == "jackknife") R <- length(cli)
## actually refit
cf <- applyfun(1L:R, bootfit, ...)
## aggregate across cluster variables
if(type == "jackknife") {
cf <- do.call("cbind", cf)
center <- match.arg(center, c("mean", "estimate"))
rval <- rval + sign[i] * (R - 1L)/R * tcrossprod(cf - if(center == "mean") rowMeans(cf) else cf0)
} else {
cf <- do.call("rbind", cf)
rval <- rval + sign[i] * cov(cf, use = use)
}
}
## clean up starting values again
remove(".vcovBSstart", envir = .vcovBSenv)
## check (and fix) if sandwich is not positive semi-definite
if(fix && any((eig <- eigen(rval, symmetric = TRUE))$values < 0)) {
eig$values <- pmax(eig$values, 0)
rval[] <- crossprod(sqrt(eig$values) * t(eig$vectors))
}
return(rval)
}
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