Nothing
ci.boot.lmf <-
function(x, clevel = 0.05)
{
#Check class
if(class(x) != "boot.lmf")
stop("This is not bootstrap replicates from a 'lmf' model")
#Keep the call
ret <- list(call = match.call())
#Keep the number of bootstrap replicates
ret$nboot <- x$nboot
#Keep the what argument from x$call
ret$what <- x$call$what
#Keep the level argument
ret$clevel <- clevel
#Keep the unique ages from x$uage
ret$uage <- x$uage
#Keep the number of age classes from x$nage
ret$nage <- x$nage
#Set up quantile function
qfn <- function(a, clevel) {paste("(", paste(format(
quantile(a, c(clevel/2, 1 - clevel/2)), digits = getOption("digits") - 3),
collapse = ","), ")", sep = "")}
#Calculate confidence intervals after checking which parameters
#has been bootstrapped
if(!is.null(x$lboot))
{
#lboot - CI for transition matrix
lt <- array(Reduce(cbind, x$lboot),
dim = c(dim(x$l)[1], dim(x$l)[2], x$nboot))
ret$l <- apply(lt, 1:2, qfn, clevel = clevel)
#luvboot - CI for lambda, u and v
ret$luv <- apply(x$luvboot, 2, qfn, clevel = clevel)
}
if(!is.null(x$djboot))
{
#djboot - CI for sigma2.dj
ret$sigma2.dj <- apply(x$djboot, 2, qfn, clevel = clevel)
#dboot - CI for sigma2.d
ret$sigma2.d <- qfn(x$dboot, clevel = clevel)
#atboot
#No CI possible
#Atboot
#No CI possible
#Mboot - CI for temporal covariance matrix
Mt <- array(Reduce(cbind, x$Mboot),
dim = c(x$npar, x$npar, x$nboot))
ret$M <- apply(Mt, 1:2, qfn, clevel = clevel)
#Inherit names
dimnames(ret$M) <- dimnames(x$Mboot[[1]])
#aMboot - CI for temporal alpha estimates
aMt <- do.call(rbind, x$aMboot)
ret$aM <- apply(aMt, 2, qfn, clevel = clevel)
#atCboot
#No CI possible
#eboot - CI for environmental variance (sigma2.e)
ret$sigma2.e <- qfn(x$eboot, clevel = clevel)
#Anfboot - CI for temporal covariance matrix
#assuming M = 0 (no fluctuating selection)
Anft <- array(Reduce(cbind, x$Anfboot),
dim = c(x$npar, x$npar, x$nboot))
ret$Anf <- apply(Anft, 1:2, qfn, clevel = clevel)
#Inherit names
dimnames(ret$Anf) <- dimnames(x$Anfboot[[1]])
#anfboot
anft <- do.call(rbind, x$anfboot)
ret$anf <- apply(anft, 2, qfn, clevel = clevel)
}
class(ret) <- "ci.boot.lmf"
ret
}
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