Nothing
plot.boot.lmf <-
function(x,
what = c("all"),
...)
{
#Check if x is of class "boot.lmf"
if(class(x) != "boot.lmf")
stop("'x' does not contain bootstrap replicates from a 'lmf' model")
#Plot the parameter distribution from the bootstrap replicates for "leslie"
if(!is.null(x$lboot) & (what == "projection" | what == "all"))
{
#Plot lambda
plot(density(x$luvboot[, 1]), main = "Growth rate", xlab =
expression(lambda), col = "blue")
#Set the option to click to see next plot and the plot window to have
#nage numbers of plots
par(ask = TRUE, mfrow = c(1, x$nage))
#Plot stable age distribution
for(i in 1 : x$nage)
{
plot(density(x$luvboot[, 1 + i]), main = "Stable age distribution",
xlab = bquote(u[.(x$uage[i])]), col = "blue")
}
#Plot reproductive values
for(i in 1 : x$nage)
{
plot(density(x$luvboot[, x$nage + 1 + i]), main = "Reproductive value",
xlab = bquote(v[.(x$uage[i])]), col = "blue")
}
#Set the plot window to have "nage^2" number of plots (maximum 4 * 4 number of plots)
par(mfrow = pmin(dim(x$l), c(4, 4)))
#Plot projection matrix
for(i in 1 : ifelse(x$nage == 1, dim(x$l)[1], dim(x$l)[1]^2))
{
plot(density(sapply(x$lboot, '[', i)),
main = "Projection matrix (l)", xlab = paste("Component ", i,
sep = ""), col = "blue")
}
}
#Plot the parameter distribution from the bootstrap replicates for "alpha"
if(!is.null(x$aMboot) & (what == "alpha" | what == "all"))
{
#Set the plot window to have one plots
par(mfrow = c(1, 1))
#Plot environmenal variance
plot(density(x$eboot), main = "Environmental variance",
xlab = bquote(sigma[e]^2), col = "blue")
#Set the option to click to see next plot and the plot window to have
#nage + 1 numbers of plots
par(ask = TRUE, mfrow = c(1, x$nage + 1))
#Plot demographic variances
for(i in 1 : x$nage)
{
plot(density(x$djboot[, i]), main = "Demographic variance",
xlab = bquote(sigma[paste("d", .(x$uage[i]), sep = "")]^2), col = "blue")
}
plot(density(x$dboot), main = "Demographic variance",
xlab = bquote(sigma[d]^2), col = "blue")
#Set the plot window to have "npar" number of plots
par(mfrow = c(1, x$npar))
#Plot temporal mean alphas
for(i in 1 : x$npar)
{
plot(density(sapply(x$aMboot, '[', i)),
main = expression("Temporal"~alpha~"-estimates"),
xlab = bquote(alpha[.(i - 1)]~"(M)"),
col = "blue")
}
#Set the plot window to have "npar^2" number of plots
#(maximum 4 * 4 number of plots)
par(mfrow = c(min(4, x$npar), min(4, x$npar)))
#Plot components of the temporal covariance matrix (M)
for(i in 1 : x$npar^2)
{
plot(density(sapply(x$Mboot, '[', i)),
main = "Temporal covariance matrix (M)", xlab = paste("Component ", i,
sep = ""), col = "blue")
}
#Set the plot window to have "npar" number of plots
par(mfrow = c(1, x$npar))
#Plot temporal mean alphas
for(i in 1 : x$npar)
{
plot(density(sapply(x$anfboot, '[', i)),
main = expression("Temporal"~alpha~"-estimates (M = 0)"),
xlab = bquote(alpha[.(i - 1)]~"(M = 0)"),
col = "blue")
}
#Set the plot window to have "npar^2" number of plots
#(maximum 4 * 4 number of plots)
par(mfrow = c(min(4, x$npar), min(4, x$npar)))
#Plot components of the temporal covariance matrix (M)
for(i in 1 : x$npar^2)
{
plot(density(sapply(x$Anfboot, '[', i)),
main = "Temporal covariance matrix (M = 0)", xlab = paste("Component ", i,
sep = ""), col = "blue")
}
}
}
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