Nothing
"view.te" <-
function(coef, plotform = "pdf") {
done0 <- tkmessageBox(message="View all taxon-environment relationships?",
icon="question",type="yesno",default="yes")
if (as.character(done0) != "yes") {
tnames0 <- tklist.modal("Select taxa.", coef$tnames, selectmode = "multiple")
}
else {
tnames0 <- coef$tnames
}
if (! is.null(coef$raw.data)) {
nlist <- as.list(rep(NA, times = length(coef$raw.data)))
for (i in 1:length(coef$raw.data)) {
nlist[[i]] <- names(coef$raw.data[[i]])
}
}
if (plotform == "pdf") {
pdf(file = "taxon.env.pdf", width = 9, height = 6.5, pointsize = 10)
par(mfrow = c(2,3), pty = "s", mar = c(4,4,3,2))
}
else {
if (plotform == "windows") {
# windows(width = 6, height = 3, pointsize = 10)
par(mfrow = c(1,2), pty = "m", mar = c(4,4,2,0))
}
}
np <- 100
xnew <- seq(from = 0, to = 1, length = np)
ynew <- seq(from = 0, to = 1, length = np)
df1 <- expand.grid(x = xnew, y = ynew)
if (length(tnames0) > 0) {
for (i in 1:length(tnames0)) {
if ((plotform == "windows") & (i > 2) & (floor((i-1)/2) == (i-1)/2)) {
dev.new()
par(mfrow = c(1,2), pty = "m", mar = c(4,4,2,0))
}
isel <- match(tnames0[i], coef$tnames)
cc <- coef$csave[isel,]
if (length(coef$xvar) == 2) {
z <- cc[1] + cc[2]*df1$x + cc[3]*(df1$x^2) + cc[4]*df1$y +
cc[5]*(df1$y^2) + cc[6]*df1$x*df1$y
z2 <- exp(z)/(1+exp(z))
dim(z2) <- c(np,np)
contour(xnew, ynew, z2, axes = FALSE)
at0 <- seq(from = 0, to = 1, length = 5)
xlims <- coef$xlims
lab1 <- round(at0*diff(xlims[[1]]) + xlims[[1]][1], digits = 0)
lab2 <- round(at0*diff(xlims[[2]]) + xlims[[2]][1], digits = 0)
box()
axis(1, at = at0, labels = lab1)
axis(2, at = at0, labels = lab2)
mtext(toupper(coef$xvar[1]), side = 1, line=2.3)
mtext(toupper(coef$xvar[2]), side = 2, line = 2.3)
mtext(tnames0[i], side = 3, line = 0.5)
}
else {
if (length(coef$xvar) == 1) {
z <- cc[1] + cc[2]*xnew + cc[3]*xnew^2
z2 <- exp(z)/(1+exp(z))
ylim0 <- range(z2)
if (! is.null(coef$raw.data)) {
imatch <- NA
j <- 0
while ((is.na(imatch)) & (j < length(coef$raw.data))) {
j <- j + 1
imatch <- match(tnames0[i], names(coef$raw.data[[j]]))
}
cutp <- quantile(coef$raw.data[[j]][, coef$xvar[1]],
probs = seq(from = 0, to = 1,
length = floor(nrow(coef$raw.data[[j]])/40)))
cutm <- 0.5*(cutp[-1] + cutp[-length(cutp)])
cutf <- cut(coef$raw.data[[j]][, coef$xvar[1]], cutp,
include.lowest = TRUE)
vals <- tapply(coef$raw.data[[j]][, imatch], cutf,
function(x) mean(as.numeric(x>0)))
ylim0 <- range(c(ylim0, vals), na.rm = TRUE)
}
plot(xnew, z2, axes = FALSE, type = "l", xlab = "", ylab = "",
ylim = ylim0)
if (! is.null(coef$raw.data)) {
points(cutm, vals)
}
at0 <- seq(from = 0, to = 1, length = 5)
xlims <- coef$xlims
lab1 <- round(at0*diff(xlims[[1]]) + xlims[[1]][1], digits = 1)
box(bty = "l")
axis(1, at = at0, labels = lab1)
axis(2)
mtext(toupper(coef$xvar[1]), side = 1, line = 2.3)
mtext("Capture Probability", side = 2, line = 2.3)
mtext(tnames0[i], side = 3, line = 0.5)
}
else {
print("Coefficient file not suitable.")
}
}
}
}
if (plotform == "pdf") {
dev.off()
}
return()
}
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