aMiAD.plot <-
function (fit, filename = "filename.pdf", fig.title = "figtitle")
{
out <- as.data.frame(rbind(round(fit$ItembyItem.out[, c(1,
5)], 3), round(fit$aMiAD.out[c(1, 5)], 3)))
es <- out[, 2]
ind.neg <- which(es < 0)
ind.pos <- which(es >= 0)
cols <- rep(NA, length(es))
cols[ind.neg] <- "lightgreen"
cols[ind.pos] <- "lightpink"
if (es[length(es)] < 0)
cols[length(es)] <- "green2"
if (es[length(es)] >= 0)
cols[length(es)] <- "red2"
pvs <- out[, 1]
ind.zero <- which(pvs == 0)
pvs[ind.zero] <- "<.001"
names.arg.v <- c(paste("Richness\n", "(p:", pvs[1], ")",
sep = ""), paste("Shannon\n", "(p:", pvs[2], ")", sep = ""),
paste("Simpson\n", "(p:", pvs[3], ")", sep = ""), paste("PD\n",
"(p:", pvs[4], ")", sep = ""), paste("PE\n", "(p:",
pvs[5], ")", sep = ""), paste("PQE\n", "(p:", pvs[6],
")", sep = ""), paste("aMiAD\n", "(p:", pvs[7], ")",
sep = ""))
pdf(file = filename, width = 4, height = 3.5)
par(mai = c(1.1, 0.7, 0.4, 0.2))
par(oma = c(0, 0, 0.5, 0))
barplot(es, names.arg = names.arg.v, ylim = c(-ceiling(max(abs(es)) *
1.1), ceiling(max(abs(es)) * 1.1)), col = cols, xpd = FALSE,
axes = TRUE, cex.names = 0.7, axis.lty = 1, ylab = "MiDivES",
space = 1, las = 2, tck = -0.02, cex.axis = 0.7, cex.lab = 0.7,
mgp = c(2, 1, 0), srt = 45)
title(fig.title, adj = 0.06, outer = TRUE, line = -1, cex.main = 1.5)
graphics.off()
}
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