# Analysis of community ecology data in R

David Zelený

### Others

en:numecolr:panelutils

This script is part of supporting materials, coming with the book of Borcard et al. 2011.

To import the function definition directly into R, use the following:

```source ('http://www.davidzeleny.net/anadat-r/doku.php/en:numecolr:panelutils?do=export_code&codeblock=1')
```
panel.cor
```# panelutils.R
#
# Author: Francois Gillet, 23 August 2012
#
## Put Pearson, Spearman or Kendall correlations on the upper panel
panel.cor <- function(x, y, method="pearson", digits=3, cex.cor=1.2, no.col=FALSE)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r <- cor(x, y, method=method)
ra <- cor.test(x, y, method=method)\$p.value
txt <- round(r, digits)
prefix <- ""
if(ra <= 0.1) prefix <- "."
if(ra <= 0.05) prefix <- "*"
if(ra <= 0.01) prefix <- "**"
if(ra <= 0.001) prefix <- "***"
if(no.col)
{
color <- 1
if(r < 0) { if(ra <= 0.001) sig <- 4 else sig <- 3 }
else { if(ra <= 0.001) sig <- 2 else sig <- 1 }
}
else
{
sig <- 1
if(ra <= 0.001) sig <- 2
color <- 2
if(r < 0) color <- 4
}
txt <- paste(txt, prefix, sep="\n")
text(0.5, 0.5, txt, cex = cex.cor, font=sig, col=color)
}

## Put histograms on the diagonal
panel.hist <- function(x, no.col=FALSE, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
his <- hist(x, plot=FALSE)
breaks <- his\$breaks; nB <- length(breaks)
y <- his\$counts
y <- y/max(y)
if(no.col) rect(breaks[-nB], 0, breaks[-1], y, col="gray", ...)
else rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
}

## Add black lowess curves to scatter plots
panel.smoothb <- function (x, y, col=par("col"), bg=NA, pch=par("pch"),
cex=1, col.smooth="black", span=2/3, iter=3, ...)
{
points(x, y, pch=pch, col=col, bg=bg, cex=cex)
ok <- is.finite(x) & is.finite(y)
if (any(ok))
lines(stats::lowess(x[ok], y[ok], f=span, iter=iter), col=col.smooth, ...)
}

#Usage:
#pairs(num.mat, lower.panel=panel.smooth, upper.panel=panel.cor, diag.panel=panel.hist)
#pairs(num.mat, lower.panel=panel.smooth, upper.panel=panel.cor, method="kendall")
```