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## Community matrix comm.matrix: n x m matrix with n=time step, m=species
meancorr <- function (data, nrands = 0,
alternative=c("two.tailed", "greater", "less"),
method=c("pearson", "kendall", "spearman"),
type=1, quiet = FALSE, ...) {
data=as.matrix(data)
results=list()
methods=c("pearson", "kendall", "spearman")
method=match.arg(method, methods)
alternatives=c("two.tailed", "greater", "less")
alternative=match.arg(tolower(alternative), alternatives)
results$obs=meancorr.aux (data, method=method, ...)
if (nrands > 0) {
nr=NROW(data)
nc=NCOL(data)
if (!quiet)
prog.bar=txtProgressBar(min = 0, max = nrands, style = 3)
results$rands=numeric(length=nrands+1)*NA
for (i in 1:nrands) {
if (type==1)
rand.mat=apply(data, 2, sample)
else {
lags=sample(1:nr, size=nc, replace=TRUE)
rand.mat=mlag(data, lags)
}
results$rands[i]=meancorr.aux(rand.mat, method=method, ...)
if (!quiet)
setTxtProgressBar(prog.bar, i)
}
results$rands[nrands+1]=results$obs
if (alternative == "two.tailed") {
pvals=sum(abs(results$rands) >= abs(results$obs))/(nrands+1)
}
else {
if (alternative=="greater")
pvals=sum(results$rands >= results$obs)/(nrands+1)
else
pvals=sum(results$rands <= results$obs)/(nrands+1)
}
results$pval=pvals
results$alternative=alternative
}
results$method=method
class(results)="synchrony"
return (results)
}
meancorr.aux <- function (data, method=method, ...) {
mean.corr=suppressWarnings(cor(data, method=method, ...))
mean.corr=mean(mean.corr[lower.tri(mean.corr)], na.rm=TRUE)
return (mean.corr)
}
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