# Analysis of community ecology data in R

David Zelený

### Others

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Author: David Zelený

Function used to adjust the p-values in results of `envfit` function (from `vegan`) for the multiple test problem (by default using Bonferroni's correction).

```# Function p.adjust.envfit
# Calculates adjusted P values for results stored in envfit object,
# created using envfit function from vegan, which fits supplementary variables
# onto axes of unconstrained ordination.
# Arguments:
# x - envfit object
# method - method for correction of multiple testing issue (default = 'bonferroni',
#          see ''?p.adjust' for more options)
# n - optional, number of tests for which to correct; if not given, the number is
#          taken as the number of tests conducted by envfit function (for both vectors and factors).
# Author: David Zeleny
p.adjust.envfit <- function (x, method = 'bonferroni', n)
{
x.new <- x
if (!is.null (x\$vectors)) pval.vectors <- x\$vectors\$pvals else pval.vectors <- NULL
if (!is.null (x\$factors)) pval.factors <- x\$factors\$pvals else pval.factors <- NULL
if (missing (n)) n <- length (pval.vectors) + length (pval.factors)
if (!is.null (x\$vectors)) x.new\$vectors\$pvals <- p.adjust (x\$vectors\$pvals, method = method, n = n)
if (!is.null (x\$factors)) x.new\$factors\$pvals <- p.adjust (x\$factors\$pvals, method = method, n = n)
cat ('Adjustment of significance by', method, 'method')
return (x.new)
}```