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).

The definition of the function can be sourced from here:

source ('https://raw.githubusercontent.com/zdealveindy/anadat-r/master/scripts/p.adjust.envfit.r')
 

and the script is here:

p.adjust.envfit.r

# 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)
}