permute {pTITAN2}

Permute

Description

Permute treatment labels for a taxa and associated environmental gradients.

Usage

permute(taxa, envs, sid)

permute2(..., minTaxonFreq = 3L, trys = 100L)

Arguments

taxa

a list of data.frames with the taxa. See Details.

envs

a list of data.frames with the environmental gradients. See Details

sid

a character vector of length one with the name of the column identifying the station id.

...

passed to permute

minTaxonFreq

min number of occurrences for each taxon

trys

maximum number of attempts to generate a meaningful permutation

Details

The taxa and envs lists are expected to be of equal length and that the ith element of taxa list is associated with the ith element of the envs list. That is, the taxa and environmental gradient for treatment 1 are both the first elements of the respective lists, the taxa and environmental gradient for treatment 2 are the second elements for the respective lists, etc.

The environmental gradient data.frames are expected to have two columns, one with the station ID and one with the data defining the gradient.

The taxa data.frames are expected to have the station ID column as well. Important The station ID column name needs to be the same for all the taxa and environmental gradient data.frames.

Value

A list of lists of lists. At the top level the elements are the treatment groups. There are as many elements as the length of the lists taxa and envs.

The second level are the taxa and environmental gradient.

See Also

vignette(topic = "pTITAN2", package = "pTITAN2")

Examples

example_permutation <-
 permute(taxa = list(CD_06_Mall_wID, CN_06_Mall_wID),
         envs = list(C_IC_D_06_wID, C_IC_N_06_wID),
         sid  = "StationID")
str(example_permutation, max.level = 2)