organize.pcps: Function for organize data for Package PCPS

Description

Package PCPS requires that the species and community sequence in the data.frame or matrix must be the same for all data.frame/matrices. This function use the function organize.syncsa to organize the data.

Usage

organize.pcps(comm, phylodist = NULL, envir = NULL, check.comm = TRUE, ...)

Arguments

comm

Community data, with species as columns and sampling units as rows.

phylodist

Matrix containing phylogenetic distance between species. Must be a complete matrix (not a half diagonal matrix).This matrix can be larger than community data (more species) as long as it has at least all species that are in community data (Default phylodist = NULL).

envir

Environmental variables for each community, with variables as columns and sampling units as rows (Default envir = NULL).

check.comm

Logical argument (TRUE or FALSE) to remove sampling units and species with total sums equal or less than zero (Default check.comm = TRUE).

...

Other parameters for the organize.syncsa function.

Value

A object of class metacommunity.data (also of the class list) with all result returned by organize.syncsa. Featured for:

call

The arguments used.

community

Community data.

phylodist

Phylogenetic distance.

environmental

Environmental variables.

Details

The function, as well as organize.syncsa, organizes the data for the functions of the package PCPS, placing the matrices of community, phylogenetic distance and environmental varibles in the same order.

Essentially this function is the same as function organize.syncsa. This use as reference the community data for organize all data.frame or matrices in the same order that the sampling units names and species names found in community data set. For this all data sets entered must be correctly named, with rows and columns named. The matrices phylodist and envir can be larger than community data (more species and/or more sampling units) as long as it has at least all species and/or sampling units that are in community data. The function organizes the data despite the absence of one of the data.frames or matrices, provided that the community data had been entered. Unspecified data will appear as NULL. All arguments this funtion will be passed to organize.syncsa, see more details in organize.syncsa.

Examples

Run this code

# NOT RUN {
data(ADRS)
organize.pcps(ADRS$community, phylodist = ADRS$phylo)
# }