organize.syncsa: Function for organize data for Package SYNCSA

In vanderleidebastiani/SYNCSA: Analysis of Functional and Phylogenetic Patterns in Metacommunities

Description

Package SYNCSA requires that the species and community sequence in the data.frame or matrix must be the same for all data.frame/matrices.

Usage

organize.syncsa(
  comm,
  traits = NULL,
  phylodist = NULL,
  envir = NULL,
  strata = NULL,
  spp.weights = NULL,
  check.comm = TRUE,
  convert.traits = FALSE,
  ranks = TRUE
)

Arguments

comm	Community data, with species as columns and sampling units as rows.
traits	Matrix or data.frame of species described by traits, with traits as columns and species as rows (Default traits = NULL).
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).
strata	Strata named vector to specify restricting permutations within species groups (Default strata = NULL).
spp.weights	Named vector to specify individual species weights (Default spp.weights = 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).
convert.traits	Logical argument (TRUE or FALSE) to convert factor traits in dummy traits and/or convert ordinal variables in numeric (see ranks argument) (Default convert.traits = FALSE).
ranks	Logical argument (TRUE or FALSE) to specify if ordinal variables are convert to ranks. If ranks = TRUE all ordered variable are replaced by their ranks and if ranks = FALSE all ordinal variables are simply treated as continuous variables (Default ranks = TRUE).

Details

The function organizes the data for the functions of the package SYNCSA, placing the matrices of community, traits, phylogenetic distance, environmental varibles, species weights and strata vectors in the same order. The function 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, traits, 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.

When trait is a data.frame with different types of variables correctly identified and the argument convert.traits is TRUE factor traits are expanded in dummy traits and ordinal variables are converted in numeric according to ranks argument.

The individual species weights (spp.weights) and strata must be named vectors. The strata vector is a vector for restrict permutation within species groups, insofar as the SYNCSA package the null models are based in permutation of species rather than permutation of sample units.

Value

A object of class metacommunity.data (also of the class list) with the data.frames or matrices:

call	The arguments used.
community	Community data.
traits	Traits data.
phylodist	Phylogenetic distance.
environmental	Environmental variables.
community.var.type	Type of each varible in community data, where 'c' to continuous/numeric, 'o' to ordinal, 'b' to binary and 'f' to factor. Nominal are not allowed.
traits.var.type	Type of each varible in traits data. See labels above.
phylodist.var.type	Type of each varible in phylodist. See labels above.
environmental.var.type	Type of each varible in environmental data. See labels above.
strata	The strata vector for permutations.
put.together	A list with suggestion to group of traits that are analyzed together, only if convert.traits is TRUE and if some traits are of factor class.
spp.weights	The individual species weights vector.
list.warning	A list of warning.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

See Also

syncsa, var.dummy, var.type

Examples

data(ADRS)
organize.syncsa(ADRS$community, ADRS$traits, ADRS$phylo, ADRS$envir)

vanderleidebastiani/SYNCSA documentation built on Sept. 4, 2020, 10:57 p.m.