beta_deviation: Computing Beta-Deviation

In RodolfoPelinson/PredatorIsolationStochasticity: Data Analyses for Pelinson et al 2021B

Description

This function computes observed beta-diversity (community variability), expected beta-diversity and beta-deviation for a given grouping factor. It strongly rely on functions from package vegan

Usage

beta_deviation(
  com,
  method = "quasiswap",
  dist = "bray",
  fixedmar = "both",
  shuffle = "both",
  group,
  strata = NULL,
  mtype = "count",
  times = 1000,
  burnin = 0,
  thin = 1,
  transform = NULL,
  seed = NULL
)

Arguments

com	The community data. A species by site matrix containing abundance or presence/absence data.
method	The chosen null model algorithm. See help file from the permatswap function in package vegan. Defaut is set to "quasiswap"
dist	The beta-diversity metric to be used. Default is set to bray-curtis beta dissimilarity.
fixedmar	character, stating which of the row/column sums should be preserved ("none", "rows", "columns", "both"). Defaut is to "both".
shuffle	Character, indicating whether individuals ("ind"), samples ("samp") or both ("both") should be shuffled, see details.
group	a grouping factor to compute community variability
strata	Numeric vector or factor with length same as nrow(m) for grouping rows within strata for restricted permutations. Unique values or levels are used. It is usefull to keep gamma-diversity within treatments constant. Defaut is set to "NULL".
mtype	Matrix data type, either "count" for count data, or "prab" for presence-absence type incidence data. Defaut is set to "count".
times	Number of permuted matrices. Defaut is set to 1000.
thin	Number of discarded permuted matrices between two evaluations in sequential ("swap", "tswap") methods. Defaut is set to 1.
transform	A character. Should the community matrix values be transformed? Default is set to "NULL". Options here are the same as for the decostand function from vegan.
seed	Do you wish set a seed? Defaut is to "NULL"
burning	Number of null communities discarded before proper analysis in sequential ("swap", "tswap") methods. Defaut is set to 0.

RodolfoPelinson/PredatorIsolationStochasticity documentation built on Feb. 21, 2022, 12:03 p.m.