nullPerm: Generate statistical null expectations for the variograms
In mcglinnlab/vario: Community variograms and associated null models

nullPerm

R Documentation

Generate statistical null expectations for the variograms

Description

Generate statistical null expectations for the variograms

Usage

nullPerm(
  x,
  vobject,
  nperm,
  coords = NULL,
  meth = "both",
  sp = TRUE,
  all = FALSE,
  snap = NULL,
  npar = 1,
  linux = FALSE,
  RPargs = FALSE,
  breaks = NA
)

Arguments

`x`	is either an output of class 'sim' that is the output of 'sim.neut.uni' OR an site x species matrix
`vobject`	is the output of 'vario', this informs the function of what parameterization of vario to use specifically it indiates if the pos.neg components and median should be calculated
`nperm`	is the number of permutations
`coords`	the spatial coordinates of the sites, not needed if x is of class 'sim'
`meth`	the type of permutation to use, options include: reflect: random reflection/rotations of species (only makes sence when sp are not fixed shift: random torodial shifting with or with sp fixed both: both reflection and shifting random: random shuffle randpat: random patterns algo of Roxburgh and Chesson 1998, must parameterize RPargs (See below)
`sp`	boolean, if FALSE then obs composition of quadrats is fixed to the observed pattern, if TRUE then species are each shuffled independently
`all`	boolean, if TRUE then all relevant nulls calculated
`snap`	is the time period of the simulation to analyze,defaults to NULL val, if not set gets internally set to last time period
`npar`	number of processors to run the function on
`linux`	if TRUE then function assumes you are on a linux cluster and therefore exports a different compiled code
`RPargs`	is a vector of arguments that are needed to perform the Random Patterns spatial null model
`breaks`	gives either the number or the position of the breaks for the function vario Notes: 1) see the notes associated with the function 'nullGen' that indicate how 'RPargs" should be parameterized 2) 'meth' and 'sp' are arguments to randomization function 'spatPerm2D'
`median`	if TRUE then median is also calculated in addition to mean