plot_null: Plotting null ordinations

In RodolfoPelinson/PredatorIsolationComm: Data Analysis of Pelinson et al 2020

Description

This function is just for visualization of null generated communities. It is useful to see if your permutation design is doing what it is suppose to! It relies on the plot_ordination function.

Usage

plot_null(
  com,
  x1,
  x2,
  nperm = 1,
  family,
  num.lv = 2,
  strata = F,
  orig_n.init = 1,
  perm_n.init = 1,
  refit_perm = F,
  ...
)

Arguments

x1	A vector containing the identity of fish treatments.
x2	A vector containing the identity of isolation treatments.
nperm	The number of permutations.
family	Family distribution to fit the GLLVMs.
num.lv	Number of latent variables used to compute GLLVMs.
strata	Should communities be permuted freely or be restricted by fish treatment? Default to TRUE.
orig_n.init	Number of iterations used to compute the original GLLVM? Default to 30.
perm_n.init	Number of iterations used to compute the permuted GLLVMs? Default to 1.
refit_perm	If TRUE, the rows of the original community matrix will be permuted and for every permutation a gllvm will be computed. It can take too much time. If false, only the rows of a matrix with the original latent variables are permuted.
comm	The community data. A species by site matrix containing abundance data.

RodolfoPelinson/PredatorIsolationComm documentation built on June 7, 2021, 6:19 p.m.