DNCI.ses_overall: DNCI Function : Dispersal-Niche Continuum Index computation...

In Corentin-Gibert-Paleontology/DNCImper: Assembly process identification based on SIMPER analysis

DNCI Function : Dispersal-Niche Continuum Index computation for overall dissimilarity analysis of 3 groups or more

Description

Quantitative identification of the main assembly process driving the overall dissimilarity contribution distribution (i.e. the empirical SIMPER profile structure). This function is based on PerSIMPER_overall function and its E index return(). -Under development- The three distributions of E index (corresponding to the three hypothesis: niche, dispersal, niche+dispersal) are used to compute the DNCI index. If DNCI is significantly < 0 : dispersal || DNCI significantly > 0 : niche || DNCI +- CI ~~ 0 : dispersal+niche -under development-

Usage

DNCI.ses_overall(
  x,
  grouping,
  id = "no_name",
  Nperm = 1000,
  count = TRUE,
  dataTYPE = "prab",
  plotSIMPER = TRUE,
  parallelComputing = FALSE
)

Arguments

x	Sample/Taxa matrix with sample in row and taxa in column
grouping	Grouping vector, ex : c(1,1,1,1,2,2,2,2,2,3,3,3) : 3 groups or more
id	Name of the dataset, default = "no_name"
Nperm	Number of permutation, default = 1000, should be change to 100 for robustness analysis
count	Display the number of permutation done, can be usefull with very large or small matrix, default = TRUE
dataTYPE	Need to be set for presence/absence or abundance data ("count"), default = "prab" (presence_absence)
plotSIMPER	Display the SIMPER, PerSIMPER and E index plots, default = TRUE
parallelComputing	Run PerSIMPER on half of the available cores/nodes

Examples

A <- DNCImper:::DNCI.ses_overall(DNCImper::Matrix_4groups, DNCImper::Group4)
#where Matrix is a presence/absence matrix with taxa in column and sample in row
#and Group is a vector with length() == number of rows/samples in Matrix, 3 groups or more.
#
B <- DNCImper:::DNCI.ses_overall(DNCImper::Matrix_4groups, DNCImper::Group4, Nperm = 100, count = FALSE, plotSIMPER = FALSE)
#In this example, same data are analysed, with 100 permutations, with no countdown and no plots

Corentin-Gibert-Paleontology/DNCImper documentation built on Feb. 8, 2025, 10:20 a.m.