DNCI.ses_overall_symmetrized: 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 with randomly even groups

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 DNCI.ses_overall() PerSIMPER_overall function and its E index return(). -Under development- -under development- Group are made even by subsampling largest group to the size of the smallest ! CAUTION ! Do rerun for robust results -under development-

Usage

DNCI.ses_overall_symmetrized(
  Mat,
  Group,
  id = "no_name",
  NbrReRun = 100,
  dataTYPE = "prab",
  Nperm = 100,
  plotSIMPER = TRUE,
  count = FALSE,
  parallelComputing = FALSE
)

Arguments

Mat	Sample/Taxa matrix with sample in row and taxa in column
Group	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"
NbrReRun	Number of iteration to obtain mean DNCI_overall values with even groups
dataTYPE	Need to be set for presence/absence or abundance data ("count"), default = "prab" (presence_absence)
Nperm	Number of permutation, default = 1000, should be change to 100 for robustness analysis
plotSIMPER	Display the SIMPER, PerSIMPER and E index plots, default = TRUE
count	Display the number of permutation done, can be usefull with very large or small matrix, default = TRUE
parallelComputing	Run PerSIMPER_overall on half of the available cores/nodes

Examples

A <- DNCImper:::DNCI.ses_overall_symmetrized(DNCImper::Matrix_4groups, DNCImper::Group4, NbrReRun = 10)
#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; 10 reruns (default NbrReRun is 100).
#
B <- DNCImper:::DNCI.ses_overall_symmetrized(DNCImper::Matrix_4groups, DNCImper::Group4, NbrReRun = 10, Nperm = 100, count = FALSE, plotSIMPER = FALSE)
#In this example, same data are analysed, with 100 permutations and 10 reruns (default NbrReRun is 100), with no countdown and no plots

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