IDIP: Function for decomposing diversity (genetic or species...

View source: R/IDIP.R

IDIPR Documentation

Function for decomposing diversity (genetic or species diversity) and differentiation into different hierarchical levels

Description

This function comes from Information-based Diversity Partitioning (Chao et al, 2017). It allows you to decompose diversity under a specified multi-level hierarchical structure.

Usage

IDIP(abun, struc)

Arguments

abun

The count or frequency data, raw or relative species/allele abundances.

struc

The hierarchial structure.

Details

This function is definitely an useful tool to do analysis of any information based diversity decomposition. Whether the data is genetic allele/species count/abundance or other frequency data in ecology, chemistry or economy.

Value

IDIP can be applied to any arbitrary number of hierarchical levels. The output consists of a basic data summary and decomposition results, with the latter including (1) gamma (or total) diversity; alpha and beta diversity at each level; (2) proportion of total beta information (Shannon information) found at each level; (3) mean differentiation (dissimilarity) among aggregates at each level (Chao et al, 2017).

Author(s)

chao@stat.nthu.edu.tw

References

Qin, X., & Gaggiotti, O. E. (2022). Information-based summary statistics for spatial genetic structure inference. Molecular Ecology Resources, 22(6), 2183-2195.

Chao, A., & Chiu, C. H. User's Guide for Online program iDIP (Information-based Diversity Partitioning).

Gaggiotti, O. E., Chao, A., Peres-Neto, P., Chiu, C. H., Edwards, C., Fortin, M. J., ... & Selkoe, K. A. (2018). Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evolutionary Applications.

Examples

str=Str(nreg=4,r=c(7,4,2,3),n=16)
abu=matrix(data=runif(16*3,min=0,max=1),nrow = 20,ncol = 16)
IDIP(abu,str)

xinghuq/HierDpart documentation built on March 21, 2023, 6:43 p.m.