HierDpart (version 1.5.0)

IDIP: 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.

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).

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.

References

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

# NOT RUN {
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)
# }