IDIP | R Documentation |
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.
IDIP(abun, struc)
abun |
The count or frequency data, raw or relative species/allele abundances. |
struc |
The hierarchial structure. |
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.
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).
chao@stat.nthu.edu.tw
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.
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)
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