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

In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

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)

[e-mail]

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

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)

Example output

Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 
Registered S3 methods overwritten by 'huge':
  method    from   
  plot.sim  BDgraph
  print.sim BDgraph
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4
Warning message:
In matrix(data = runif(16 * 3, min = 0, max = 1), nrow = 20, ncol = 16) :
  data length [48] is not a sub-multiple or multiple of the number of rows [20]
                        [,1]
D_gamma           19.3212184
D_alpha.2         18.6457070
D_alpha.1         15.6677460
D_beta.2           1.0362288
D_beta.1           1.1900695
Proportion.2       0.1697901
Proportion.1       0.8302099
Differentiation.2  0.0277419
Differentiation.1  0.1174719

HierDpart documentation built on March 31, 2021, 5:09 p.m.