Description Usage Arguments Details Value Author(s) References Examples
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.
1 | 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
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.
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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
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