Last data update: 2014.03.03

 R: Rao's quadratic entropy
rao.diversityR Documentation

Rao's quadratic entropy

Description

Calculates Rao's quadratic entropy, functional and phylogenetic redundancy.

Usage

rao.diversity(comm, traits = NULL, phylodist = NULL, checkdata = TRUE, ...)

Arguments

comm

Community data, with species as columns and sampling units as rows. This matrix can contain either presence/absence or abundance data.

traits

Matrix data of species described by traits, with traits as columns and species as rows (optional).

phylodist

Matrix containing phylogenetic distance between species (optional).

checkdata

Logical argument (TRUE or FALSE) to check if species sequence in the community data follows the same order as the one in the trait and in the phylodist matrices (Default checkdata = TRUE).

...

Parameters for gowdis function.

Details

Rao's quadratic entropy is a measure of diversity of ecological communities defined by Rao (1982) and is based on the proportion of the abundance of species present in a community and some measure of dissimilarity among them. The dissimilarity range from 0 to 1 and is based on a set of specified functional traits or in the phylogenetic dissimilarity.

For the trait data , the function calculates the square root of the one-complement of Gower’s similarity index, in order to have a dissimilarity matrix with Euclidean metric properties. Gower’s index ranges from 0 to 1 and can handle traits measured indifferent scales. When the species are completely different in terms of their traits, Rao quadratic entropy is equivalent to the Gini–Simpson index.

Functional redundancy is defined purely as the difference between species diversity and Rao’s quadratic entropy based on their functional dissimilarity (de Bello et al. 2007). The same definition is used for phylogenetic redundancy.

Value

Simpson

Gini-Simpson index within each community (equivalent to Rao quadratic entropy with null, crisp, similarities).

FunRao

Rao quadratic entropy within each community, considering trait distance.

FunRedundancy

Functional redundancy in each community.

PhyRao

Rao quadratic entropy within each community, considering phylogenetic distance.

PhyRedundancy

Phylogenetic redundancy in each community.

Note

IMPORTANT: The sequence species show up in community data matrix MUST be the same as they show up in traits and phylodist matrices. See organize.syncsa.

Author(s)

Vanderlei Júlio Debastiani <vanderleidebastiani@yahoo.com.br>

References

de Bello, F.; Leps, J.; Lavorel, S. & Moretti, M. (2007). Importance of species abundance for assessment of trait composition: an example based on pollinator communities. Community Ecology, 8, 163–170.

Pillar, V.D.; Blanco, C.C.; Muler, S.C.; Sosinski, E.E.; Joner, F. & Duarte, L.d.S. (2013). Functional redundancy and stability in plant communities. Journal of Vegetation Science, 24, 963-974.

Rao, C.R. (1982). Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24–43.

See Also

organize.syncsa, gowdis, syncsa

Examples

data(flona)
rao.diversity(flona$community)
rao.diversity(flona$community,traits=flona$traits)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SYNCSA)
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
Loading required package: mice
Loading required package: Rcpp
mice 2.25 2015-11-09
Loading required package: FD
Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:vegan':

    cca

Loading required package: ape
Loading required package: geometry
Loading required package: magic
Loading required package: abind
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/SYNCSA/rao.diversity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rao.diversity
> ### Title: Rao's quadratic entropy
> ### Aliases: rao.diversity
> ### Keywords: SYNCSA
> 
> ### ** Examples
> 
> data(flona)
> rao.diversity(flona$community)
$Simpson
     uni1      uni2      uni3      uni4      uni5      uni6      uni7      uni8 
0.9166667 0.8333333 0.9166667 0.8888889 0.9411765 0.9090909 0.8888889 0.7500000 
     uni9     uni10     uni11     uni12     uni13     uni14     uni15     uni16 
0.8571429 0.8888889 0.8333333 0.8888889 0.8750000 0.9230769 0.9285714 0.9285714 
    uni17     uni18     uni19     uni20     uni21     uni22     uni23     uni24 
0.8888889 0.6666667 0.8571429 0.9000000 0.9090909 0.8888889 0.9444444 0.9411765 
    uni25     uni26     uni27     uni28     uni29     uni30     uni31     uni32 
0.8888889 0.9285714 0.9444444 0.9230769 0.9090909 0.9411765 0.8000000 0.5000000 
    uni33     uni34     uni35     uni36     uni37     uni38     uni39 
0.6666667 0.7500000 0.9166667 0.8000000 0.8571429 0.8888889 0.9285714 

> rao.diversity(flona$community,traits=flona$traits)
$Simpson
     uni1      uni2      uni3      uni4      uni5      uni6      uni7      uni8 
0.9166667 0.8333333 0.9166667 0.8888889 0.9411765 0.9090909 0.8888889 0.7500000 
     uni9     uni10     uni11     uni12     uni13     uni14     uni15     uni16 
0.8571429 0.8888889 0.8333333 0.8888889 0.8750000 0.9230769 0.9285714 0.9285714 
    uni17     uni18     uni19     uni20     uni21     uni22     uni23     uni24 
0.8888889 0.6666667 0.8571429 0.9000000 0.9090909 0.8888889 0.9444444 0.9411765 
    uni25     uni26     uni27     uni28     uni29     uni30     uni31     uni32 
0.8888889 0.9285714 0.9444444 0.9230769 0.9090909 0.9411765 0.8000000 0.5000000 
    uni33     uni34     uni35     uni36     uni37     uni38     uni39 
0.6666667 0.7500000 0.9166667 0.8000000 0.8571429 0.8888889 0.9285714 

$FunRao
     uni1      uni2      uni3      uni4      uni5      uni6      uni7      uni8 
0.4690524 0.4263351 0.4654569 0.4688354 0.4660832 0.4286874 0.4769802 0.4178346 
     uni9     uni10     uni11     uni12     uni13     uni14     uni15     uni16 
0.4009167 0.4053195 0.4274385 0.4280875 0.3897610 0.4777808 0.4831594 0.4868864 
    uni17     uni18     uni19     uni20     uni21     uni22     uni23     uni24 
0.3893573 0.2765344 0.3760857 0.4064176 0.4669158 0.3912312 0.4774189 0.4813512 
    uni25     uni26     uni27     uni28     uni29     uni30     uni31     uni32 
0.4881358 0.4784518 0.4715757 0.4453332 0.3814591 0.4413601 0.3254530 0.2533968 
    uni33     uni34     uni35     uni36     uni37     uni38     uni39 
0.1834921 0.3002263 0.2997412 0.2483362 0.4596980 0.3679820 0.4209772 

$FunRedundancy
     uni1      uni2      uni3      uni4      uni5      uni6      uni7      uni8 
0.4476142 0.4069983 0.4512098 0.4200535 0.4750933 0.4804035 0.4119086 0.3321654 
     uni9     uni10     uni11     uni12     uni13     uni14     uni15     uni16 
0.4562262 0.4835694 0.4058949 0.4608013 0.4852390 0.4452961 0.4454120 0.4416850 
    uni17     uni18     uni19     uni20     uni21     uni22     uni23     uni24 
0.4995316 0.3901323 0.4810571 0.4935824 0.4421751 0.4976577 0.4670256 0.4598253 
    uni25     uni26     uni27     uni28     uni29     uni30     uni31     uni32 
0.4007531 0.4501196 0.4728687 0.4777437 0.5276318 0.4998164 0.4745470 0.2466032 
    uni33     uni34     uni35     uni36     uni37     uni38     uni39 
0.4831745 0.4497737 0.6169255 0.5516638 0.3974449 0.5209069 0.5075942 

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> dev.off()
null device 
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