CODEWITHSUNDEEP
rvegan
shuixia100
shuixia100

Reputation: 3

How to calculate the checkerboard score (C-score) under a null model by vegan package in R

I recently want to follow the checkerboard score under a null model method to calculate the pvalue for co-occurrence analysis as adopted by this paper "Using network analysis to explore co-occurrence patterns in soil microbial communities".

Unfortunately, the usage of commands and arguments of vegan package was not well described in the paper.

I believe there must be some expert of vegan package in R to do such co-occurrence analysis based on checkerboard score under a null model.

Could any one help with the scripts or the commands and arguments I should use to calculate the C-score under a null model in R?

Will this C-score thing return me a matrix of pvalue that I could use to indicate the co-occurrence?

Upvotes: 0

Views: 4066

Answers (2)

Razz Rakali
Razz Rakali

Reputation: 16

this should give a quick estimate of C-score

library(vegan)
library(bipartite)
C.score(species, normalise=T, FUN=mean, na.rm=T)->cscore.speciesN
C.score(species, normalise=F, FUN=mean, na.rm=T)->cscore.speciesS
cscore.speciesN
cscore.speciesS

Upvotes: 0

Bob
Bob

Reputation: 21

I guess this may answer your question:

library(vegan)

library(bipartite)

null.model <- oecosimu(species, bipartite::C.score, "swap", burnin=100, thin=10, statistic="evals", nsimul=10000) #where species is you species by sites matrix

print(null.model)

Upvotes: 2

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