Bio381/test.R at master · mws19/Bio381 · GitHub

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# read in associated species data
sppDat <- read.table("AssociatedSppData_Serp.csv",header=TRUE,sep=",",stringsAsFactors = FALSE)
head(sppDat)

# reshape data using dcast function in reshape2 package
library(reshape2)
PA <- dcast(sppDat,formula=SpeciesName~SitePatch)
head(PA)

library(EcoSimR)
library(MASS)

# Run null model with SIM9 algorithm & CHECKER index
adMod1 <- cooc_null_model(PA,algo= "sim9",metric="checker",nReps=1000,suppressProg=T)

# Summary and plots
summary(adMod1)
mean(adMod1$Sim)
plot(adMod1,type="hist")
plot(adMod1,type="cooc")
plot(adMod1,type="burn_in")

## Run null model with SIM9 algorithm and C score index
adMod2 <- cooc_null_model(PA,algo= "sim9",metric="c_score",nReps=1000)

# Summary and plots
summary(adMod2)
plot(adMod2,type="hist")
plot(adMod2,type="cooc")
plot(adMod2,type="burn_in")

# Run null model with SIM9 algorithm and COMBO index
adMod3 <- cooc_null_model(PA,algo= "sim9",metric="species_combo",nReps=1000)

# Summary and plots
summary(adMod3)
plot(adMod3,type="hist")
plot(adMod3,type="cooc")