setwd("~/Desktop/communityDimensions/R/simulation_setup/test_data")
load(file="testData_correctlySpecified.RData")
numSpecies <- c(5, 10, 15, 20, 25, 30)
numFactors <- c(1, 2, 5, 10, 20)
scenarios = expand.grid(numSpecies, numFactors)
require(boral)
for(i in 1:18){ ## 5 latent factors
## use correct number of latent variables
fit.boral <- boral(simulatedData[[i]], family = "binomial", lv.control=list(num.lv=scenarios[i,2]), row.eff = "none", save.model = FALSE)
save(fit.boral,file=paste("correctlySpecifiedResults/r",i,".RData", sep=""))
#mcmc.control = list(n.burnin = 10000, n.iteration = 40000, n.thin = 30, seed = 123)
}
## boral can't handle more than 5 latent variables, so the rest are going to be misspecified
for(i in 19:nrow(scenarios)){ ## 5 latent factors
## use correct number of latent variables
fit.boral <- boral(simulatedData[[i]], family = "binomial", lv.control=list(num.lv=5), row.eff = "none", save.model = FALSE)
save(fit.boral,file=paste("correctlySpecifiedResults/r",i,".RData", sep=""))
#mcmc.control = list(n.burnin = 10000, n.iteration = 40000, n.thin = 30, seed = 123)
}
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