ecoBayesIRT: Helper functions for ecological Bayesian item response theory...

In stevencarlislewalker/ecoBayesIRT: Helper functions for ecological Bayesian item response theory in R using MCMCpack

Description

Steps: (1) Fit a model using functions from the MCMCpack package such as MCMCirt1d or MCMCirtKd. (2) Do diagnostics and convergence checks on the resulting MCMC objects. (3) Separate the three types of parameters (site scores, x, species intercepts, a, and species scores, b), by passing the MCMC through the getBO function. (4) Use the other functions of this package to analyze the results (BOeta; BOflip; BOp; BOrotate; BOswitch).

Examples

## simulate data
nSite <- 25
nSpec <- 10
nIter <- 10000
set.seed(1)
x <- rnorm(nSite)
a <- rnorm(nSpec)
b <- rnorm(nSpec)
eta <- cbind(1, x) %*% rbind(a, b)
e <- matrix(rnorm(nSite*nSpec), nSite, nSpec)
p <- pnorm(eta + e)
Y <- matrix(rbinom(nSite*nSpec, 1, p), nSite, nSpec)
rownames(Y) <- letters[1:nSite]
colnames(Y) <- LETTERS[1:nSpec]

## fit model
Yirt <- MCMCirt1d(Y, mcmc = nIter, store.item = TRUE)

## getBO
BO <- getBO(Yirt, Y)

## fix identifiability
(refSite <- findRefSite(BO))
BO <- BOflip(BO, refSite)

## get fitted values
pFit <- BOp(BO)
pFitMean <- apply(pFit, c(2, 3), mean)
boxplot(pFitMean ~ Y)

## ordination plot
ordInt <- t(apply(BO$x, c(2, 3), quantile, probs = c(0.025, 0.975))[,,1])

stevencarlislewalker/ecoBayesIRT documentation built on May 30, 2019, 4:42 p.m.