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##################################################################
## Illustrate faecal egg count reduction modelling
##################################################################
# load libraries
library('eggCounts')
require('coda',quietly = TRUE)
require('rstan',quietly = TRUE)
# simulate faecal egg counts
set.seed(1)
counts <- simData2s(n = 15, preMean = 500, delta = 0.07, kappa = 1,
f = 15, paired = TRUE)
# look at simulated counts: dataframe with columns
head(counts, 5)
# plot FECs
plotCounts(counts[,c("obsPre","obsPost")])
# run a paired model with individual efficacy
model <- fecr_stan(counts$obsPre, counts$obsPost, rawCounts = FALSE, preCF = 15,
paired = TRUE, zeroInflation = FALSE, indEfficacy = TRUE)
# compute the probability that the reduction is below 95%
fecr_probs(model$stan.samples, threshold = 0.95, plot = TRUE)
# extract posterior samples
model_mcmc <- stan2mcmc(model$stan.samples)
# check the traceplots and densities of posterior samples
plot(model_mcmc[,c("kappa","delta_mu","delta_shape")])
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