Nothing
## ----global_options, include=FALSE--------------------------------------------
knitr::opts_chunk$set(fig.width=8.5, fig.height=5.5, fig.align='center', warning=FALSE, message=FALSE)
## ---- echo = F, message = F---------------------------------------------------
library(DHARMa)
set.seed(123)
## ---- eval = F----------------------------------------------------------------
# library(rjags)
# library(BayesianTools)
#
# set.seed(123)
#
# dat <- DHARMa::createData(200, overdispersion = 0.2)
#
# Data = as.list(dat)
# Data$nobs = nrow(dat)
# Data$nGroups = length(unique(dat$group))
#
# modelCode = "model{
#
# for(i in 1:nobs){
# observedResponse[i] ~ dpois(lambda[i]) # poisson error distribution
# lambda[i] <- exp(eta[i]) # inverse link function
# eta[i] <- intercept + env*Environment1[i] # linear predictor
# }
#
# intercept ~ dnorm(0,0.0001)
# env ~ dnorm(0,0.0001)
#
# # Posterior predictive simulations
# for (i in 1:nobs) {
# observedResponseSim[i]~dpois(lambda[i])
# }
#
# }"
#
# jagsModel <- jags.model(file= textConnection(modelCode), data=Data, n.chains = 3)
# para.names <- c("intercept","env", "lambda", "observedResponseSim")
# Samples <- coda.samples(jagsModel, variable.names = para.names, n.iter = 5000)
#
# x = BayesianTools::getSample(Samples)
#
# colnames(x) # problem: all the variables are in one array - this is better in STAN, where this is a list - have to extract the right columns by hand
# posteriorPredDistr = x[,3:202] # this is the uncertainty of the mean prediction (lambda)
# posteriorPredSim = x[,203:402] # these are the simulations
#
# sim = createDHARMa(simulatedResponse = t(posteriorPredSim), observedResponse = dat$observedResponse, fittedPredictedResponse = apply(posteriorPredDistr, 2, median), integerResponse = T)
# plot(sim)
## ---- eval=F------------------------------------------------------------------
# # Posterior predictive simulations
# for (i in 1:nobs) {
# observedResponseSim[i]~dpois(lambda[i])
# }
## ---- eval = F----------------------------------------------------------------
# for(i in 1:nobs){
# observedResponse[i] ~ dpois(lambda[i]) # poisson error distribution
# lambda[i] <- exp(eta[i]) # inverse link function
# eta[i] <- intercept + env*Environment1[i] + RE[group[i]] # linear predictor
# }
#
# for(j in 1:nGroups){
# RE[j] ~ dnorm(0,tauRE)
# }
## ---- eval=F------------------------------------------------------------------
# for(j in 1:nGroups){
# RESim[j] ~ dnorm(0,tauRE)
# }
#
# for (i in 1:nobs) {
# observedResponseSim[i] ~ dpois(lambdaSim[i])
# lambdaSim[i] <- exp(etaSim[i])
# etaSim[i] <- intercept + env*Environment1[i] + RESim[group[i]]
# }
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