我有一个模型，可以计算带有生存数据的标记重新捕获数据的样条曲线。该模型运行良好，但计算样条曲线的参数混合得非常糟糕。
mean 2.5% 97.5% That n.eff
...
m[1] 1.667899656 -0.555606 4.18479 2.8829 4
m[2] 1.293023680 -0.951046 3.90294 2.8476 4
m[3] 1.717855378 -0.484097 4.23105 2.8690 4
m[4] 1.723899423 -0.474260 4.23869 2.8686 4
m[5] 1.747050770 -0.456455 4.26314 2.8578 4
...
基本上，我正在计算p由物种特定效果p.sp和采样努力组成的重新捕获率p.effort。我还计算了phi具有特定物种术语phi.sp、年份影响phi.year、气候因素phi.sum.preci和样条曲线的适应度分量m。
run.model <- function(d, ## incoming data (packaged up in src/analyses.R)
ni=1100, ## number of iterations to run ## number of draws per chain
nt=10, ## thinning rate ##to save space on computer disk space see p.61 Kéry
nb=100, ## burn in ## should be large enough to discard initial part of Markov chains that have not yet converged
nc=3, ## number of chains to run ## multiple chain to check the convergence
n.cluster = 3) {
model.jags <- function() {
## Priors ------------------------------------------------------------------
## Random effect species-specific intercept (survival)
mu.phi.sp ~ dnorm(0,0.01)
sigma.phi.sp ~ dunif(0,10)
tau.phi.sp <- 1/(sigma.phi.sp)^2
## Random effect for recapture rate
mu.p.sp ~ dnorm(0,0.01)
## Random effect of year and fixed effect of precipitation & abundance
sigma.phi.year ~ dunif(0,10)
tau.phi.year <- 1/(sigma.phi.year)^2
## fixed effect of effort
p.effort ~ dnorm(0, 0.01) ## fixed effect
## Fixed precipitation per year
phi.sum.preci ~ dnorm(0, 0.01) ## fixed effect
# Prior spline ------------------------------------------------------------
###BEGIN SPLINE###
# prior distribution for the fixed effects parameters
for (l in 1:3) {
beta[l] ~ dnorm(0,0.1)
}
prior.scaleeps <- 1
xi ~ dnorm(0, tau.xi)
tau.xi <- pow(prior.scaleeps, -2)
for (k in 1:nknotsb) {
b[k] <- yi*etab[k]
etab[k] ~ dnorm(0, tau.etab) # hierarchical model for theta
} # closing k
prior.scaleb <- 1
yi ~ dnorm (0, tau.yi)
tau.yi <- pow(prior.scaleb, -2)
tau.etab ~ dgamma(.5, .5) # chi^2 with 1 d.f.
sigmab <- abs(xi)/sqrt(tau.etab) # cauchy = normal/sqrt(chi^2)
###END SPLINE###
for(sp in 1:nsp) {
## Random species-specific intercept
phi.sp[sp] ~ dnorm(mu.phi.sp, tau.phi.sp)
## Random recapture rate
p.sp[sp] <- mu.p.sp # Changed from a comment from Luke Jan. 9 2017
}
for (yr in 1:nyear) {
## random year
phi.year[yr] ~ dnorm(0, tau.phi.year)
}
## Likelihood!
for(sp in 1:nsp) { ## per species
## Rates -------------------------------------------------------------------
## recapture rate
for (yr in 1:nyear) {
logit(p[sp,yr]) <- # added logit here
p.sp[sp] +
p.effort*effort[yr]
} ## closing for (year in 1:nyear)
} ## closing for (sp in 1:nsp)
## Each ID ----------------------------------------------------------------
## Likelihood!
for(ind in 1:nind) { ## nind = nrow(d$X)
### BEGIN SPLINE ###
## mean function model
m[ind] <-mfe[ind] + mre1[ind] + mre2[ind]
# fixed effect part
mfe[ind] <- beta[1] * Xfix[ind,1] +beta[2] * Xfix[ind,2] + beta[3] * Xfix[ind,3]
mre1[ind] <- b[1]*Z[ind,1] + b[2]*Z[ind,2] + b[3]*Z[ind,3] + b[4]*Z[ind,4] + b[5]*Z[ind,5] + b[6]*Z[ind,6] + b[7]*Z[ind,7] + b[8]*Z[ind,8] + b[9]*Z[ind,9] + b[10]*Z[ind,10]
mre2[ind] <- b[11]*Z[ind,11] + b[12]*Z[ind,12] + b[13]*Z[ind,13] + b[14]*Z[ind,14] + b[15]*Z[ind,15]
###END SPLINE###
}
## for each individual
for(ind in 1:nind) { ## nind = nrow(d$X)
for(yr in 1:nyear) {
logit(phi[ind,yr]) <-
phi.sp[species[ind]] + ## effect of species
phi.year[yr] + ## effect of year
# Effect of the traits on survival values
m[ind]+ # spline
phi.sum.preci*sum.rainfall[yr] # effect of precipitation per sampling event
} ## (yr in 1:nyear)
## First occasion
for(yr in 1:first[ind]) {
z[ind,yr] ~ dbern(1)
} ## (yr in 1:first[ind])
## Subsequent occasions
for(yr in (first[ind]+1):nyear) { # (so, here, we're just indexing from year "first+1" onwards).
mu.z[ind,yr] <- phi[ind,yr-1]*z[ind,yr-1]
z[ind,yr] ~ dbern(mu.z[ind,yr])
## Observation process
sight.p[ind,yr] <- z[ind,yr]*p[species[ind],yr] ## sightp probability of something to be seen
X[ind,yr] ~ dbern(sight.p[ind,yr]) ## X matrix : ind by years
} ## yr
} ## closing for(ind in 1:nind)
} ## closing model.jags function
## Calling Jags ------------------------------------------------------------
jags.parallel(data = d$data,
inits = d$inits,
parameters.to.save = d$params,
model.file = model.jags,
n.chains = nc, n.thin = nt, n.iter = ni, n.burnin = nb,
working.directory = NULL,
n.cluster = n.cluster)
} ## closing the run.model function
# Monitored parameters ----------------------------------------------------
get.params <- function()
c('phi.sp','mu.phi.sp','sigma.phi.sp','mu.p.sp','sigma.p.sp','phi.year','phi','p', 'phi.sum.preci','p.sp','p.effort','z',
# Spline parameters
"m","sigmab","b","beta")