Description Usage Arguments Value Author(s) Examples
View source: R/simsList_from_mcmcList.R
Takes an object of class mcmc.list
and converts it to a list with one component for each parameter present. Parameters which are not scalar are stored as arrays of the appropriate dimension. Ragged arrays in the JAGS output result in all-NA columns in the output - see Examples.
We now recommend the use of mcmcOutput
objects instead of simsList
. This function will be removed in future versions.
1 | simsList(mc)
|
mc |
an object of class |
A list with one component for each parameter monitored. This is the same format as the sims.list
component in the output of other JAGS wrappers.
Mike Meredith.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | # Salamander occupancy again:
sal <- rep(0:4, c(21,12,1,4,1))
# JAGS code for psi(.) p(.) occupancy model but with additional parameters:
# p appears to be a 2x2 matrix but p[1,1] is undefined;
# this will be a ragged array in the output.
modelText <- "
model {
for(i in 1:nSites) {
z[i] ~ dbern(psi)
y[i] ~ dbin(p[1,2] * z[i], n)
}
psi ~ dbeta(1, 1)
p[1,2] ~ dbeta(1, 1)
p[2,1] ~ dbeta(1, 1)
p[2,2] <- 3
} "
writeLines(modelText, con = "JAGSmodel.txt")
JAGSdata <- list(y = sal, n = 5, nSites = length(sal))
inits <- function(chain) list(z = rep(1, 39))
wanted <- c("p", "psi")
res1 <- saveJAGS(JAGSdata, inits, wanted, "JAGSmodel.txt",
chains=2, sample2save=1000, nSaves=4, burnin=1000, thin=1,
fileStub="testing")
str(res1)
summary(res1)
# p has 3 elements
# Load the results into R as an mcmc.list object
mcmc <- combineSaves(res1)
str(mcmc)
#... and convert to a sims.list:
sl <- simsList(mcmc)
str(sl)
# sl$p is an 8000 x 2 x 2 array, with sl$p[, 1, 1] filled with NAs
apply(sl$p, 2:3, mean)
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