mcmc-output | R Documentation |
MCMC
callThis environment holds a copy of the last call to MCMC, including the start
and end time (to compute total elapsed time) of the call. Since the resulting
object of MCMC
is an object of class coda::mcmc, this is a way to capture
more information in case the user needs it.
get_(x)
get_logpost()
get_draws()
get_elapsed()
get_initial()
get_fun()
get_nsteps()
get_seed()
get_nchains()
get_burnin()
get_thin()
get_kernel()
get_multicore()
get_conv_checker()
get_cl()
get_progress()
get_chain_id()
x |
Character scalar. Name of an argument to retrieve. If |
The function get_logpost
returns the logposterior
value at each
iteration. The values correspond to a named numeric vector. If nchains > 1
then it will return a list of length nchains
with the corresponding logpost
values for each chain.
The function get_draws()
retrieves the proposed states from the
kernel function.
# Getting the logpost -------------------------------------------------------
set.seed(23133)
x <- rnorm(200)
y <- -4 + x*2 + rnorm(200)
f <- function(p) {
sum(dnorm(y - p[1] - x*p[2], log = TRUE))
}
# Setting a RAM kernel
kern <- kernel_am(eps = 1e-2)
ans <- MCMC(fun = f, initial = c(0, 1), nsteps = 2000, kernel = kern)
plot(
# Plotting the logpost from the last run
-get_logpost(),
# Getting the number of chains
main = paste0("nchains: ", get_nchains()),
# And the elapsed time
sub = sprintf("Run time: %.4f(s)", get_elapsed()[3]),
type = "l",
log = "y"
)
# This also works using multiple chains
ans <- MCMC(fun = f, initial = c(0, 0), nsteps=2000, nchains = 2, kernel = kern)
# In this case, just like -ans-,
draws <- get_draws()
# Plotting proposed points vs accepted
plot(
draws[[1]], pch = 20,
col = adjustcolor("gray", alpha = .5),
main = "Accepted vs proposed states\n(chain 1)"
)
lines(ans[[1]], pch = 20, col = "tomato", lwd = 2)
legend(
"topleft", legend = c("Accepted", "Proposed"), pch = c(NA, 20),
col = c("tomato", "black"), lty = c(1, NA), lwd = c(2, NA)
)
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