I create traceplots of my stanfit objects via mcmc_trace. I want to rename the titles of the traceplots. I already managed to change the title, but I don't know how I can rename the plots to greek letters with subscripts similar to the expression function.
array <- as.array(fit)
array[1,1,1:3]
dimnames(array)[[3]][1:3] <- c("alpha1", "alpha2", "alpha3")
trace <- mcmc_trace(array, pars = c("alpha1", "alpha2", "alpha3")
I want to replace alpha1 with expression(gamma[0]), but it doesn't work.
Okay, so after a little digging, it simply seems like bayesplott::mcmc_trace
doesn't have an option for greek lettering.
However, the much similar mcmcplots::traplot
package has an option greek = TRUE
.
I did a random example for you to see:
library(mcmcplots)
nc <- 3; nr <- 1000
pnames <- c(paste('alpha[', 1:2, ']', sep = ''), paste('gamma[1]', sep = ''))
means <- rpois(10, 20)
fakemcmc <- coda::as.mcmc.list(
lapply(1:3, function(i) coda::mcmc(matrix(rnorm(nc*nr, rep(means, each=nr)),
nrow=nr, dimnames=list(NULL,pnames)))))
traplot(fakemcmc, greek = TRUE)
Which produces this output: