Return a tidy data summary of an MCMC object

`tidy.mcmc.list` is a function that behaves like those from `broom`. It takes an mcmc.list object from `coda.samples` and return a data frame that summarises each parameters with its mean and quantiles and returns the output as a data.table object. This can be called as `tidy`. Currently summarises over all chains.

# S3 method for mcmc.list
tidy(x, conf_level = 0.95, chain = FALSE,
  colnames = NULL, ...)

Arguments

x

object of class "mcmc.list", as you would find with fitting a model using `jags.model()`, and `coda.samples`.
conf_level

level of the credible interval to be calculuated
chain

whether or not to summarise each parameter for each chain
colnames

which parameters we want from `mcmc_object`, if `NULL` then all columns get selected
...

extra arguments

Value

a data.table containing parameter summaries

Examples

library(coda)
data(line)
tidy(line)
#>    parameter      mean        sd      2.5%    median    97.5%
#> 1:     alpha 2.9875644 0.4983950 1.9650403 3.0188300 3.876589
#> 2:      beta 0.7991864 0.3366834 0.1430713 0.7962500 1.469723
#> 3:     sigma 0.9680519 0.7413014 0.4249618 0.7911975 2.559520
# Optionally ask for a subset of parameters with a vector of `colnames`,
# and summarise for each chain:
tidy(line,
     chain = TRUE,
     colnames=c("alpha"))
#>    parameter chain     mean        sd     2.5%   median    97.5%
#> 1:     alpha     1 2.982615 0.5313900 2.085719 2.973115 3.838839
#> 2:     alpha     2 2.992514 0.4643476 1.965040 3.063630 3.890256