MCMC Derive — mcmc_derive • mcmcderive

Generates an MCMC object with derived parameters from an MCMC object.

mcmc_derive(object, ...)

# S3 method for class 'nlist'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

# S3 method for class 'nlists'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

# S3 method for class 'mcmc'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

# S3 method for class 'mcmc.list'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  parallel = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

# S3 method for class 'mcmcr'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  parallel = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

# S3 method for class 'mcmcrs'
mcmc_derive(
  object,
  expr,
  values = list(),
  monitor = ".*",
  primary = FALSE,
  parallel = FALSE,
  silent = getOption("mcmcderive.silent", FALSE),
  ...
)

Arguments

object: An MCMC object.
...: Unused.
expr: A string of the R code defining the values of the derived parameter(s) with respect to the parameters in object.
values: A named list of additional R objects to evaluate in the R expression.
monitor: A regular expression specifying the derived parameter(s) in expr to monitor.
primary: A flag specifying whether to include the original primary parameters in the new MCMC object.
silent: A flag specifying whether to suppress messages and warnings.
parallel: A flag specifying whether to generate the derived parameters for each chain in parallel.

Value

An MCMC object with the derived parameter(s).

Details

It's important to note that parameters in the expression that also occur in the original object are not included in the new object unless primary = TRUE in which case they are simply copied from the original object to the new one. This applies even when the primary parameters are redefined in values.

Methods (by class)

mcmc_derive(nlist): Get derived parameters for an nlist::nlist-object()
mcmc_derive(nlists): Get derived parameters for an nlist::nlists-object()
mcmc_derive(mcmc): Get derived parameters for an coda::mcmc() object
mcmc_derive(mcmc.list): Get derived parameters for an coda::mcmc.list() object
mcmc_derive(mcmcr): Get derived parameters for an mcmcr::mcmcr-object()
mcmc_derive(mcmcrs): Get derived parameters for an mcmcr::mcmcrs-object()

Examples

mcmcr::mcmcr_example
#> $alpha
#> [1] 3.718025 4.718025
#> 
#> nchains:  2 
#> niters:  400 
#> 
#> $beta
#>           [,1]     [,2]
#> [1,] 0.9716535 1.971654
#> [2,] 1.9716535 2.971654
#> 
#> nchains:  2 
#> niters:  400 
#> 
#> $sigma
#> [1] 0.7911975
#> 
#> nchains:  2 
#> niters:  400 
#> 

expr <- "
 log(alpha2) <- alpha
 gamma <- sum(alpha) * sigma"

mcmc_derive(mcmcr::mcmcr_example, expr, silent = TRUE)
#> $alpha2
#> [1]  41.18352 111.94841
#> 
#> nchains:  2 
#> niters:  400 
#> 
#> $gamma
#> [1] 6.60742
#> 
#> nchains:  2 
#> niters:  400 
#>