Derive MCMC Parameters.
mcmcderive
Why mcmcderive
?
mcmcderive
is an R package to generate derived parameter(s) from Monte Carlo Markov Chain (MCMC) samples using R code.
This is useful because it means Bayesian models can be fitted without the inclusion of derived parameters which add unnecessary clutter and slows model fitting. For more information on MCMC samples see Brooks et al. (2011).
Installation
To install the latest release version from CRAN
install.packages("mcmcderive")
To install the latest development version from GitHub
remotes::install_github("poissonconsulting/mcmcderive")
Demonstration
library(mcmcderive)
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
Parallel Chains
If the MCMC object has multiple chains the run time can be substantially reduced by generating the derived parameters for each chain in parallel. In order for this to work it is necessary to:
- Ensure plyr and doParallel are installed using
install.packages(c("plyr", "doParallel"))
. - Register a parallel backend using
doParallel::registerDoParallel(4)
. - Set
parallel = TRUE
in the call tomcmc_derive()
.
Extras
To facilitate the translation of model code into R code the extras
package provides the R equivalent to common model functions such as pow()
, phi()
and log() <-
.
Contribution
Please report any issues.
Pull requests are always welcome.
Code of Conduct
Please note that the mcmcderive project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
References
Brooks, S., Gelman, A., Jones, G.L., and Meng, X.-L. (Editors). 2011. Handbook for Markov Chain Monte Carlo. Taylor & Francis, Boca Raton.