BMHE

A utility package for post-processing of Bayesian models performed in OpenBUGS or JAGS

Installation

The package is only available from this GitHub repository, for now. It is possible to install bmhe_utils via r-universe using the following commands.

install.packages(
  'bmhe', 
  repos = c('https://giabaio.r-universe.dev', 'https://cloud.r-project.org')
)

(NB: You can replace the CRAN mirror to any other, e.g. https://www.stats.bris.ac.uk/R/ --- see here).

Alternatively, on Windows machines, you need to install a few dependencies, including Rtools first, e.g. by running

pkgs <- c("MASS", "Rtools", "remotes")
repos <- c("https://cran.rstudio.com", "https://inla.r-inla-download.org/R/stable") 
install.packages(pkgs, repos=repos, dependencies = "Depends")

before installing the package using remotes:

remotes::install_github("giabaio/bmhe_utils")

Under Linux or MacOS, it is sufficient to install the package via remotes:

install.packages("remotes")
remotes::install_github("giabaio/bmhe_utils")

Use

Load the package into the R workspace as usual

library(bmhe)

and use all the available functions. Roughly speaking, these can be divided into "plotting", "printing" and "utility".

Plotting

• betaplot Trial-and-error Beta plot (using [manipulate](https://cran.r-project.org/web/packages/manipulate/index.html))
• coefplot "Coefplot" for the parameters in the model (using [tidyverse](https://www.tidyverse.org/))
• diagplot Specialised diagnostic plots to check convergence and autocorrelation of the MCMC run
• gammaplot Trial-and-error Gamma plot (using [manipulate](https://cran.r-project.org/web/packages/manipulate/index.html))
• posteriorplot Various plots for the posteriors in a 'bugs' or 'jags' object
• traceplot Makes a traceplot (eg to visualise MCMC simulations from multiple chains, using [tidyverse](https://www.tidyverse.org/))
• acfplot Autocorrelation plot

Printing

• print.bugs Modifies the built-in print method for the R2OpenBUGS package to provide a few more options and standardisation
• print.rjags Modifies the built-in print method for the R2jags package to provide a few more options and standardisation
• stats Computes and prints summary statistics for a vector or matrix of simulated values

Utility

• betaPar Computes the parameters of a Beta distribution so that the mean and standard dev are the input (m,s)
• betaPar2 Compute the parameters of a Beta distribution, given a prior guess for key parameters. Based on "Bayesian ideas and data analysis", page 100. Optimisation method to identify the values of a,b that give required conditions on the Beta distribution
• ilogit Computes the inverse logit of a number between -infinity and +infinity
• logit Computes the logit of a number
• lognPar Computes mean and variance of a logNormal distribution so that the parameters on the natural scale are mu and sigma
• odds2probs Maps from odds to probabilities
• OR Computes the odds ratio between two probabilities
• dlogitnorm, plogitnorm, qlogitnorm, rlogitnorm Computes the density, probability distribution, quantiles and random numbers from the logit-Normal distribution. The code is lifted from the graybox package (with attribution)
• change_of_variable Computes the density for a variable y=f(x) using the rule of the change of variable and given as inputs the functions f, g=f^{-1} and the distribution p = p_X(x)

Licence

Contributing

Please submit contributions through Pull Requests. To report issues and/or seek support, please file a new ticket in the issue tracker.