In libbi/RBi: Interface to 'LibBi'

rbi is an R interface to libbi, a library for Bayesian inference.

It mainly contains:

• various functions to retrieve and process the results from libbi (which are in NetCDF format)
• a bi_model class, to manipulate libbi models
• a libbi wrapper class, to perform Bayesian using libbi inference from within R,

Installation

The easiest way to install the latest stable version of rbi is via CRAN:

install.packages("rbi")

Alternatively, the current development version can be installed using the remotes package

# install.packages("remotes")
library("remotes")
install_github("sbfnk/rbi")

The rbi package has only been tested on GNU/Linux and OS X, but it should mostly work everywhere R works.

If you want to use rbi as a wrapper to LibBi then you need a working version of LibBi. To install LibBi on a Mac, the easiest way is to install Homebrew, followed by (using a command shell, i.e. Terminal or similar):

```{sh install-libbi, eval = FALSE} brew install libbi

On linux, follow the [instructions](https://github.com/lawmurray/LibBi/blob/master/INSTALL_LINUX.md) provided with LibBi.

The path to `libbi` script can be passed as an argument to **rbi**, otherwise the package tries to find it automatically using the `which` linux/unix command.

If you just want to process the output from **LibBi**, then you do not need to have **LibBi** installed.

Getting started
==============

A good starting point is to look at the included demos:

```r
demo(PZ_generate_dataset) ## generating a data set from a model
demo(PZ_PMMH) ## particle Markov-chain Metropolis-Hastings
demo(PZ_SMC2) ## SMC^2
demo(PZ_filtering) ## filtering

For further information, have a look at the introductory vignette from the link from the rbi CRAN package.

Using coda

LibBi contains the get_traces method which provides an interface to coda.

Other packages

For higher-level methods to interact with LibBi, have a look at rbi.helpers.

libbi/RBi documentation built on June 3, 2024, 12:22 p.m.