StanBase.jl

Common components for a family of wrapper packages using Stan's cmdstan executable from Julia.
Author StanJulia
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2 Months Ago
Started In
July 2019

StanBase.jl

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Introduction

This package contains all the common components for several application packages wrapping Stan's cmdstan executable.

Stan methods supported are in StanSample, StanOptimize, StanVariational, StanDiagnose and generated_quantities (included in StanSample.jl).

StanBase.jl, HelpModel.jl, help_types.jl and cmdline.jl are the templates that have been used in the cmdstan application packages to support cmdstan options such as stan_sample, stan_variational, etc.

Note that help_types.jl is a bit degenerated, a more complete version can be found here.

These five application packages support all features and options currently available in the cmdstan exacutable.

The intention is that users of Stan's cmdstan executable will never have to install Stanbase.jl, they can simply install any of the application packages listed here.

The currenly existing package CmdStan.jl v5.x.x will continue to exists. A new version of Stan.jl, v6 using this newer setup is in the pipeline.

Installation

This package is registered yet. Install with

pkg> add StanBase

This package is loaded automatically when using ... any of the application packages.

This package is derived from Tamas Papp's StanRun.jl package. It also uses StanDump.jl.

This and all the application packages need a working cmdstan installation, the path of which you should specify in JULIA_CMDSTAN_HOME, eg in your ~/.julia/config/startup.jl have a line like

# CmdStan setup
ENV["JULIA_CMDSTAN_HOME"] = expanduser("~/src/cmdstan-2.19.1/") # replace with your path