Throughout this manual, we refer to this top-level CmdStan source directory as. cmdstan-2.23.0.Ĭloning CmdStan from GitHub creates a directory simply called cmdstan. Version string consists of the version numbers, e.g. The CmdStan release unpacks into a directory called cmdstan- where the To use the current development version you can clone the GitHub repo. The most recent CmdStan release is always available as. The CmdStan C++ source code and libraries.ĬmdStan releases are available from GitHub as a compressed tarfile containing all C++ source code and libraries. On Windows, mingw32-make is installed as part of RTools. On macOS, this is part of the XCode command line tools installed via command xcode-select -install. Utility program or the Windows equivalent mingw32-make. Windows: g++ 8.1 (available with RTools 4.0) is recommended alternatively, g++ 4.9.3 (available with RTools 3.5).21.6.2 Infinite and Not-a-Number Values.21.6 Integer- and Real-Valued Variables.21.5 Matrix- and Vector-Valued Variables.18 print (deprecated): MCMC Output Analysis.17.3.3 Low E-BFMI values - sampler transitions HMC potential energy.17.3.1 Divergent transitions after warmup.17.3 diagnose Warnings and Recommendations.17 diagnose: Diagnosing Biased Hamiltonian Monte Carlo Inferences.16.2.2 Model Parameters and Quantities of Interest.13 Diagnosing HMC by Comparison of Gradients.11 Variational Inference Algorithm: ADVI.9.5.9 Suppressing progress updates to the console.9.5.8 Capturing Hamiltonian diagnostics and gradients.9.5.6 Changing the NUTS-HMC adaptation parameters.9.5.5 Specifying the metric and stepsize.9.5.2 Changing the default warmup and sampling iterations.9.5.1 Running multiple chains with a specified RNG seed. 9.3.1 Samples from a set of fixed parameters.9.2.1 Step size optimization configuration.9 MCMC Sampling using Hamiltonian Monte Carlo.8.3 Initialize Model Parameters Argument.7 Generating Quantities of Interest from a Fitted Model.4.4 Summarizing Sampler Output(s) with stansummary.3.5 C++ compilation and linking optimizations flags.3.4 Troubleshooting C++ Compiler or Linker Errors.1.3 Clone the GitHub CmdStan Repository.
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