This is a fork of CmdStan for some custom calculations! If you come here looking for cmdstan, you're in the wrong place! Head over to [https://github.com/stan-dev/cmdstan].
For the input files, L is a function of P according to this table:
| P | L |
|---|---|
| 8 | 165 |
| 10 | 286 |
| 12 | 455 |
| 14 | 680 |
| 16 | 969 |
| 18 | 1330 |
| 20 | 1771 |
L = (P + 1) * (P + 2) * (P + 3) / 6
CmdStan is the command line interface to Stan, a package providing
- full Bayesian inference using the No-U-Turn sampler (NUTS), a variant of Hamiltonian Monte Carlo (HMC),
- penalized maximum likelihood estimation (MLE) using optimization, either Newton or quasi-Newton algorithms BFGS and L-BFGS,
- approximate Bayesian inference using automatic differentiation variational inference (ADVI),
- a full first- and higher-order automatic differentiation library based on C++ template overloads, and
- a supporting fully-templated matrix, linear algebra, and probability special function library.
Stan's home page, with links to everything you'll need to use Stan is:
There are separate repositories here on GitHub for interfaces:
- CmdStan (command-line/shell interface)
- CmdStanPy (a lightweight interface to CmdStan for Python users)
- CmdStanR (a lightweight interface to CmdStan for R users)
- PyStan (Python interface)
- RStan (R interface)
CmdStan's source-code repository is hosted here on GitHub.
The Stan-to-C++ compiler written in OCaml, core Stan C++ code, and CmdStan are licensed under new BSD.
Note that the Stan math library depends on the Intel TBB library which is licensed under the Apache 2.0 license. This dependency implies an additional restriction as compared to the new BSD lincense alone. The Apache 2.0 license is incompatible with GPL-2 licensed code if distributed as a unitary binary. You may refer to the Apache 2.0 evaluation page on the Stan Math wiki.
- Download the latest release tarball (use the "green" link) from: CmdStan releases
- Unpack the tarball.
- From the folder, type
makefor a quick tutorial on how to build models.
See Getting Started with CmdStan for instructions how to clone both CmdStan and Stan submodule.
As of version 2.22, CmdStan has switched to the new Stan-to-C++ compiler, called stanc3. This compiler is intended to be backwards compatible with the existing Stan language and should accept all models that compile under the release 2.21 compiler, (see this list of bug fixes).
The old C++ compiler is still available as program bin/stanc2.
This compiler is not longer being maintained, i.e., existing bugs will not be fixed
and new functions and features are only available in the stanc3 compiler.
Its intended use is as a diagnostic tool and backup for the new stanc3 compiler and
If you experience any problems or noticeable changes in compilation, execution, or outputs of model after switching to CmdStan 2.22, you can use the stanc2 compiler via the make option STANC2:
> make STANC2=TRUE my_program
If using the old compiler fixes the issues in your model, please report a bug on the stanc3 repository. Otherwise, report the issue to the CmdStan repository.
To permanently enable the stanc2 compiler, add the following to your make/local file:
STANC2=true
to the make/local file.
If using the old compiler fixes the issues in your model, please report a bug on the stanc3 repository. Otherwise, report the issue to the CmdStan repository.
Further information is available on the CmdStan wiki page https://github.com/stan-dev/cmdstan/wiki/Troubleshooting-the-stanc3-compiler