Andrew Johnson

Generalised Hypergeometric (pFq) function

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## Description One of the pre-requisites for implementing the inverse-CDF (quantile) of the Gamma distribution is the hypergeometric 2F2 function, which is needed for the gradients. The gradients are the...

Update log_prob method to take constrained_params in init format

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#### Submisison Checklist - [x] Run tests: `./runCmdStanTests.py src/test` - [x] Declare copyright holder and open-source license: see below #### Summary: Updates the recently added `log_prob` method so that the...

Add install target for Linux/OSX systems

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#### Summary: A request that's come up before is the ability to centrally install cmdstan after building. I've put together an initial attempt at a makefile target, so that a...

WSL - Run `cmdstan` and models under WSL filesystem

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#### Submission Checklist - [x] Run unit tests - [x] Declare copyright holder and agree to license (see below) #### Summary This PR refactors the WSL functionality introduced in #677...

Expose `log_prob` and `grad_log_prob` methods

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I'm opening this as a reference issue/reminder to myself to add a `log_prob` method to `CmdStanFit` once [the PR](https://github.com/stan-dev/cmdstan/pull/1107) has been merged. As for the implementation/design, I'm thinking of simply...

With the merge of #74, it's now possible for users to add new marginals as needed. Add some documentation and worked examples for this with both discrete and continuous marginals

Delegate installation/configuration to rstantools

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This PR updates the `rstanarm` installation to fully delegate to `rstantools`. This will help ensure ongoing compatibility with `rstan` and its updates, and simplify some of the maintenance involved with...

External c++ example fails

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#### Summary: Attempting to run the [external c++ example](https://mc-stan.org/docs/cmdstan-guide/using-external-cpp-code.html) fails with: ``` andrew@Andrews-MacBook-Air cmdstan-2.30.1 % make STANCFLAGS=--allow-undefined USER_HEADER=examples/bernoulli/make_odds.hpp examples/bernoulli/bernoulli # on Windows add .exe --- Translating Stan model to C++...

As mentioned by a student in Zulip, installing `pystan` on an M1 Mac requires building `httpstan` from source first. This PR updates the FAQ to walk through the process -...

Hopefully this is just me misunderstanding the adjustment, but it looks like the CQC limits aren't being back-transformed to the original scale. Given that it uses a square-root transform, shouldn't...