Python

[Saang-Yoon Hyun]

Hi. 

As you know, TMB, a R package, evolved from ADMB, whose hard cores include the auto differentiation algorithm and Laplace approximation for the joint likelihood of random effects and parameters.   How can we call those hard cores in Python?  In other words, if you use the TMB or ADMB functions *in Python*, can you share the ways? 

Saang-Yoon

[John Sibert]

Saang-Yoon,

I think this idea is worth exploring. Python has a number of ways to invoke C/C++ land Fortran libraries, but I have never tried any of them. And I have no idea of what the speed problems might be. Python is more strictly object- oriented, the Pandas package provides easier manipulation of data structures, and the graphics seem nicer to my eye. So, I hope someone gives it a try.

John

Contact me on Signal at +1 808 294 3842 (text, voice, or video; UTC-8)

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[Ben Bolker]

This wasn't hard to find:

https://github.com/kforeman/PyMB

I took a brief swing at testing it but ran into Python environment
problems that I didn't feel like troubleshooting ...


The README says

## Current

PyMB is currently just a light wrapper around Template Model Builder,
allowing users to run TMB models directly from Python by transparently
passing numpy and other numeric data into an embedded rpy2 instance. TMB
models are specified using C++ templates, requiring the user to be at
least somewhat familiar with C++.

## Future

We intend to make a fully Pythonic modeling library that closely mirrors
PyMC2 in syntax and ease of model specification, but uses either CppAD
mixed or TensorFlow under the hood.
"

It doesn't look active, I don't know if any effort would

>> https://groups.google.com/d/msgid/tmb-users/CAFh292OyUn3zFLSggiC6q8o5c_8JE1moOWi07C-sosbrMaKKOQ%40mail.gmail.com <https://groups.google.com/d/msgid/tmb-users/CAFh292OyUn3zFLSggiC6q8o5c_8JE1moOWi07C-sosbrMaKKOQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.

>
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--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of
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[Saang-Yoon Hyun]

Dear John and Ben. 

Thank you for your information.

Saang-Yoon 

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