santisoler / lapis2019-afonso-homework

Solutions to Juan Afonso's Homework for LAPIS 2019

Solutions to Juan Afonso's Homework for LAPIS 2019

This repo contains the Jupyter notebooks that perform the tasks left as homework by Juan Afonso on the LAPIS 2019 School.

It contains:

• 01. MTMIS Multiple Try Metropolis Independent Sampler.ipynb: Jupyter notebook that implements a simple Multiple Try Metropolis Independent Sampler.
• 02. Parallel Tempering with Multiple Chains.ipynb: Jupyter notebook that implements a simple Parallel Tempering with multiple chains.
• 03. Non linear inverse problem.ipynb: Jupyter notebook that creates a synthetic model from a non linear forward model and perform an MCMC inversion to recover the first one.
• environment.yml: Configuration file for creating Anaconda environment.

All notebooks have been written by Santiago Soler and Sebastian Correa-Otto in order to pass the LAPIS 2019 assignments.

How to run?

Use Binder

The easiest way to run the notebook is through Binder. Just follow this link and wait until Binder loads the notebook.

Download the repo and run it locally

You'll need a Python distribution to make it run with the following dependencies:

• numpy
• scipy
• matplotlib

The easiest way to get Python and all of these dependencies installed is through Anaconda. Download the latest Anaconda 3 distribution for your OS.

Then clone the repo:

git clone https://github.com/santisoler/lapis2019-afonso-homework

or download it as a zip file.

Change your working directory to the cloned repo and create the conda environment to get all the dependencies:

cd lapis2019-afonso-homework
conda env create

Once all the packages have been downloaded and installed, activate the repository:

conda activate lapis2019

Finally, start a Jupyter Notebook kernel:

jupyter-notebook

This will open a new page on your web browser where you will be able to find all the notebooks. You'll be able to open it and run any cell. If you want to reproduce our results, run all cells in order.

License

All code is licensed under the MIT License.

Copyright (c) 2019 Santiago Soler, Sebastian Correa-Otto

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

lapis2019-afonso-homework's Issues

Revise report.txt

The file report.txt needs to be revised and edited before sending for evaluation. Final form of presentation must be chosen as well.

Add current point in MTM and MTMIS even if was rejected

Remember to create binder when finished

Remove numba from dependencies

Remove it from the README.md and environment.yml.

Should we rename the "likelihood" function?