Bayesian CBIOMES workshop

This repository contains notebooks and files for the Bayesian CBIOMES workshop.

Preparation

In preparation for the meeting and if Stan is not yet installed on your system follow the installation instructions for your operating system of choice.

Schedule

Tips and tricks

• Turn any jupyter notebook into a script using

jupyter nbconvert --to script notebook_name.ipynb

• Some introductions to using Git

  MITgcm manual Git intro section

  Github guides collection

• Steps to bring your github fork master branch up to date with main repo

  1. If you have not done so already, download your fork to some directory (e.g. ~/projects/gits/github.com/YOUR-GITHUB-ORG-NAME/bayesian_cbiomes) using command such as

       $ git clone https://github.com/YOUR-GITHUB-ORG-NAME/bayesian_cbiomes.git 
     

  2. If you have not done so already, set the upstream repo for your download of the fork

       $  cd ~/projects/gits/github.com/YOUR-GITHUB-ORG-NAME/bayesian_cbiomes
       $  git remote add upstream https://github.com/jpmattern/bayesian_cbiomes
     

  3. Now you are set to bring the local copy up to date.

     1. Make sure you are in the relevant directory and have the master branched checked out

       $  cd ~/projects/gits/github.com/YOUR-GITHUB-ORG-NAME/bayesian_cbiomes
       $  git checkout master
     

     2. Now fetch the changes from the upstream repo and merge

       $ git fetch upstream master
       $ git merge upstream/master
     

     3. Finally push changes back to your github.com organization

       $ git push
     

  4. Awesome, you should now be done! It is possible that the git merge upstream/master step will report a merge conflict error. This happens when the git algorithms can't figure out how to merge some changes you have made yourself in the master branch. One practice to manage this is to make your own changes on a feature branch. The feature branch workflow is described here.

For fun

• Some timely videos just added on this years viralest math site on the web 3blue1brown recently!

  Intro to Bayes, includes references to the SS Central America and other Bayes legends.

  Testing Bayes, simple visual working through of Bayes algebra - with nice graphics!