Repo for Marion and Hamm (2016) "A hierarchical Bayesian approach to estimate endosymbiont infection rates" for a special issue of in Frontiers in Microbiology

Release 1.0 of code.

Major commits by date (2016):

• 15 February - First commit
• 11 April - First calculatoin of vcv matrix based on phylogeny
• 20 April - Corrected Erebidae naming error in Regier et al. (2013) data
• 24 April - Added OU correction with multiple alpha value
• 25 April - Phylogenetically corrected model, early code for simulating data
• 26 April - Models incorporating phylogenetic correction working, full simuation code working for BM and OU models
• 27 April - Made tree ultrametric, calculated vcv from ultrametric tree, ran models with different vcv corrections
• 28 April - Made figures, barplots by samples and proportion of species in family, added updated .tex files.
• 29 April - Updated stan files and modified plots
• 4 May - Updated plots, added model averaging
• 8 May - Updated ms latex files
• 14 May - Corrected model averaging error for family level predictions
• 24 May - Added correlation and plots for association between CI and sample size
• 14 June - Updated repo to reflect state upon submission of ms. Latex docs in folder, code in submitted state. Fingers crossed.
• 20 June - Removed the paper files, too soon to have them posted on git (should have been on ArXiv, honestly)
• 11 October - Ammended code to accomodate changes in stan, added code for posterior predictive checks of the model.
• 1 November - Ammended code to work with new "yaRrr" package
• 15 November - Release version of cade created.

Major commits by date (2017):

• 21 January - Updated code to use spaceMovie color palette, started issue to correct depreciate (but still functional) code for stan.