Disturbance and recovery: microbial community (re)assembly following disturbance across realms

This repository includes R code to reproduce the analyses shown in the article:

Disturbance and recovery: a synthesis of microbial community assembly following disturbance across realms

by Stephanie D. Jurburg, Shane A. Blowes, Ashley Shade, Nico Eisenhauer, Jonathan M. Chase

Here we give a brief overview on the code and data files in this repository. Note that most analyses were repeated for two different standardisations of sample-effort: one used a single standardisation across all studies, the second standardised effort within studies. Results were qualitatively similar, and we present the across study standardisation in the main text. There are two versions of most things in the repo, one for each standardisation.

Data

Files in the data folder contain the processed data following the bioinformatics, effort standardisation, and null modelling (code for these steps available at:https://github.com/drcarrot/DisturbanceSynthesis)

dispersions-across.txt: disperion data standardised across studies

dispersions-within.txt: disperion data standardised within studies

dispersions.zscores-across.txt: null model results for disperion data standardised across studies

dispersions.zscores-within.txt: null model results for disperion data standardised within studies

Resilience-across.txt: turnover data standardised across studies

Resilience-within.txt: turnover data standardised within studies

Resilience.zscores-across.txt: null model results for turnover data standardised across studies

Resilience.zscores-within.txt: null model results for turnover data standardised within studies

Rich-across.txt: richness data standardised across studies

Rich-within.txt: richness data standardised within studies

Code

Files in the code folder include:

01_: code to fit models (written to run on scientific computing cluster)

02_: scripts to examine model fit (convergence, posterior predictive checks), examine results and make figures

03_: script to combine model output of two different responses and plot

04_: scripts to wrangle and visually inspect models fit to the different data standardisations

Results

Files in the model-fits-across folder have the model objects for models fit to data standardised across all studies

Files in the model-fits-within folder have the model objects for models fit to data standardised within each studies