This is the GitHub repository for code and data associated with the manuscript "Sustained drought, but not short-term warming, alters the gut microbiome of wild Anolis lizards"
Data: contains all data outputs associated with this manuscript. Raw data files are available under NCBI Bioproject PRJNA.
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liz-micro-metadata.tsv is the metadata file associated with the sequences
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Panama-Weather-Data-2017-through-2019 is the data for analyses about weather on the mainland and islands, as measured from the weather station on BCI and operative temperature models.
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PICRUST2/Kegg contains all the outputs associated with the functional inference analysis.
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QIIME2 contains all outputs from QIIME2. Within this folder are the overarching outputs for the entire dataset as well as subsets of the data for various comparisons contained in subfolders.
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ShortTermWarming contains all the data associated with the short term warming experiment - lizard temperatures throughout the experiment, lizard ids, and physiology data.
Figures: contains all figures for this publication
QIIME2 Commands: contains a script detailing all the analyses performed in QIIME2
R and Python Scripts: contain the scripts for all the analyses performed in R and Python. Data called in each of these scripts is found in the data folder.
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2020_02_04_rdecontamscript.R is the script for performing decontam on the dataset.
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2020_07_05_Regression_Physiology.Rmd is the script for the regressions on physiological data.
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2021_05_25_Weather_Analysis_Script.Rmd is the script for performing analysis on the climate data.
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2021_05_28_Python_and_RCombined_KeggProcessing.Rmd and KeggSortingScript.ipynb are the scripts for sorting and analyzing the outputs of PICRUST2
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2021_06_05_Figures.Rmd is the script for producing the majority of figures in the publication.