This repository contains all the code necessary to replicate the figures in Scale Reliant Inference by Nixon, Letourneau, David, Lazar, Mukherjee, and Silverman (2021+).
To run, first make sure the correct packages are installed. All packages are available on CRAN and/or Bioconductor. CRAN packages needed: fido, tidyverse, gghighlight, ggpattern, cowplot, directlabels, matrixNormal, and LaplacesDemon. Bioconductor packages needed: phyloseq, DESeq2, and ALDEx2.
To rerun the results, first make sure that you have the packages in the first few lines of 02_simulations.R and 03_realAnalysis.R installed. If you are unsure of how to install packages from BioConductor (such as the DESeq2 and ALDEx2 package), see the instructions here.
Once the packages are installed, replication should be easy. Simply run the functions in 01a_main_functions.R and 01b_helper_functions.R. Both the simulations and real data analysis files can then be run with these two files alone. They do not depend on each other, so run order does not matter.