R code for Prokounter paper

This resource presents code used for analysis for the Prokounter manuscript.

The src/ folder provides some utility functions. The rest of the code is organized into the following files.

• Paper_AmplificationSequencing*Rmd presents code used in modeling amplification and sequencing processes.

• Paper_SSandLoessTrends.Rmd presents within-genus taxa accumulation data trends.

• Paper_GenusEffectsWhenTesting*Rmd presents code to characterize systematic genus effects when fitting overall within-genus taxa accumulation data.

• Paper_WGTACsLinearSDtermsAls*Rmd presents code to compute main text and supplementary tables.

• Paper_WGTACsHigherOrder*.Rmd presents accumulation trends at higher taxonomic orders.

• Paper_AsymptoticAndObservedRichness*Rmd, Paper_Chao1CC16Behavior.Rmd, Paper_undetectedRichness.Rmd presents code used for characterizing various richness estimators, their correlations to observed richness estimators and the behavior of undetected richness estimates.

• Paper_FoldChangeDistributionTec*Rmd presents code to characterize the relative abundance fold change distribution across study samples.

• Paper_Simulations.Rmd presents code on simulating differential richness.