# A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers

## Documentation for package ‘BRCore’ version 2.0.7

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add_rarefaction_metrics | Calculate and append pre-rarefaction statistics to microbiome data
bcse | 16S amplicon dataset from the GLBRC Biofuel Cropping System Experiment (BCSE) at Michigan State University, Kellogg Biological Station
bean | 16S amplicon dataset from common bean (Phaseolus vulgaris)
fit_neutral_model | Fit a Neutral Model to Microbial Community Data
identify_core | Identify Core Microbiome Using Bray-Curtis Similarity biological samples. Core taxa are selected using either a "last % increase" or "elbow" method implementing the method developed by Shade and Stopnisek (2019) Curr Opin Microbiol, see below for details.
mimulus | 16S amplicon dataset from yellow monkeyflower (Mimulus guttatus)
multi_rarefy | Run rarefaction for microbiome count tables
plot_abundance_occupancy | Plot Abundance-Occupancy Curve and Display the Core Taxa
plot_core_distribution | Plot Core Taxa Occupancy Across Metadata Groups
plot_identified_core | Plot Bray-Curtis increase over ranked OTU/ASVs
plot_neutral_model | Plot a fitted Neutral Model to Microbial Community Data
plot_rarefaction_metrics | Plot pre-rarefaction diagnostics
plot_variance_propagation | Variance propagation diagnostic for rarefaction
sncm.fit | Fit Sloan Neutral Community Model (SNCM)
switchgrass | 16S amplicon dataset from Switchgrass (Panicum virgatum)
switchgrass_core | Identified core microbiome members for the switchgrass dataset
update_otu_table | Add a rarefied otu_table to a phyloseq object