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

Documentation for package ‘BRCore’ version 2.0.4

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