Package index • BRCore

Core Identification Functions

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.
plot_identified_core(): Plot Bray-Curtis increase over ranked OTU/ASVs
plot_core_distribution(): Plot Core Taxa Occupancy Across Metadata Groups

plot_rarefaction_metrics(): Plot pre-rarefaction diagnostics
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_variance_propagation(): Variance propagation diagnostic for rarefaction
plot_neutral_model(): Plot a fitted Neutral Model to Microbial Community Data

fit_neutral_model(): Fit a Neutral Model to Microbial Community Data
plot_neutral_model(): Plot a fitted Neutral Model to Microbial Community Data
sncm.fit(): Fit Sloan Neutral Community Model (SNCM)

add_rarefaction_metrics(): Calculate and append pre-rarefaction statistics to microbiome data
multi_rarefy(): Run rarefaction for microbiome count tables
plot_rarefaction_metrics(): Plot pre-rarefaction diagnostics

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)
mimulus: 16S amplicon dataset from yellow monkeyflower (Mimulus guttatus)
switchgrass: 16S amplicon dataset from Switchgrass (Panicum virgatum)
switchgrass_core: Identified core microbiome members for the switchgrass dataset