Reference

Handling Datasets Functions for manipulating Dataset objects.
clean()	Remove samples and taxons from a Dataset
collapse_by_taxonomy()	Collapse by taxonomy
create_dataset()	Create Dataset object
find_good_samples()	Find good samples
measurable_taxa()	Identify measurable taxa
normalize()	Normalize
remove_samples()	Remove samples from a Dataset object.
remove_taxons()	Remove taxa from a Dataset object.
samples()	Get sample names
pool_samples()	Pool samples
rarefaction()	Rarefaction
taxa()	Get taxa names
variables()	Get metadata variables
Visualization Plotting functions.
heatgg()	Heatmap with ggplot2
phylogram()	Phylogram
plotgg(<PCA>)	Plot a PCA
plotgg(<PCO>)	Plotting a PCoA
plotgg()	Make ggplot2 plot
plotgg(<site.diversity>)	Plot diversity across sites.
plotgg_rankabun()	Make rank abundance plot
plotgg_rankabun2()	Make rank abundance plot with Poisson confidence intervals.
plotgg_taxon()	Plot single taxon.
plotgg_var()	Plot single variable.
theme_blackbox()	Blackbox theme
Analysis Functions for statistical analysis.
beta_diversity()	Beta diversity
bootstrap_glm()	Bootstrap estimation of Generalized Linear Models on a matrix of observations
compare_site_diversity()	Compare diversity accross sites and groups of samples.
matrix_glm()	Fit Generalized Linear Models on a matrix of observations
matrix_glmNB()	Fit Negative Binomial Generalized Linear Models on a matrix of observations
PCA()	Principal Component Analysis
PCO()	Principal Coordinates Analysis
site_diversity()	Diversity across sites.
subset(<Dataset>)	Subset samples from a Dataset object.
summary(<bootglm>)	Summarize bootstrap_glm model fits
summary(<matrix.glm>)	Summarize matrix GLM results
I/O Functions for reading and writing data.
read.am()	Read abundance matrix
write.qiime()	Write a QIIME abundance table file
Miscellaneous Miscellaneous functions.
AMOR-package	Abundance Matrix Operations in R
collapse_matrix()	Collapse matrix
get_tax_level()	Get tax level
print(<summary.bootglm>)	Print summary.bootglm object
total_richness()	Calculate richness of an abundance table.
Data Data objects