Unsupervised Learning Based Definition of Microbial Rare Biosphere

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Documentation for package ‘ulrb’ version 0.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ulrb-package	ulrb: Unsupervised Learning Based Definition of Microbial Rare Biosphere
check_avgSil	Check average Silhouette score index
check_CH	Check Calinski-Harabasz index
check_DB	Check Davies-Bouldin Index
define_rb	Define Rare Biosphere
evaluate_k	Evaluate k from all samples in a dataset
evaluate_sample_k	Evaluate sample k
nice	V4-V5 16S rRNA gene amplicons, clean OTU table (N-ICE, 2015)
nice_env	Metadata of samples from OTU tables (N-ICE, 2015)
nice_raw	V4-V5 16S rRNA gene amplicons, raw OTU table (N-ICE, 2015)
nice_tidy	V4-V5 16S rRNA gene amplicons, clean OTU table in tidy/long format (N-ICE, 2015)
plot_ulrb	Plot ulrb clustering results and silhouette scores
plot_ulrb_clustering	Plot Rank Abundance Curve of classification results
plot_ulrb_silhouette	Plot silhouette scores from clustering results
prepare_tidy_data	Prepare data in tidy format
suggest_k	Suggest k