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