Ecological analysis of microbial rare biosphere defined by ulrb | Quick overview of N-ICE dataset | (a) Load and clean OTU table | (b) Rarefy samples | (b) Classify OTUs into rare, undetermined or abundant (with define_rb() function); | (c) Merge OTU table with metadata information | (e) Calculate and plot diversity metrics against environmental variables. | Alpha diversity plots | Beta diversity | Final considerations | References

Explore alternative classifications | Index | Classical example | Prepare data | Default is k = 3 | Apply 2 classifications: Rare vs Abundant | Apply more complicated classification, k>3 | Why k = 1 is non-sense | What is the maximum value of k and why? | Approaches to evaluate k | Fine grained analysis | Automatic k selection | Everything automatic | How each index behaves across all possible values of k? | References

Unsupervised Learning Based Definition Of Microbial Rare Biosphere | Brief note on nomenclature | Pre-processing of data prior to clustering algorithm | Load and clean abundance table | Transform abundance table into tidy/long format | Apply definition of rare biosphere with unsupervised learning | Fully automated version | Verify results | (1) Rank Abunddance Curve (RAC) to verify clustering | (2) Silhouette plots | Sanity check summary | References

Why we made this tutorial | Phylogenetic units | Phylogenetic units translated to machine learning | Variables and features | Abundance classification | Summary