qiime diversity core-metrics (version 2019.4)

--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]:

--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]:

--m-metadata-file [required]s

--m-metadata-file [required] 0

Core diversity metrics (non-phylogenetic)

Applies a collection of diversity metrics (non-phylogenetic) to a feature table.

Parameters

table : FeatureTable[Frequency]: The feature table containing the samples over which diversity metrics should be computed.
sampling_depth : Int % Range(1, None): The total frequency that each sample should be rarefied to prior to computing diversity metrics.
metadata : Metadata: The sample metadata to use in the emperor plots.

Returns

rarefied_table : FeatureTable[Frequency]: The resulting rarefied feature table.
observed_otus_vector : SampleData[AlphaDiversity]: Vector of Observed OTUs values by sample.
shannon_vector : SampleData[AlphaDiversity]: Vector of Shannon diversity values by sample.
evenness_vector : SampleData[AlphaDiversity]: Vector of Pielou's evenness values by sample.
jaccard_distance_matrix : DistanceMatrix: Matrix of Jaccard distances between pairs of samples.
bray_curtis_distance_matrix : DistanceMatrix: Matrix of Bray-Curtis distances between pairs of samples.
jaccard_pcoa_results : PCoAResults: PCoA matrix computed from Jaccard distances between samples.
bray_curtis_pcoa_results : PCoAResults: PCoA matrix computed from Bray-Curtis distances between samples.
jaccard_emperor : Visualization: Emperor plot of the PCoA matrix computed from Jaccard.
bray_curtis_emperor : Visualization: Emperor plot of the PCoA matrix computed from Bray-Curtis.