skbio.diversity.alpha_diversity¶
-
skbio.diversity.
alpha_diversity
(metric, counts, ids=None, validate=True, **kwargs)[source]¶ Compute alpha diversity for one or more samples
State: Experimental as of 0.4.1.
- Parameters
metric (str, callable) – The alpha diversity metric to apply to the sample(s). Passing metric as a string is preferable as this often results in an optimized version of the metric being used.
counts (1D or 2D array_like of ints or floats) – Vector or matrix containing count/abundance data. If a matrix, each row should contain counts of OTUs in a given sample.
ids (iterable of strs, optional) – Identifiers for each sample in
counts
. By default, samples will be assigned integer identifiers in the order that they were provided.validate (bool, optional) – If False, validation of the input won’t be performed. This step can be slow, so if validation is run elsewhere it can be disabled here. However, invalid input data can lead to invalid results or error messages that are hard to interpret, so this step should not be bypassed if you’re not certain that your input data are valid. See
skbio.diversity
for the description of what validation entails so you can determine if you can safely disable validation.kwargs (kwargs, optional) – Metric-specific parameters.
- Returns
Values of
metric
for all vectors provided incounts
. The index will beids
, if provided.- Return type
pd.Series
- Raises
ValueError, MissingNodeError, DuplicateNodeError – If validation fails. Exact error will depend on what was invalid.
TypeError – If invalid method-specific parameters are provided.