skbio.math.stats.distance.pwmantel

skbio.math.stats.distance.pwmantel(dms, labels=None, strict=True, lookup=None, method='pearson', permutations=999, alternative='two-sided')[source]

Run Mantel tests for every pair of distance matrices.

Runs a Mantel test for each pair of distance matrices and collates the results in a data frame. Distance matrices do not need to be in the same ID order (contrary to how the mantel function behaves). Distance matrices will be re-ordered prior to running each pairwise test, and if strict=False, IDs that don’t match between a pair of distance matrices will be dropped prior to running the test (otherwise a ValueError will be raised if there are non-matching IDs between any pair of distance matrices).

Parameters:

dms : iterable of DistanceMatrix objects

DistanceMatrix instances to perform pairwise Mantel tests upon.

labels : iterable of str or int, optional

Labels for each DistanceMatrix in dms. These are used in the results data frame to identify the pair of distance matrices used in a pairwise Mantel test. If None, defaults to monotonically-increasing integers starting at zero.

strict : bool, optional

If True, raises a ValueError if IDs are found that do not exist in both distance matrices for the current pairwise test. If False, these “extra” (nonmatching) IDs are discarded before running the pairwise Mantel test.

lookup : dict, optional

Maps each ID in the distance matrices to a new ID. Used to match up IDs across distance matrices prior to running the Mantel test. If the IDs already match between the distance matrices in dms, this parameter is not necessary.

method : {‘pearson’, ‘spearman’}

Correlation method. See mantel function for more details.

permutations : int, optional

Number of permutations. See mantel function for more details.

alternative : {‘two-sided’, ‘greater’, ‘less’}

Alternative hypothesis. See mantel function for more details.

Returns:

pandas.DataFrame

Data frame containing the results of each pairwise test (one per row). Includes the number of objects considered in each test as column n (after applying lookup and filtering non-matching IDs if strict=False). Column p-value has the p-values formatted as strings with the correct number of decimal places, or N/A if a p-value could not be computed.

See also

mantel