skbio.tree.TreeNode.compare_tip_distances#
- TreeNode.compare_tip_distances(other, sample=None, dist_f=<function distance_from_r>, shuffle_f=<bound method RandomState.shuffle of RandomState(MT19937)>)[source]#
Compare self to other using tip-to-tip distance matrices.
Value returned is dist_f(m1, m2) for the two matrices. Default is to use the Pearson correlation coefficient, with +1 giving a distance of 0 and -1 giving a distance of +1 (the maximum possible value). Depending on the application, you might instead want to use distance_from_r_squared, which counts correlations of both +1 and -1 as identical (0 distance).
Note: automatically strips out the names that don’t match (this is necessary for this method because the distance between non-matching names and matching names is undefined in the tree where they don’t match, and because we need to reorder the names in the two trees to match up the distance matrices).
- Parameters:
- otherTreeNode
The tree to compare
- sampleint or None
Randomly subsample the tips in common between the trees to compare. This is useful when comparing very large trees.
- dist_ffunction
The distance function used to compare two the tip-tip distance matrices
- shuffle_ffunction
The shuffling function used if sample is not None
- Returns:
- float
The distance between the trees
- Raises:
- ValueError
A ValueError is raised if there does not exist common tips between the trees
See also
Examples
>>> from skbio import TreeNode >>> # note, only three common taxa between the trees >>> tree1 = TreeNode.read(["((a:1,b:1):2,(c:0.5,X:0.7):3);"]) >>> tree2 = TreeNode.read(["(((a:1,b:1,Y:1):2,c:3):1,Z:4);"]) >>> dist = tree1.compare_tip_distances(tree2) >>> print("%.9f" % dist) 0.000133446