lingpy.test.evaluate.EvalPSA

class lingpy.test.evaluate.EvalPSA(gold, test)

Base class for the evaluation of automatic pairwise sequence analyses.

Parameters :

gold, test : lingpy.compare.Pairwise

The Pairwise objects which shall be compared. The first object should be the gold standard and the second object should be the test set.

See also

lingpy.test.evaluate.EvalMSA

Notes

Moste of the scores which can be calculated with help of this class are standard evaluation scores in evolutionary biology. For a close description on how these scores are calculated, see, for example, Thompson1999, List2012, and Rosenberg2009b.

Methods

c_score()	Calculate column (C) score.
diff([filename])	Write all differences between two sets to a file.
jc_score()	Calculate the Jaccard (JC) score.
pir_score([mode])	Compute the percentage of identical rows (PIR) score.
sp_score()	Calculate the sum-of-pairs (SP) score.