cassiopeia.critique.triplets_correct#
- cassiopeia.critique.triplets_correct(tree1, tree2, number_of_trials=1000, min_triplets_at_depth=1)[source]#
Calculate the triplets correct accuracy between two trees.
Takes in two newick strings and computes the proportion of triplets in the tree (defined as a set of three leaves) that are the same across the two trees. This procedure samples the same number of triplets at every depth such as to reduce the amount of bias of sampling triplets randomly.
- Parameters:
- tree1
CassiopeiaTree Input CassiopeiaTree
- tree2
CassiopeiaTree CassiopeiaTree to be compared to the first tree.
- number_of_trials
int(default:1000) Number of triplets to sample at each depth
- min_triplets_at_depth
int(default:1) The minimum number of triplets needed with LCA at a depth for that depth to be included
- tree1
- Returns:
all_triplets_correct: the total triplets correct resolvable_triplets_correct: the triplets correct for resolvable
triplets
- unresolved_triplets_correct: the triplets correct for unresolvable
triplets
- proportion_resolvable: the proportion of unresolvable triplets per
depth
- Return type:
Four dictionaries storing triplet information at each depth