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A library for working with phylogenetic and population genetic data.
v0.32.0
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measures.cpp File Reference

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Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::placement
 

Functions

double edpl (Pquery const &pquery, utils::Matrix< double > const &node_distances)
 Calculate the EDPL uncertainty values for a Pquery. More...
 
std::vector< double > edpl (Sample const &sample)
 Calculate the expected distance between placement locations (EDPL) for all Pqueries in a Sample. More...
 
double edpl (Sample const &sample, Pquery const &pquery)
 Calculate the EDPL uncertainty values for a Pquery. More...
 
std::vector< double > edpl (Sample const &sample, utils::Matrix< double > const &node_distances)
 Calculate the edpl() for all Pqueries in the Sample. More...
 
double pairwise_distance (const Sample &smp_a, const Sample &smp_b, bool with_pendant_length=false)
 Calculate the normalized pairwise distance between all placements of the two Samples. More...
 
double variance (const Sample &smp, bool with_pendant_length=false)
 Calculate the variance of the placements on a tree. More...
 
static double variance_partial_ (PqueryPlain const &pqry_a, std::vector< PqueryPlain > const &pqrys_b, utils::Matrix< double > const &node_distances, bool with_pendant_length)
 Internal function that calculates the sum of distances contributed by one pquery for the variance. See variance() for more information. More...