#include "genesis/placement/function/measures.hpp"
#include "genesis/placement/function/distances.hpp"
#include "genesis/placement/function/functions.hpp"
#include "genesis/placement/function/helper.hpp"
#include "genesis/placement/function/masses.hpp"
#include "genesis/placement/function/operators.hpp"
#include "genesis/placement/placement_tree.hpp"
#include "genesis/placement/pquery/plain.hpp"
#include "genesis/placement/sample_set.hpp"
#include "genesis/placement/sample.hpp"
#include "genesis/tree/common_tree/distances.hpp"
#include "genesis/tree/function/distances.hpp"
#include "genesis/tree/function/operators.hpp"
#include "genesis/tree/function/tree_set.hpp"
#include "genesis/tree/iterator/node_links.hpp"
#include "genesis/tree/iterator/postorder.hpp"
#include "genesis/tree/mass_tree/functions.hpp"
#include "genesis/tree/mass_tree/tree.hpp"
#include "genesis/tree/tree_set.hpp"
#include "genesis/tree/tree.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/core/options.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/matrix/operators.hpp"
#include <algorithm>
#include <cassert>
#include <map>
#include <stdexcept>
Go to the source code of this file.
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... | |