`lmpy.statistics.pam_stats`

Module containing base PAM statistic functionality.

Module Contents

Classes

`CovarianceMatrixMetric`	Constructor.
`DiversityMetric`	Constructor.
`PamDistMatrixMetric`	Constructor.
`PamStats`	Constructor for PAM stats computations.
`PamStatsMetric`	Constructor.
`SiteMatrixMetric`	Constructor.
`SpeciesMatrixMetric`	Constructor.
`TreeDistanceMatrixMetric`	Constructor.
`TreeMetric`	Constructor.

Functions

`alpha`(pam)	Calculate alpha diversity, the number of species in each site.
`alpha_proportional`(pam)	Calculate proportional alpha diversity.
`c_score`(pam)	Calculate the checker board score for the PAM.
`lande`(pam)	Calculate Lande's beta diversity metric for a PAM.
`legendre`(pam)	Calculate Legendre's beta diversity metric for a PAM.
`mean_nearest_taxon_distance`(phylo_dist_mtx)	Calculates the nearest neighbor distance.
`mean_pairwise_distance`(phylo_dist_mtx)	Calculates mean pairwise distance between species present at a site.
`num_sites`(pam)	Get the number of sites with presences.
`num_species`(pam)	Get the number of species with presences.
`omega`(pam)	Calculate the range size per species.
`omega_proportional`(pam)	Calculate the mean proportional range size of each species.
`pearson_correlation`(pam, phylo_dist_mtx)	Calculates the Pearson correlation coefficient for each site.
`phi`(pam)	Calculate phi, the range size per site.
`phi_average_proportional`(pam)	Calculate proportional range size per site.
`phylogenetic_diversity`(tree)	Calculate phylogenetic diversity of a tree.
`psi`(pam)	Calculate the range richness of each species.
`psi_average_proportional`(pam)	Calculate the mean proportional species diversity.
`schluter_site_variance_ratio`(pam)	Calculate Schluter's site variance ratio.
`schluter_species_variance_ratio`(pam)	Calculate Schluter's species variance ratio.
`sigma_sites`(pam)	Compute the site sigma metric for a PAM.
`sigma_species`(pam)	Compute the species sigma metric for a PAM.
`sum_pairwise_distance`(phylo_dist_mtx)	Calculates the sum pairwise distance for all species present at a site.
`whittaker`(pam)	Calculate Whittaker's beta diversity metric for a PAM.

class lmpy.statistics.pam_stats.CovarianceMatrixMetric(func)[source]

Bases: PamStatsMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.DiversityMetric(func)[source]

Bases: PamStatsMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.PamDistMatrixMetric(func)[source]

Bases: _SiteStatMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.PamStats(pam, tree=None, tree_matrix=None, node_heights_matrix=None, tip_lengths_matrix=None)[source]

Constructor for PAM stats computations.

Parameters

pam (Matrix) – A presence-absence matrix to use for computations.
tree (TreeWrapper) – A tree to use for phylogenetic distance computations.
tree_matrix (Matrix) – A matrix of tip / node presence absence values.
node_heights_matrix (Matrix) – A matrix of node height values.
tip_lengths_matrix (Matrix) – A matrix of tip length values.

covariance_stats = [None, None][source]

diversity_stats = [None, None, None, None, None, None][source]

site_matrix_stats = [None, None, None, None][source]

site_pam_dist_mtx_stats = [None][source]

site_tree_distance_matrix_stats = [None, None, None][source]

site_tree_stats = [None][source]

species_matrix_stats = [None, None, None, None][source]

calculate_covariance_statistics(self)[source]

Calculate covariance statistics matrices.

Returns: A list of metric name, value tuples for covariance stats.
Return type: list of tuple

calculate_diversity_statistics(self)[source]

Calculate diversity statistics.

Returns: A list of metric name, value tuples for diversity metrics.
Return type: list of tuple

calculate_site_statistics(self)[source]

Calculate site-based statistics.

Returns: A matrix of site-based statistics for the selected metrics.
Return type: Matrix

calculate_species_statistics(self)[source]

Calculate species-based statistics.

Returns: A matrix of species-based statistics for the selected metrics.
Return type: Matrix

register_metric(self, name, metric_function)[source]

Register a new metric.

Parameters

name (str) – A name for this metric that will be used for a header.
metric_function (function) – A decorated metric generating function.

Raises

TypeError – Raised if the metric function type cannot be processed.

class lmpy.statistics.pam_stats.PamStatsMetric(func)[source]

Constructor.

Parameters: func – The function to call.

__call__(self, *args, **kwargs)[source]

Call the wrapped function.

Parameters

*args – Positional arguments passed to the function.
**kwargs – Keyword arguments passed to the function.

Returns

The output of the wrapped function.

Return type

object

class lmpy.statistics.pam_stats.SiteMatrixMetric(func)[source]

Bases: _SiteStatMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.SpeciesMatrixMetric(func)[source]

Bases: _SpeciesStatMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.TreeDistanceMatrixMetric(func)[source]

Bases: _SiteStatMetric

Constructor.

Parameters: func – The function to call.

class lmpy.statistics.pam_stats.TreeMetric(func)[source]

Bases: _SiteStatMetric

Constructor.

Parameters: func – The function to call.

lmpy.statistics.pam_stats.alpha(pam)[source]

Calculate alpha diversity, the number of species in each site.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: A column of alpha diversity values for each site in the PAM.
Return type: Matrix

lmpy.statistics.pam_stats.alpha_proportional(pam)[source]

Calculate proportional alpha diversity.

Parameters

pam (Matrix) – The presence-absence matrix to use for the computation.

Returns

A column of proportional alpha diversity values for each site in the: PAM.

Return type

Matrix

lmpy.statistics.pam_stats.c_score(pam)[source]

Calculate the checker board score for the PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: The checkerboard score for the PAM.
Return type: float

lmpy.statistics.pam_stats.lande(pam)[source]

Calculate Lande’s beta diversity metric for a PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: Lande’s beta diversity for the PAM.
Return type: float

lmpy.statistics.pam_stats.legendre(pam)[source]

Calculate Legendre’s beta diversity metric for a PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: Legendre’s beta diversity for the PAM.
Return type: float

lmpy.statistics.pam_stats.mean_nearest_taxon_distance(phylo_dist_mtx)[source]

Calculates the nearest neighbor distance.

Parameters: phylo_dist_mtx (Matrix) – A matrix of distances between the species present at a site.
Returns: The average distance from each taxa to taxa nearest to it.
Return type: float

lmpy.statistics.pam_stats.mean_pairwise_distance(phylo_dist_mtx)[source]

Calculates mean pairwise distance between species present at a site.

Parameters: phylo_dist_mtx (Matrix) – A matrix of distances between the species present at a site.
Returns: The average distance from each taxa all of the other co-located taxa.
Return type: float

lmpy.statistics.pam_stats.num_sites(pam)[source]

Get the number of sites with presences.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: The number of sites that have present species.
Return type: int

lmpy.statistics.pam_stats.num_species(pam)[source]

Get the number of species with presences.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: The number of species that are present in at least one site.
Return type: int

lmpy.statistics.pam_stats.omega(pam)[source]

Calculate the range size per species.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: A row of range sizes for each species in the PAM.
Return type: Matrix

lmpy.statistics.pam_stats.omega_proportional(pam)[source]

Calculate the mean proportional range size of each species.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: A row of the proportional range sizes for each species in the PAM.
Return type: Matrix

lmpy.statistics.pam_stats.pearson_correlation(pam, phylo_dist_mtx)[source]

Calculates the Pearson correlation coefficient for each site.

Parameters

pam (Matrix) – A presence-absence matrix to use for the computation.
phylo_dist_mtx (Matrix) – A matrix of distance between species.

Returns

A column of Pearson correlation values for each site in a PAM.

Return type

Matrix

lmpy.statistics.pam_stats.phi(pam)[source]

Calculate phi, the range size per site.

Parameters

pam (Matrix) – The presence-absence matrix to use for the computation.

Returns

A column of the sum of the range sizes for the species present at each: site in the PAM.

Return type

Matrix

lmpy.statistics.pam_stats.phi_average_proportional(pam)[source]

Calculate proportional range size per site.

Parameters

pam (Matrix) – The presence-absence matrix to use for the computation.

Returns

A column of the proportional value of the sum of the range sizes for: the species present at each site in the PAM.

Return type

Matrix

lmpy.statistics.pam_stats.phylogenetic_diversity(tree)[source]

Calculate phylogenetic diversity of a tree.

Parameters: tree (TreeWrapper) – A phylogenetic tree to compute phylogenetic diversity for.
Returns: The sum of the edge lengths of the nodes of the provided tree.
Return type: float

lmpy.statistics.pam_stats.psi(pam)[source]

Calculate the range richness of each species.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: A row of range richness for the sites that each species is present in.
Return type: Matrix

lmpy.statistics.pam_stats.psi_average_proportional(pam)[source]

Calculate the mean proportional species diversity.

Parameters

pam (Matrix) – The presence-absence matrix to use for the computation.

Returns

A row of proportional range richness for the sites that each species in: the PAM is present.

Return type

Matrix

lmpy.statistics.pam_stats.schluter_site_variance_ratio(pam)[source]

Calculate Schluter’s site variance ratio.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: The Schluter site variance ratio for the PAM.
Return type: float

lmpy.statistics.pam_stats.schluter_species_variance_ratio(pam)[source]

Calculate Schluter’s species variance ratio.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: The Schluter species variance ratio for the PAM.
Return type: float

lmpy.statistics.pam_stats.sigma_sites(pam)[source]

Compute the site sigma metric for a PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: Matrix of covariance of composition of sites.
Return type: Matrix

lmpy.statistics.pam_stats.sigma_species(pam)[source]

Compute the species sigma metric for a PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: Matrix of covariance of composition of species.
Return type: Matrix

lmpy.statistics.pam_stats.sum_pairwise_distance(phylo_dist_mtx)[source]

Calculates the sum pairwise distance for all species present at a site.

Parameters: phylo_dist_mtx (Matrix) – A matrix of distances between the species present at a site.
Returns: The total distance from each taxa all of the other co-located taxa.
Return type: float

lmpy.statistics.pam_stats.whittaker(pam)[source]

Calculate Whittaker’s beta diversity metric for a PAM.

Parameters: pam (Matrix) – The presence-absence matrix to use for the computation.
Returns: Whittaker’s beta diversity for the PAM.
Return type: float

lmpy.statistics.pam_stats

Module Contents

Classes

Functions

`lmpy.statistics.pam_stats`