biotaphy.analyses.phylo_beta_diversity package

Submodules

biotaphy.analyses.phylo_beta_diversity.phylo_beta_diversity module

Module contents

Module containing code for calculating phylogenetic beta diversity.

Note

  • Numpy and Scipy may have the methods needed for these computations. Feel

    free to take advantage of those to libraries as they are already dependencies.

biotaphy.analyses.phylo_beta_diversity.calculate_phylo_beta_diversity_jaccard(pam, tree)[source]

Calculates phylogenetic beta diversity for the jaccard index family.

Parameters

  • pam (Matrix) – A Lifemapper Matrix object with presence absence values (site rows by species columns).

  • tree (TreeWrapper) – A TreeWrapper object for a wrapped Dendropy phylogenetic tree.

Returns

Phylogenetic beta diversity matrics (species by species)

  • beta_jtu: ADD DESCRIPTION

  • phylo_beta_jtu: ADD DESCRIPTION

  • beta_jne: ADD DESCRIPTION

  • phylo_beta_jne: ADD DESCRIPTION

  • beta_jac: ADD DESCRIPTION

  • phylo_beta_jac: ADD DESCRIPTION

Note

  • It looks like the scipy.spatial.distance.jaccard method may be useful

    here.

biotaphy.analyses.phylo_beta_diversity.calculate_phylo_beta_diversity_sorensen(pam, tree)[source]

Calculates phylogenetic beta diversity for the sorensen index family.

Parameters

  • pam (Matrix) – A Lifemapper Matrix object with presence absence values.

  • tree (TreeWrapper) – A TreeWrapper object for a wrapped Dendropy phylogenetic tree.

Returns

Phylogenetic beta diversity matrics (species by species)

  • beta_sim: ADD DESCRIPTION

  • phylo_beta_sim: ADD DESCRIPTION

  • beta_sne: ADD DESCRIPTION

  • phylo_beta_sne: ADD DESCRIPTION

  • beta_sor: ADD DESCRIPTION

  • phylo_beta_sor: ADD DESCRIPTION

biotaphy.analyses.phylo_beta_diversity.core_Beta_calc(pam, tree)[source]

Creates an array of core metrics to asses beta diversity components.

Parameters

  • ( (tree) – obj:’Matrix’): A Lifemapper Matrix object with presence absence values.

  • ( – obj:’TreeWrapper’): A TreeWrapper object for a wrapped Dendropy phylogenetic tree.

Returns

List of arrays, see Details.

Details:

In general, the metrics returned represent different contributions to beta diversity arising from how communities are combined together. Metrics:

shared_array: spp shared in each pairwise comm. combinations. not_shared_array: spp. not shared btwn pairwise comm. combinations. sum_not_shared: max_not_shared: min_not_shared:

biotaphy.analyses.phylo_beta_diversity.core_PD_calc(pam, tree)[source]

Creates array of core metrics to asses components of beta diversity.

Parameters

  • ( (tree) – obj:’Matrix’): A Lifemapper Matrix object with presence absence values.

  • ( – obj:’TreeWrapper’): A TreeWrapper object for a wrapped Dendropy phylogenetic tree.

Returns

Matrix object. Cols=core metrics; Rows=Pairwise comparisons.

Details:

In general, the metrics returned represent different contributions to PD arising from how communities are combined together. Metrics:

min_not_shared: smallest dist. from ind. samples to their combo. max_not_shared: largest dist. from ind. samples to their combo. sum_not_shared: total addition to PD from both comm. shared: combined contribution to PD that comm. make jointly.

biotaphy.analyses.phylo_beta_diversity.pdnew(pam, tree)[source]

Creates a lookup dictionary for PD of sites in a matrix.

Parameters

  • pam (Matrix) – A Lifemapper Matrix object with presence absence values.

  • tree (TreeWrapper) – A TreeWrapper object for a wrapped Dendropy phylogenetic tree.

Returns

Matrix object w/ PD values & spp. rch for each community in sample. Col1 = PD; Col2 = SR; Rows = Indvidual samples from pam.