Welcome to Lifemapper lmpy’s documentation!

The Lifemapper lmpy repository contains common Lifemapper objects that can be useful to the community for either developing new tools for the BiotaPhy Python Repository or for independent projects that want to use some of our performance and feature improvements.

At the time of this first release, the tools are primarily for lightly wrapped Dendropy trees, extended NumPy arrays that include header information, and presence-absence matrix (PAM) randomizations that are used to create null models.

Contents:

• Installation
  • Apt Requirements Installation
  • Conda Requirements Installation
• lmpy Installation
  • Install latest
  • Install latest release
• Alternative: Install and run with a Docker Container
  • Get from DockerHub
  • Get from GitHub Container Registry
• Tutorials
  • Build Grid
    • Introduction
    • Build a grid
  • Data Cleaning
    • Cleaning Occurrences
      • Introduction
      • Occurrence Data Wrangler Configuration
      • Example - Console Script
      • Example - Python
  • Layer Encoder
    • Introduction
    • Creating a PAM
    • Encoding Environmental Data
    • Encoding Biogeographic Hypotheses
  • Matrix Objects
    • Introduction
    • Creating Matrix Instances
      • From an existing NumPy ndarray
      • Reading a CSV file
      • Reading a saved Matrix
      • Concatenating existing Matrix objects
      • Slicing by array indices
      • Slicing by headers
    • Writing Matrix objects
      • Saving to the file system
      • Writing to a CSV file
    • Header management
      • On instantiation
      • Setting headers
      • Getting headers
    • Metadata management
      • On instantiation
      • Setting metadata
      • Getting metadata
  • Matrix Data Wrangling
    • Introduction
    • Subset a PAM for a Taxon or Group of Taxa and Export to GeoJSON
    • Subset a Matrix by Taxa, Generate Stats, and Write GeoJSON
  • Metacommunity Phylogenetics Analysis (MCPA)
    • Introduction
    • Tutorial
  • Occurrence Filters
    • Introduction
    • Bounding Box Filter
    • Disjoint Geometries Filter
    • Intersect Geometries Filter
    • Unique Localities Filter
  • PAM Randomization and Null Models
    • Introduction
    • Randomization algorithms
      • Swap
      • Trial Swap
      • Grady’s Heuristic Fill
      • Strona’s Curveball Method
    • Generating a null model
    • References
  • PAM Statistics
    • Introduction
    • Generating Default Statistics
    • Generate Statistics and Write to GeoJSON File
    • Adding New Statistics
    • Covariance Matrix Metrics
      • sigma_sites
      • sigma_species
    • Diversity Metrics
      • schluter_species_variance_ratio
      • schluter_site_variance_ratio
      • num_sites
      • num_species
      • whittaker
      • lande
      • legendre
      • c_score
    • Species Matrix Metrics
      • omega
      • omega_proportional
      • psi
      • psi_average_proportional
    • Site Matrix Metrics
      • alpha
      • alpha_proportional
      • phi
      • phi_average_proportional
    • PAM Distance Matrix Metrics
      • pearson_correlation
    • Tree Metrics
      • phylogenetic_diversity
    • Tree Distance Matrix Metrics
      • mean_nearest_taxon_distance
      • mean_pairwise_distance
      • sum_pairwise_distance
  • Running Statistics
    • Introduction
    • Instantiation
    • Tracking statistics
  • TreeWrapper Objects
    • Introduction
    • Creating TreeWrapper Instances
      • From an existing Dendropy Tree
      • Reading a file
    • Annotations
      • Adding node labels
      • Annotating tips and nodes
      • Annotating tree tips
      • Retrieving annotations
      • Retrieving tip labels
    • Getting matrices
      • Get distance matrix
      • Get distance matrix using Dendropy method
      • Get variance covariance matrix
    • Inspecting the tree
      • Checking for branch lengths
      • Checking for polytomies
      • Checking if a tree is binary
      • Checking if a tree is ultrametric
    • Pruning tree tips without an attribute
• Tools
  • aggregate_matrices - CLI interface
    • aggregate_matrices positional arguments
    • aggregate_matrices optional arguments
  • calculate_p_values - CLI interface
    • calculate_p_values positional arguments
    • calculate_p_values optional arguments
  • calculate_pam_stats - CLI interface
    • calculate_pam_stats positional arguments
    • calculate_pam_stats optional arguments
  • convert_csv_to_lmm - CLI interface
    • convert_csv_to_lmm positional arguments
    • convert_csv_to_lmm optional arguments
  • convert_lmm_to_csv - CLI interface
    • convert_lmm_to_csv positional arguments
    • convert_lmm_to_csv optional arguments
  • convert_lmm_to_geojson - CLI interface
    • convert_lmm_to_geojson positional arguments
    • convert_lmm_to_geojson optional arguments
  • create_point_heatmap - CLI interface
    • create_point_heatmap positional arguments
    • create_point_heatmap optional arguments
  • create_rare_species_model - CLI interface
    • create_rare_species_model positional arguments
    • create_rare_species_model optional arguments
  • create_scatter_plot - CLI interface
    • create_scatter_plot positional arguments
    • create_scatter_plot optional arguments
  • create_stat_heatmap - CLI interface
    • create_stat_heatmap positional arguments
    • create_stat_heatmap optional arguments
  • create_tree_matrix - CLI interface
    • create_tree_matrix positional arguments
    • create_tree_matrix optional arguments
  • encode_layers - CLI interface
    • encode_layers positional arguments
    • encode_layers optional arguments
  • encode_tree_mcpa - CLI interface
    • encode_tree_mcpa positional arguments
    • encode_tree_mcpa optional arguments
  • mcpa_run - CLI interface
    • mcpa_run positional arguments
    • mcpa_run optional arguments
  • randomize_pam - CLI interface
    • randomize_pam positional arguments
    • randomize_pam optional arguments
  • split_occurrence_data - CLI interface
    • split_occurrence_data positional arguments
    • split_occurrence_data optional arguments
  • wrangle_matrix - CLI interface
    • wrangle_matrix positional arguments
    • wrangle_matrix optional arguments
  • wrangle_occurrences - CLI interface
    • wrangle_occurrences positional arguments
    • wrangle_occurrences optional arguments
  • wrangle_species_list - CLI interface
    • wrangle_species_list positional arguments
    • wrangle_species_list optional arguments
  • wrangle_tree - CLI interface
    • wrangle_tree positional arguments
    • wrangle_tree optional arguments
• Lmpy Term Glossary
• References
• About
• API Reference
  • lmpy
    • Subpackages
      • lmpy.data_preparation
      • lmpy.data_wrangling
      • lmpy.plots
      • lmpy.randomize
      • lmpy.sdm
      • lmpy.spatial
      • lmpy.statistics
      • lmpy.tools
    • Submodules
      • lmpy._version
      • lmpy.log
      • lmpy.matrix
      • lmpy.point
      • lmpy.species_list
      • lmpy.tree

Indices and tables

• Index

• Module Index

• Search Page