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