drugcandy: Detecting punctuated evolution in taxa ranging from dinosaurs...

In suryakevin/drugcandy: Detecting Punctuated Evolution in Dinosaurs and Viruses

Detecting punctuated evolution in taxa ranging from dinosaurs to viruses

Description

This package contains the tools to simulate, detect, and visualize punctuated evolution in any clades, from co-occurring species (e.g., present-day mammals) to serially-sampled viruses (e.g., SARS-CoV-2 genomes) and long-extinct taxa (e.g., Mesozoic dinosaurs).

Function directory

• Main functions:

  • Extracting data: get_node_count and get_path_length

  • Preparing dataset: reorder_data

  • Editing the phylogenetic variance-covariance matrix: break_vcv and create_dmat

  • Detecting punctuated evolution: fit_punc_model and print_punc_model

  • Calculating test statistics: calc_r2, calc_partialr2, and est_punc_contrib

  • Comparing models: compare_models

  • Checking biases and diagnostics: calc_vif, est_node_density, print_node_density, plot_diagnostics, and plot_node_density

  • Visualizing data and results: export_plot_pdf, export_plot_svg, plot_data_2d, plot_data_3d, plot_punc_model, plot_tree, and plot_tree_color

  • Simulating data and tree: sim_punc

• Auxillary functions:

  • Importing dataset: import_data, import_data_bt, and import_data_csv

  • Importing phylogenetic tree: import_tree_nex and import_tree_nwk

  • Exporting dataset: export_data and export_data_bt

  • Exporting tree: export_tree_nex and export_tree_nwk

Author(s)

Kevin Surya

References

Surya, K., Gardner, J.D. & Organ, C. Detecting punctuated evolution in SARS-CoV-2 over the first year of the pandemic. Submitted.

suryakevin/drugcandy documentation built on May 6, 2022, 6:37 p.m.