R/drugcandy.r

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).
#'
#' @section Function directory:
#' \itemize{
#'   \item Main functions:
#'     \itemize{
#'       \item Extracting data: `get_node_count` and `get_path_length`
#'       \item Preparing dataset: `reorder_data`
#'       \item Editing the phylogenetic variance-covariance matrix: `break_vcv`
#'         and `create_dmat`
#'       \item Detecting punctuated evolution: `fit_punc_model` and
#'         `print_punc_model`
#'       \item Calculating test statistics: `calc_r2`, `calc_partialr2`, and
#'         `est_punc_contrib`
#'       \item Comparing models: `compare_models`
#'       \item Checking biases and diagnostics: `calc_vif`, `est_node_density`,
#'         `print_node_density`, `plot_diagnostics`, and `plot_node_density`
#'       \item 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`
#'       \item Simulating data and tree: `sim_punc`
#'     }
#'   \item Auxillary functions:
#'     \itemize{
#'       \item Importing dataset: `import_data`, `import_data_bt`, and
#'         `import_data_csv`
#'       \item Importing phylogenetic tree: `import_tree_nex` and
#'         `import_tree_nwk`
#'       \item Exporting dataset: `export_data` and `export_data_bt`
#'       \item Exporting tree: `export_tree_nex` and `export_tree_nwk`
#'     }
#' }
#'
#' @author 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.
#'
#' @docType package
#'
#' @name drugcandy
#'
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