Based on the models and algorithms described in Durbin et
Imports: graphics, openssl, kmer (>= 1.0.0), Rcpp (>= 0.12.5), stats

Suggests: ape (>= 4.0), knitr, rmarkdown, testthat

Title: Statistical Inference and Prediction of Annotations in
Authors@R: c(person("George", "Vega Yon", role=c("aut","cre"),
email="g.vegayon@gmail.com", comment = c(ORCID = "0000-0002-3171-0844")),
Cancer Institute (NCI)", role = "fnd", comment = "Grant Number
person("USC Biostatistics", role = "cph")
Description: Implements a parsimonious evolutionary model to analyze and
predict gene-functional annotations in phylogenetic trees as described in Vega
Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. With a focus on
computational efficiency, 'aphylo' makes it possible to estimate pooled
phylogenetic models, including thousands (hundreds) of annotations (trees) in
the same run. The package also provides the tools for visualization of
annotated phylogenies, calculation of posterior probabilities (prediction,)
and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc, utils, MASS,
Suggests: covr, knitr, tinytest, AUC, rmarkdown,
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>),
National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),

Title: Functions and Data Sets for the Book "A Progressive Introduction
Maintainer: Joshua P. French <joshua.french@ucdenver.edu>
Description: Simplifies aspects of linear regression analysis, particularly simultaneous inference. Additionally, supports "A Progressive Introduction to Linear Models" by Joshua French (<https://jfrench.github.io/LinearRegression/>).
Suggests: testthat (>= 3.0.0), ggplot2, knitr

Title: Interface to 'episensr' for Sensitivity Analysis of
Description: API for using 'episensr', Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. See <https://cran.r-project.org/package=episensr>.
Imports: shiny, golem, config, processx, attempt, DT, glue, htmltools,
shinymaterial, shinyjs, rhandsontable, rmarkdown, ggraph,
Author: Denis Haine [aut, cre] (<https://orcid.org/0000-0002-6691-7335>)