Title: Using Tip Dates with Phylogenetic Trees in BEAST
Author: Adrien Rieux, Camilo Khatchikian
Description: Assist performing tip-dating of phylogenetic trees with BEAST.

Title: Using Tip Dates with Phylogenetic Trees in BEAST (Software for
Imports: mclust, TeachingDemos, DescTools, utils, stats

Packaged: 2017-11-22 03:29:08 UTC; ckhatchikian

Packaged: 2018-01-30 01:05:04 UTC; ckhatchikian

Packaged: 2018-03-29 04:28:40 UTC; ckhatchikian

Description: Assists performing tip-dating of phylogenetic trees with BEAST
BEAST is a popular software for phylogenetic analysis.
The package assists the implementation of various phylogenetic tip-
dating tests using BEAST. It contains two main functions.
The first one allows preparing date randomization analyses,
which assess the temporal signal of a data set.
The second function allows performing leave-one-out analyses,
which test for the consistency between independent calibration sequences
and allow pinpointing those leading to potential bias.
The included tutorial provides detailed step-by-step instructions.
An expanded description of the package can be found in article:
TIPDATINGBEAST: an R package to assist the implementation of phylogenetic
tip-dating tests using BEAST. Molecular Ecology Resources, 17: 608-613.

Title: Enhanced Tipping Point Displays the Results of Sensitivity
Description: Using the idea of "tipping point" (proposed in
Gregory Campbell, Gene Pennello and Lilly Yue(2011)
of sensitivity analysis for missing data, the package provides
a set of functions to list out all the possible combinations
of the values of missing data in two treatment arms, calculate
corresponding estimated treatment effects and p values and draw
a colored heat-map to visualize them. It could deal with randomized
experiments with a binary outcome or a continuous outcome. In addition,
the package provides a visualized method to compare various imputation
methods by adding the rectangles or convex hulls on the basic plot.
Imports: ggplot2 (>= 2.0.0), RColorBrewer, bayesSurv, reshape2, Rcpp