Comparative Phylogeographic Analysis using the Community Tree
Framework
ape (>= 3.1-4), ggplot2 (>= 1.0.0), gridExtra, phangorn,
reshape
Provides functions to measure the difference between constrained and unconstrained gene tree distributions using various tree distance metrics. Constraints are enforced prior to this analysis via the estimation of a tree under the community tree model.

Useful libraries for building a Java based GUI under R

Kornelius Rohmeyer (author only of two libraries and of the R code for loading them), see the documentation for the authors of the other java libraries

Kornelius Rohmeyer (R package), see COPYRIGHTS file for the authors of the java libraries

Useful Libraries for Building a Java Based GUI under R
Useful libraries for building a Java based GUI under R are provided.

Estimate bivariate common mean vector under copula models with known correlation. In the current version, available copulas include the Clayton, Farlie-Gumbel-Morgenstern (FGM), and Gaussian copulas. See Shih et al. (2019) <doi:10.1080/02331888.2019.1581782> for details under the FGM copula.

Estimate bivariate common mean vector under copula models with known correlation. In the current version, available copulas are the Clayton, Farlie-Gumbel-Morgenstern (FGM), and normal copulas. See Shih et al. (2019) <doi:10.1080/02331888.2019.1581782> and Shih et al. (2021) <under review> for details under the FGM and general copulas, respectively.

Estimate bivariate common mean vector under copula models with known correlation. In the current version, available copulas are the Clayton, Gumbel, Frank, Farlie-Gumbel-Morgenstern (FGM), and normal copulas. See Shih et al. (2019) <doi:10.1080/02331888.2019.1581782> and Shih et al. (2021) <under review> for details under the FGM and general copulas, respectively.

Extract and plot common trends from a cointegration system
Directly extract and plot common trends from cointegration systems using different approaches, currenctly including Kasa (1992) and Gonzalo and Granger (1995). The approach proposed by Gonzalo and Granger, also known as Permanent-Transitory Decomposition, is widely used in Macroeconomics and Market Microstructure literature. The Kasa's approach has a nice property that it only uses the super consistent estimater \eqn{\beta}.
'GG.ComT.R' 'Kasa.ComT.R' 'optimlag.R' 'plotComT.R'
'print.ComT.R' 'print.optimlag.R'