Suggests: extraDistr, SkewHyperbolic, testthat, covr, EQL, knitr,

Suggests: extraDistr, SkewHyperbolic, testthat, covr, knitr, rmarkdown

Title: Nonparametric method for identifying discordant trees
Author: Grady Weyenberg and Peter Huggins
Description: Given a set of phylogenetic trees on a group of taxa (for
example trees based on individual gene sequences), we present a
method for identifying a subset of trees which are discordant
with the other trees in the set. These discordant trees may
arise from either biologically interesting phenomena
(horizontal gene transfers, for example) or more mundane
Collate: 'bw.R' 'dist.diss.R' 'kde.R' 'kdetrees-package.R' 'kernels.R'

Description: Given a set of phylogenetic trees on a group of taxa (for example
trees based on individual gene sequences), we present a method for
identifying a subset of trees which are discordant with the other trees in
the set. These discordant trees may arise from either biologically
interesting phenomena (horizontal gene transfers, for example) or more
mundane sequencing or annotation errors.

Title: Nonparametric method for identifying discordant phylogenetic
Author: Grady Weyenberg and Ruriko Yoshida
Description: A non-parametric method for identifying potential
outlying observations in a collection of phylogenetic trees based
on the methods of Owen and Provan (2011). Such discordant trees
may indicate problems with sequence annotation or tree
reconstruction, or they may represent interesting biological
phenomena, such as horizontal gene transfers.

Title: Multivariate Kernel Density Estimation with Vine Copulas
Authors@R: person("Thomas", "Nagler", ,"thomas.nagler@tum.de", c("aut", "cre"))
Description: Implements a vine copula based kernel density estimator. The
estimator does not suffer from the curse of dimensionality and is therefore
well suited for high-dimensional applications.
Imports: kdecopula, VineCopula, Rcpp, qrng, doParallel, parallel,

Description: Implements the vine copula based kernel density estimator of
Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does
not suffer from the curse of dimensionality and is therefore well suited for
Imports: graphics, stats, utils, MASS, Rcpp, qrng, ks, cctools,
kdecopula (>= 0.8.1), VineCopula, doParallel, parallel, foreach