Maintainer: Kehui Chen <khchen@wald.ucdavis.edu> Matt Yang
Description: The core program of this package is Functional Principal
Component Analysis (FPCA), a key technique for functional data
analysis, for sparsely or densely sampled random trajectories
and time courses, via the Principal Analysis by Conditional

Title: Penalized and Constrained Lasso Optimization
Authors@R: c(person("Courtney", "Paulson", email = "cpaulson@rhsmith.umd.edu", role = c("aut", "cre")),person("Gareth","James",role="ctb"),person("Paat","Rusmevichientong",role="ctb"))
Description: An implementation of both the equality and inequality constrained lasso
functions for the algorithm described in "Penalized and Constrained Optimization"
by James, Paulson, and Rusmevichientong (Journal of the American Statistical Association, 2019;
see <http://www-bcf.usc.edu/~gareth/research/PAC.pdf> for a full-text version of the paper).
The algorithm here is designed to allow users to define linear constraints (either equality
or inequality constraints) and use a penalized regression approach to solve the constrained
problem. The functions here are used specifically for constraints with the lasso formulation,
but the method described in the PaC paper can be used for a variety of scenarios. In addition
to the simple examples included here with the corresponding functions, complete code to
entirely reproduce the results of the paper is available online through the Journal of the
Imports: MASS (>= 7.3), lars (>= 1.2), quadprog (>= 1.5), limSolve (>=

Title: Variational Bayes (VB) Approximation of Gibbs Posteriors with
Description: Variational Bayesian approximations of Gibbs measures with hinge losses for classification and ranking.

Title: Plastome Assembly Coverage Visualization
Authors@R: c(person("Michael", "Gruenstaeudl", role = c("aut", "cre"), email = "m.gruenstaeudl@fu-berlin.de"),
person("Nils", "Jenke", role = c("ctb"), email = "nilsj24@zedat.fu-berlin.de"))
Author: Michael Gruenstaeudl [aut, cre],
Description: Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2019) <doi:10.1101/697821>.
License: BSD 3-clause License + file LICENSE