Title: Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Description: This package evaluates DNA copy number data, using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.

Title: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
Description: DNA copy number data evaluation using both their initial form
(copy number as a noisy function of genomic position) and their
approximation by a piecewise-constant function (segmentation),
for the purpose of identifying genomic regions where the copy number
Depends: R (>= 2.10), parallel, mclust, rlecuyer, stats

Title: Fast Algorithms for Frequency-Preserving Null Models in Ecology
Authors@R: c(person("Constantinos", "Tsirogiannis", role = c("aut", "cre"),
person("Adrija", "Kalvisa", role = "aut"))
Author: Constantinos Tsirogiannis [aut, cre], Adrija Kalvisa [aut]
Description: Efficient computations for null models that require shuffling columns on big matrix data.
This package provides functions for faster computation of diversity measure statistics
when independent random shuffling is applied to the columns of a given matrix.
Given a diversity measure f and a matrix M, the provided functions can generate random samples
(shuffled matrix rows of M), the mean and variance of f, and the p-values of this measure
for two different null models that involve independent random shuffling of the columns of M.
The package supports computations of alpha and beta diversity measures.
Imports: Rcpp (>= 0.12.9), ape, PhyloMeasures, Matrix

Title: Nonlinear Aggregation of Predictors
Description: This package performs prediction for regression-oriented
problems, aggregating in a nonlinear scheme any basic
regression machines suggested by the context and possibly
provided by the user. If necessary, the computations may be
parallelized. The method is described in Biau, Fischer, Guedj
and Malley (2013), "COBRA: A Nonlinear Aggregation Strategy".
Suggests: snowfall, lars, ridge, FNN, tree, randomForest