Thu, 18 Jun 2015

Package SharpeR updated to version 1.0.0 with previous version 0.1501 dated 2014-12-23

Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of trading strategies, based on the Sharpe ratio and overfit of the same.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>

Diff between SharpeR versions 0.1501 dated 2014-12-23 and 1.0.0 dated 2015-06-18

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Package riverplot updated to version 0.5 with previous version 0.3 dated 2014-08-29

Title: Sankey or Ribbon Plots
Description: Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings.
Author: January Weiner <january.weiner@gmail.com>
Maintainer: January Weiner <january.weiner@gmail.com>

Diff between riverplot versions 0.3 dated 2014-08-29 and 0.5 dated 2015-06-18

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Package rAvis updated to version 0.1.3 with previous version 0.1.2 dated 2014-08-28

Title: Interface to the Bird-Watching Dataset Proyecto AVIS
Description: Interface to <http://proyectoavis.com> database. It provides means to download data filtered by species, order, family, and several other criteria. Provides also basic functionality to plot exploratory maps of the datasets.
Author: Javier González Hernández <javigzz@yahoo.es>, Sara Varela <svarela@paleobiogeography.org>
Maintainer: Sara Varela <svarela@paleobiogeography.org>

Diff between rAvis versions 0.1.2 dated 2014-08-28 and 0.1.3 dated 2015-06-18

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Package oapackage updated to version 2.0.20 with previous version 2.0.17 dated 2015-06-17

Title: Orthogonal Array Package
Description: Interface to D-optimal design generation code of the Orthogonal Array package. Can generate D-optimal designs with specified number of runs and factors. The optimality of the designs is defined in terms of a user specified optimization function based on the D-efficiency and Ds-efficiency.
Author: P. T. Eendebak
Maintainer: P. T. Eendebak <pieter.eendebak@gmail.com>

Diff between oapackage versions 2.0.17 dated 2015-06-17 and 2.0.20 dated 2015-06-18

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New package modQR with initial version 0.1.0
Package: modQR
Encoding: UTF-8
Version: 0.1.0
Date: 2015-06-17
Title: Multiple-Output Directional Quantile Regression
Authors@R: c(person("Miroslav","Šiman", role=c("aut")), person("Pavel","Boček", role=c("aut", "cre"), email="bocek@utia.cas.cz"))
Author: Miroslav Šiman [aut], Pavel Boček [aut, cre]
Maintainer: Pavel Boček <bocek@utia.cas.cz>
Copyright: The Institute of Information Theory and Automation of the Czech Academy of Sciences Pod Vodárenskou věží 4, CZ-182 08 Prague 8, Czech Republic email: utia@utia.cas.cz, phone: +420 266 053 111
Description: Contains basic tools for performing multiple-output quantile regression and computing regression quantile contours by means of directional regression quantiles. In the location case, one can thus obtain halfspace depth contours in two to six dimensions.
Classification/MSC: 62H05, 62J99, 62G08, 65C60
Keywords: quantile regression, multivariate regression, semiparametric regression, nonparametric regression, data depth, regression depth, halfspace depth, Tukey depth, depth contour, multivariate quantile, regression quantile, quantile-based inference
Repository: CRAN
Depends: R (>= 2.5.0), lpSolve (>= 5.6.1), geometry (>= 0.3-1)
Suggests: rgl
License: LGPL-2
Collate: addItem.R findItem.R delItem.R addRow.R findRow.R checkArray.R checkCTechSTu.R getCTechSTM1u.R getCTechSTM2u.R getCharSTM1u.R getCharSTM2u.R findOptimalBasisM1FromScratch.R findOptimalBasisM2FromScratch.R compContourM1u.R compContourM2u.R evalContour.R
NeedsCompilation: no
Packaged: 2015-06-18 12:04:54 UTC; bocek
Date/Publication: 2015-06-18 18:00:31

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Package joint.Cox updated to version 2.0 with previous version 1.1 dated 2015-05-24

Title: Penalized Likelihood Estimation under the Joint Cox Models Between Tumour Progression and Death for Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis. The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between joint.Cox versions 1.1 dated 2015-05-24 and 2.0 dated 2015-06-18

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Package james.analysis updated to version 1.0.1 with previous version 1.0.0 dated 2015-03-19

Title: Analysis Tools for the 'JAMES' Framework
Description: Analyze and visualize results of studies performed with the analysis tools in 'JAMES', a modern object-oriented Java framework for discrete optimization using local search metaheuristics (see http://www.jamesframework.org).
Author: Herman De Beukelaer
Maintainer: Herman De Beukelaer <Herman.DeBeukelaer@UGent.be>

Diff between james.analysis versions 1.0.0 dated 2015-03-19 and 1.0.1 dated 2015-06-18

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Package hsdar updated to version 0.2 with previous version 0.1.5 dated 2015-05-22

Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [ctb], Joerg Bendix [ctb]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>

Diff between hsdar versions 0.1.5 dated 2015-05-22 and 0.2 dated 2015-06-18

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Package GPLTR updated to version 1.2 with previous version 1.1 dated 2014-12-19

Title: Generalized Partially Linear Tree-Based Regression Model
Description: Combining a generalized linear model with an additional tree part on the same scale. A four-step procedure is proposed to fit the model and test the joint effect of the selected tree part while adjusting on confounding factors. We also proposed an ensemble procedure based on the bagging to improve prediction accuracy and computed several scores of importance for variable selection.
Author: Cyprien Mbogning <cyprien.mbogning@inserm.fr> and Wilson Toussile
Maintainer: Cyprien Mbogning <cyprien.mbogning@gmail.com>

Diff between GPLTR versions 1.1 dated 2014-12-19 and 1.2 dated 2015-06-18

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Package directPA updated to version 1.2 with previous version 1.1 dated 2015-03-19

Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to integrate multiple experimental treatments for analyzing pathways and kinases from microarray, RNA-seq, proteomics, or phosphoproteomics data.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>

Diff between directPA versions 1.1 dated 2015-03-19 and 1.2 dated 2015-06-18

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Package stepR updated to version 1.0-3 with previous version 1.0-2 dated 2015-04-29

Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut], Thomas Hotz [aut], Hannes Sieling [aut], Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>

Diff between stepR versions 1.0-2 dated 2015-04-29 and 1.0-3 dated 2015-06-18

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Package migest updated to version 1.7 with previous version 1.6 dated 2014-07-27

Title: Methods for the Indirect Estimation of Bilateral Migration
Description: Indirect methods for estimating bilateral migration flows in the presence of partial or missing data. Methods might be relevant to other categorical data situations on non-migration data, where for example, marginal totals are known and only auxiliary bilateral data is available.
Author: Guy J. Abel
Maintainer: Guy J. Abel <g.j.abel@gmail.com>

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Package lfl updated to version 1.2 with previous version 1.1 dated 2015-06-03

Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>

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Package HHG updated to version 1.5 with previous version 1.4 dated 2014-05-06

Title: Heller-Heller-Gorfine Tests of Independence and Equality of Distributions
Description: Heller-Heller-Gorfine (HHG) tests are a set of powerful statistical tests of multivariate k-sample homogeneity and independence. For the univariate case, the package also offers implementations of the MinP DDP and MinP ADP tests, which are consistent against all continuous alternatives but are distribution-free, and are thus much faster to apply.
Author: Barak Brill & Shachar Kaufman, based in part on an earlier implementation by Ruth Heller and Yair Heller.
Maintainer: Barak Brill <barakbri@mail.tau.ac.il>

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Package FatTailsR updated to version 1.2-0 with previous version 1.0-3 dated 2014-07-14

Title: Kiener Distributions and Fat Tails in Finance
Description: Kiener distributions of type I, II, III and IV tailored to distributions with left and right fat tails like those that occur in financial markets. These distributions can be used to estimate with a high accuracy market risks and value-at-risk. Also include power hyperbolas and power hyperbolic functions.
Author: Patrice Kiener
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>

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New package CopyNumber450kCancer with initial version 1.0.3
Package: CopyNumber450kCancer
Type: Package
Title: Baseline Correction for Copy Number Data from Cancer Samples
Version: 1.0.3
Date: 2015-06-17
Author: Nour-al-dain Marzouka [aut, cre]
Maintainer: Nour-al-dain Marzouka <nour.marzouka@medsci.uu.se>
Description: The 450k arrays are frequently used in the epigenetic studies, the copy number calling from the 450k data is possible but it faces some difficulties in cancer samples regarding the determination of the copy number status due to the false sample centering and baseline shifting. Without solving this issue the CN calling will be inaccurate. CopyNumber450kCancer-package was designed to correct the baseline in cancer samples using the Maximum Density Peak Estimation (MDPE) method. The main advantages for CopyNumber450kCancer-package are: Fast (few seconds per sample), high accuracy rate, in-sample correction, no input parameters needed, low computer sources required, and adaptable for 450k-similar technologies.
Depends: R (>= 3.1.0)
License: GPL (>= 2)
Packaged: 2015-06-18 09:45:21 UTC; nouma923
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-18 13:38:49

More information about CopyNumber450kCancer at CRAN
Permanent link

Package bcrypt updated to version 0.2 with previous version 0.1 dated 2015-06-16

Title: 'Blowfish' Password Hashing Algorithm
Description: An R interface to the OpenBSD 'blowfish' password hashing algorithm, as described in "A Future-Adaptable Password Scheme" by Niels Provos. The implementation is derived from the 'py-bcrypt' module for Python which is a wrapper for the OpenBSD implementation.
Author: Jeroen Ooms [cre, aut], Damien Miller [cph], Niels Provos [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

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More information about bcrypt at CRAN
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Package MASS updated to version 7.3-41 with previous version 7.3-40 dated 2015-03-21

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>

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Permanent link

Package TESS updated to version 2.0.0 with previous version 1.2.1 dated 2013-04-22

Title: Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events
Description: Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Author: Sebastian Hoehna and Michael R. May
Maintainer: Sebastian Hoehna <Sebastian.Hoehna@gmail.com>

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Package kdecopula updated to version 0.0.2 with previous version 0.0.1 dated 2015-06-17

Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

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Package EcoGenetics updated to version 1.2.0-1 with previous version 1.2.0 dated 2015-05-11

Title: Analysis of Phenotypic, Genotypic and Environmental Data
Description: Easy integration of information from multiple sources with "ecogen" objects. Geostatistical tools for analyzing spatial patterns in population biology and extra functions.
Author: Leandro Roser, Juan Vilardi, Beatriz Saidman and Laura Ferreyra
Maintainer: Leandro Roser <learoser@gmail.com>

Diff between EcoGenetics versions 1.2.0 dated 2015-05-11 and 1.2.0-1 dated 2015-06-18

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Package crunch updated to version 1.3.2 with previous version 1.2.1 dated 2015-05-26

Title: Crunch.io Data Tools
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>

Diff between crunch versions 1.2.1 dated 2015-05-26 and 1.3.2 dated 2015-06-18

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 R/variable-update.R                                   |    6 
 man/appendDataset.Rd                                  |    4 
 man/catalog-extract.Rd                                |   25 +
 man/createWithMetadataAndFile.Rd                      |    8 
 man/delete.Rd                                         |    9 
 man/describe-catalog.Rd                               |   22 +
 man/describe.Rd                                       |    5 
 man/getAccountUserCatalog.Rd                          |only
 man/getTeams.Rd                                       |only
 man/teams.Rd                                          |only
 tests/testthat/api/accounts                           |only
 tests/testthat/api/datasets/dataset1/permissions.json |   56 +--
 tests/testthat/api/root.json                          |    1 
 tests/testthat/api/teams                              |only
 tests/testthat/api/teams.json                         |only
 tests/testthat/api/users/user1.json                   |    3 
 tests/testthat/conflicts.R                            |  269 ++++++++++++------
 tests/testthat/helper.R                               |   36 ++
 tests/testthat/test-add-array.R                       |    1 
 tests/testthat/test-api.R                             |   11 
 tests/testthat/test-append-arrays.R                   |   16 -
 tests/testthat/test-append-conflicts.R                |   68 ++++
 tests/testthat/test-appending.R                       |   42 +-
 tests/testthat/test-appending.R.orig                  |only
 tests/testthat/test-auth.R                            |    4 
 tests/testthat/test-hide-variables.R                  |   27 +
 tests/testthat/test-new-dataset.R                     |    5 
 tests/testthat/test-teams.R                           |only
 tests/testthat/test-update.R                          |    2 
 tests/testthat/test-user.R                            |   60 +++-
 tests/testthat/test-variable-catalog.R                |    5 
 vignettes/analyze.RData                               |binary
 vignettes/array-variables.RData                       |binary
 vignettes/derive.RData                                |binary
 vignettes/getting-started.RData                       |binary
 vignettes/variable-order.RData                        |binary
 vignettes/variables.RData                             |binary
 53 files changed, 734 insertions(+), 279 deletions(-)

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