Mon, 17 Aug 2015

New package flowr with initial version 0.9.7.5
Package: flowr
Type: Package
Title: Streamlining Design and Deployment of Complex Workflows
Description: An interface to streamline design of complex workflows and their deployment to a High Performance Computing Cluster.
Version: 0.9.7.5
Date: 2015-08-15
Depends: methods, utils
Imports: diagram, whisker, params (>= 0.2.4), tools, knitr
Suggests: reshape2, ggplot2, openxlsx, testthat
VignetteBuilder: knitr
URL: https://github.com/sahilseth/flowr
BugReports: https://github.com/sahilseth/flowr/issues
Authors@R: c( person("Sahil", "Seth", role = c("aut", "cre"), email = "me@sahilseth.com"))
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2015-08-15 17:23:30 UTC; sahilseth
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>
Repository: CRAN
Date/Publication: 2015-08-18 01:29:55

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New package RcppShark with initial version 0.1
Package: RcppShark
Type: Package
Title: R Interface to the Shark Machine Learning Library
Version: 0.1
Date: 2015-08-17
Author: Aydin Demircioglu
Maintainer: Aydin Demircioglu <aydin.demircioglu@ini.rub.de>
Description: An R interface to the C++/Boost Shark machine learning library.
License: LGPL (>= 2)
Imports: Rcpp (>= 0.11.6), checkmate (>= 1.5.1)
LinkingTo: Rcpp, BH
Suggests: knitr, testthat
VignetteBuilder: knitr
SystemRequirements: Boost 1.49 or later (via BH package)
URL: http://github.com/aydindemircioglu/RcppShark
BugReports: http://github.com/aydindemircioglu/RcppShark/issues
NeedsCompilation: yes
Packaged: 2015-08-17 20:05:31 UTC; drunkeneye
Repository: CRAN
Date/Publication: 2015-08-17 23:19:12

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New package rwirelesscom with initial version 1.0.1
Package: rwirelesscom
Title: Basic Wireless Communications
Version: 1.0.1
Authors@R: c(person("Alberto","Gutierrez", role=c("aut","cre"),email="algutier1@gmail.com"))
Maintainer: Alberto Gutierrez <algutier1@gmail.com>
Description: A basic wireless communications simulation package in R. The package includes modulation functions for BPSK, QPSK, 8-PSK, 16-QAM and 64-QAM. Also included is an AWGN noise generation function. Additionally, the package includes functions to plot an I (in-phase) and Q (quadrature) scatter diagram, or density plot. Together these functions enable the evaluation of respective bit error and symbol rates in an AWGN channel and for easily viewing the respective signals and noise in a scatter plot or density plot.
Depends: R (>= 3.1)
License: GPL (>= 2)
LazyData: true
Imports: ggplot2, stats
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-08-17 17:22:22 UTC; agutierrez
Author: Alberto Gutierrez [aut, cre]
Repository: CRAN
Date/Publication: 2015-08-17 23:08:21

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Package geostatsp updated to version 1.3.5 with previous version 1.3.4 dated 2015-07-07

Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>

Diff between geostatsp versions 1.3.4 dated 2015-07-07 and 1.3.5 dated 2015-08-17

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Package afex updated to version 0.14-2 with previous version 0.13-145 dated 2015-01-12

Title: Analysis of Factorial Experiments
Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre], Ben Bolker [aut], Jake Westfall [aut], Søren Højsgaard [ctb], John Fox [ctb], Michael A. Lawrence [ctb], Ulf Mertens [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>

Diff between afex versions 0.13-145 dated 2015-01-12 and 0.14-2 dated 2015-08-17

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New package addhazard with initial version 1.0.0
Package: addhazard
Title: Fit Additive Hazards Models for Survival Analysis
Version: 1.0.0
Authors@R: c(person("Jie (Kate)","Hu", role = c("aut", "cre"), email = "hujie0704@gmail.com"), person("Norman","Breslow", role = "aut"), person("Gary","Chan", role = "aut"))
Date: 2015-08-08
Description: Contains tools to fit additive hazards model to random sampling, two-phase sampling and two-phase sampling with auxiliary information. This package provides regression parameter estimates and their model-based and robust standard errors. It also offers tools to make prediction of individual specific hazards.
LazyData: true
Depends: R (>= 3.1.2)
Imports: ahaz, survival, rootSolve
License: GPL-2
Packaged: 2015-08-17 17:45:28 UTC; kate.hu
Author: Jie (Kate) Hu [aut, cre], Norman Breslow [aut], Gary Chan [aut]
Maintainer: Jie (Kate) Hu <hujie0704@gmail.com>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-17 23:07:27

More information about addhazard at CRAN
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Package PBC (with last version 1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-04-30 1.2
2014-02-21 1.1

Permanent link
Package fuzzyMM (with last version 1.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-07-18 1.0.1

Permanent link
Package RcmdrPlugin.StatisticalURV (with last version 1.0-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-01-25 1.0-1
2012-06-13 1.0-0

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Package kml3d updated to version 2.4 with previous version 2.3 dated 2015-05-21

Title: K-Means for Joint Longitudinal Data
Description: An implementation of k-means specifically design to cluster joint trajectories (longitudinal data on several variable-trajectories). Like 'kml', it provides facilities to deal with missing value, compute several quality criterion (Calinski and Harabatz, Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical interface for choosing the 'best' number of clusters. In addition, the 3D graph representing the mean joint-trajectories of each cluster can be exported through LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut], Bruno Falissard [ctb], Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>

Diff between kml3d versions 2.3 dated 2015-05-21 and 2.4 dated 2015-08-17

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Package simmr updated to version 0.2 with previous version 0.1 dated 2015-08-06

Title: A Stable Isotope Mixing Model
Description: Fits a stable isotope mixing model via JAGS in R. The package allows for any number of isotopes or sources, as well as concentration dependencies.
Author: Andrew Parnell
Maintainer: Andrew Parnell <andrew.parnell@ucd.ie>

Diff between simmr versions 0.1 dated 2015-08-06 and 0.2 dated 2015-08-17

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Package RcppArmadillo updated to version 0.5.400.2.0 with previous version 0.5.300.4 dated 2015-08-04

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.5.300.4 dated 2015-08-04 and 0.5.400.2.0 dated 2015-08-17

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Package fICA updated to version 1.0-3 with previous version 1.0-2 dated 2014-10-27

Title: Classical, Reloaded and Adaptive FastICA Algorithms
Description: Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>

Diff between fICA versions 1.0-2 dated 2014-10-27 and 1.0-3 dated 2015-08-17

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Package cp4p updated to version 0.3.1 with previous version 0.3 dated 2015-07-21

Title: Calibration Plot for Proteomics
Description: Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
Author: Quentin Giai Gianetto, Florence Combes, Yohann Couté, Christophe Bruley, Thomas Burger
Maintainer: Quentin Giai Gianetto <quentin2g@yahoo.fr>

Diff between cp4p versions 0.3 dated 2015-07-21 and 0.3.1 dated 2015-08-17

 DESCRIPTION             |    6 +--
 MD5                     |   12 +++----
 R/estim_pi0.R           |   82 +++++++++++++++++++++++++++++++++---------------
 man/LFQRatio2.Rd        |    8 ++--
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Package BSSasymp updated to version 1.1-1 with previous version 1.1-0 dated 2014-10-28

Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing Matrix Estimates
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric and squared symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>

Diff between BSSasymp versions 1.1-0 dated 2014-10-28 and 1.1-1 dated 2015-08-17

 DESCRIPTION                  |   12 -
 MD5                          |   40 +--
 NAMESPACE                    |    4 
 R/CRB.R                      |   32 +-
 R/FOBI_ascov.R               |  131 +++++------
 R/FastICA_ascov.R            |  502 +++++++++++++++++++++++++------------------
 R/JADE_ascov.R               |  136 +++++------
 R/SOBI_ascov.R               |  231 +++++++++----------
 R/SOBIdefl_ascov.R           |  244 +++++++++-----------
 inst/ChangeLog               |    7 
 man/ASCOV_FastICAdefl.Rd     |    2 
 man/ASCOV_FastICAdefl_est.Rd |    2 
 man/ASCOV_FastICAsym.Rd      |   15 -
 man/ASCOV_FastICAsym_est.Rd  |    6 
 man/ASCOV_JADE.Rd            |    6 
 man/ASCOV_JADE_est.Rd        |    4 
 man/ASCOV_SOBI.Rd            |    2 
 man/ASCOV_SOBI_est.Rd        |   10 
 man/BSSasymp-package.Rd      |    6 
 man/CRB.Rd                   |    2 
 man/alphas.Rd                |    2 
 21 files changed, 710 insertions(+), 686 deletions(-)

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Package Bchron updated to version 4.1.2 with previous version 4.1.1 dated 2014-04-22

Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); Age-depth modelling as per the algorithm of Haslett and Parnell (2008); Relative sea level rate estimation incorporating time uncertainty in polynomial regression models; and non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM). The package includes a vignette which can be accessed via vignette(‘Bchron’).
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@ucd.ie>

Diff between Bchron versions 4.1.1 dated 2014-04-22 and 4.1.2 dated 2015-08-17

 Bchron-4.1.1/Bchron/R/zzz.R                           |only
 Bchron-4.1.2/Bchron/DESCRIPTION                       |   19 +++++-----
 Bchron-4.1.2/Bchron/MD5                               |   34 ++++++++++--------
 Bchron-4.1.2/Bchron/NAMESPACE                         |    7 +++
 Bchron-4.1.2/Bchron/R/BchronCalibrate.R               |    8 ++--
 Bchron-4.1.2/Bchron/R/BchronDensity.R                 |   20 +++++-----
 Bchron-4.1.2/Bchron/R/Bchronology.R                   |   18 ++++-----
 Bchron-4.1.2/Bchron/R/plot.BchronCalibratedDates.R    |   16 ++++----
 Bchron-4.1.2/Bchron/R/plot.BchronDensityRun.R         |   12 +++---
 Bchron-4.1.2/Bchron/R/plot.BchronDensityRunFast.R     |   16 ++++----
 Bchron-4.1.2/Bchron/R/plot.BchronRSLRun.R             |   10 ++---
 Bchron-4.1.2/Bchron/R/plot.BchronologyRun.R           |   14 +++----
 Bchron-4.1.2/Bchron/R/predict.BchronologyRun.R        |    2 -
 Bchron-4.1.2/Bchron/R/summary.BchronCalibratedDates.R |    9 ++++
 Bchron-4.1.2/Bchron/R/summary.BchronologyRun.R        |    4 +-
 Bchron-4.1.2/Bchron/build                             |only
 Bchron-4.1.2/Bchron/inst                              |only
 Bchron-4.1.2/Bchron/man/plot.BchronCalibratedDates.Rd |   16 +++++++-
 Bchron-4.1.2/Bchron/vignettes                         |only
 19 files changed, 120 insertions(+), 85 deletions(-)

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Package ASMap updated to version 0.4-5 with previous version 0.4-4 dated 2015-06-26

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler <david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>

Diff between ASMap versions 0.4-4 dated 2015-06-26 and 0.4-5 dated 2015-08-17

 DESCRIPTION                 |   10 +++++-----
 MD5                         |   22 +++++++++++-----------
 NAMESPACE                   |    6 +++++-
 R/mstmap10.R                |    2 +-
 build/vignette.rds          |binary
 inst/NEWS.Rd                |    3 +++
 inst/doc/asmapvignette.Rnw  |   19 +++++++++++++------
 inst/doc/asmapvignette.pdf  |binary
 man/heatMap.Rd              |   14 +++++++-------
 vignettes/asmapvignette.Rnw |   19 +++++++++++++------
 vignettes/heatmap.png       |binary
 vignettes/heatmapDH.png     |binary
 12 files changed, 58 insertions(+), 37 deletions(-)

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Package multicool updated to version 0.1-7 with previous version 0.1-6 dated 2015-04-28

Title: Permutations of Multisets in Cool-Lex Order
Description: A set of tools to permute multisets without loops or hash tables and to generate integer partitions. The permutation functions are based on C code from Aaron Williams. Cool-lex order is similar to colexicographical order. The algorithm is described in Williams, A. Loopless Generation of Multiset Permutations by Prefix Shifts. SODA 2009, Symposium on Discrete Algorithms, New York, United States. The permutation code is distributed without restrictions. The code for stable and efficient computation of multinomial coefficients comes from Dave Barber. The code can be download from http://home.comcast.net/~tamivox/dave/multinomial/index.html and is distributed without conditions. The package also generates the integer partitions of a positive, non-zero integer n. The C++ code for this is based on Python code from Jerome Kelleher which can be found here http://jeromekelleher.net/partitions.php. The C++ code and Python code are distributed without conditions.
Author: James Curran, Aaron Williams, Jerome Kelleher, Dave Barber
Maintainer: James Curran <j.curran@auckland.ac.nz>

Diff between multicool versions 0.1-6 dated 2015-04-28 and 0.1-7 dated 2015-08-17

 DESCRIPTION       |    8 ++--
 MD5               |   10 ++---
 R/allPerm.R       |   22 +++++--------
 R/initMC.r        |   91 +++++++++++++++++++++++++++---------------------------
 R/nextPerm.R      |   23 +++++--------
 src/multicool.cpp |    1 
 6 files changed, 76 insertions(+), 79 deletions(-)

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New package LotkasLaw with initial version 0.0.1.0
Package: LotkasLaw
Title: Runs Lotka's Law which is One of the Special Applications of Zipf's Law
Version: 0.0.1.0
Authors@R: c( person("Kenneth", "Buker", email = "KCIV4@att.net", role = c("aut", "cre")), person("Dr. Alon", "Friedman", role = c("ctb")))
Description: Running Lotka's Law following Pao (1985)(DOI: 10.1016/0306-4573(85)90055-X). The Law is based around the proof that the number of authors making n contributions is about 1/n^{a} of those making one contribution.
Depends: R (>= 3.1.1)
License: GPL
LazyData: true
Packaged: 2015-08-17 04:53:29 UTC; Ken
Author: Kenneth Buker [aut, cre], Dr. Alon Friedman [ctb]
Maintainer: Kenneth Buker <KCIV4@att.net>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-08-17 07:53:29

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