Thu, 03 Dec 2015

Package pedometrics updated to version 0.6-6 with previous version 0.6-5 dated 2015-12-01

Title: Pedometric Tools and Techniques
Description: Functions to employ many of the tools and techniques used in the field of pedometrics.
Author: Alessandro Samuel-Rosa [aut, cre], Lúcia Anjos [ths], Gustavo Vasques [ths], Gerard Heuvelink [ths], Tony Olsen [ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo Garcia [ctb], Pablo Garcia Rodriguez [ctb], Joshua French [ctb], Ken Kleinman [ctb], Dick Brus [ctb], Frank Harrell Jr [ctb], Ruo Xu [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>

Diff between pedometrics versions 0.6-5 dated 2015-12-01 and 0.6-6 dated 2015-12-03

 DESCRIPTION                |   13 +++--
 MD5                        |   12 ++---
 R/AAAA.R                   |    1 
 R/pedometrics.R            |    4 -
 R/vgmICP.R                 |  105 +++++++++++++++++++++++----------------------
 man/pedometrics-package.Rd |    4 -
 man/vgmICP.Rd              |   46 +++++++++++--------
 7 files changed, 100 insertions(+), 85 deletions(-)

More information about pedometrics at CRAN
Permanent link

Package Luminescence updated to version 0.5.0 with previous version 0.4.6 dated 2015-09-21

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre], Michael Dietze [aut], Christoph Burow [aut], Margret C. Fuchs [aut], Christoph Schmidt [aut], Manfred Fischer [aut, trl], Rachel K. Smedley [aut], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>

Diff between Luminescence versions 0.4.6 dated 2015-09-21 and 0.5.0 dated 2015-12-03

 Luminescence-0.4.6/Luminescence/R/readBIN2R.R                            |only
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 Luminescence-0.5.0/Luminescence/DESCRIPTION                              |   53 
 Luminescence-0.5.0/Luminescence/MD5                                      |  351 +-
 Luminescence-0.5.0/Luminescence/NAMESPACE                                |  170 
 Luminescence-0.5.0/Luminescence/NEWS                                     |  648 +++
 Luminescence-0.5.0/Luminescence/R/Analyse_SAR.OSLdata.R                  |   87 
 Luminescence-0.5.0/Luminescence/R/CW2pHMi.R                              |    2 
 Luminescence-0.5.0/Luminescence/R/CW2pLM.R                               |    2 
 Luminescence-0.5.0/Luminescence/R/CW2pLMi.R                              |    2 
 Luminescence-0.5.0/Luminescence/R/CW2pPMi.R                              |    2 
 Luminescence-0.5.0/Luminescence/R/Luminescence-package.R                 |   41 
 Luminescence-0.5.0/Luminescence/R/RLum-class.R                           |   53 
 Luminescence-0.5.0/Luminescence/R/RLum.Analysis-class.R                  |  473 +-
 Luminescence-0.5.0/Luminescence/R/RLum.Data-class.R                      |    8 
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 Luminescence-0.5.0/Luminescence/R/RcppExports.R                          |    4 
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 Luminescence-0.5.0/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R    |   82 
 Luminescence-0.5.0/Luminescence/R/RisoeBINfileData-class.R               |   28 
 Luminescence-0.5.0/Luminescence/R/Second2Gray.R                          |   74 
 Luminescence-0.5.0/Luminescence/R/analyse_IRSAR.RF.R                     |  363 +-
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 Luminescence-0.5.0/Luminescence/R/apply_CosmicRayRemoval.R               |    2 
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 Luminescence-0.5.0/Luminescence/R/calc_FiniteMixture.R                   |    1 
 Luminescence-0.5.0/Luminescence/R/calc_FuchsLang2001.R                   |    2 
 Luminescence-0.5.0/Luminescence/R/calc_HomogeneityTest.R                 |    1 
 Luminescence-0.5.0/Luminescence/R/calc_IEU.R                             |    2 
 Luminescence-0.5.0/Luminescence/R/calc_MaxDose.R                         |    4 
 Luminescence-0.5.0/Luminescence/R/calc_MinDose.R                         |    2 
 Luminescence-0.5.0/Luminescence/R/calc_OSLLxTxRatio.R                    |  208 -
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 198 files changed, 7925 insertions(+), 3594 deletions(-)

More information about Luminescence at CRAN
Permanent link

Package expands updated to version 1.6.1 with previous version 1.6 dated 2015-11-02

Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. Whether or not this is the case is now decided by leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS(). Further documentation and FAQ around this package is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>

Diff between expands versions 1.6 dated 2015-11-02 and 1.6.1 dated 2015-12-03

 DESCRIPTION               |   12 ++++-----
 MD5                       |   20 ++++++++--------
 R/assignQuantityToSP.R    |   56 +++++++++++++++++++++++++++++++++-------------
 R/buildMultiSamplePhylo.R |    6 ++++
 R/buildPhylo.R            |   40 +++++++++-----------------------
 R/runExPANdS.R            |   11 ++++++---
 inst/doc/expands.R        |    2 -
 inst/doc/expands.Rnw      |    2 -
 inst/doc/expands.pdf      |binary
 man/assignQuantityToSP.Rd |    6 ++--
 vignettes/expands.Rnw     |    2 -
 11 files changed, 88 insertions(+), 69 deletions(-)

More information about expands at CRAN
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Package EpiDynamics updated to version 0.3.0 with previous version 0.2 dated 2014-08-21

Title: Dynamic Models in Epidemiology
Description: Mathematical models of infectious diseases in humans and animals. Both, deterministic and stochastic models can be simulated and plotted.
Author: Oswaldo Santos Baquero [aut, cre], Fernando Silveira Marques [aut]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>

Diff between EpiDynamics versions 0.2 dated 2014-08-21 and 0.3.0 dated 2015-12-03

 DESCRIPTION                       |   13 +++----
 MD5                               |   68 ++++++++++++++++++++------------------
 NAMESPACE                         |   14 ++++++-
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 man/SIRInducedMortality2.Rd       |    7 ++-
 man/SIRPartialImmunity.Rd         |   10 +++--
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 man/SIRSinusoidalForcing.Rd       |   12 +++---
 man/SIRTauLeap.Rd                 |    4 +-
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 man/SIRVector.Rd                  |   10 +++--
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 man/SISnRiskGroups.Rd             |   10 +++--
 man/sir2AgeClasses.Rd             |    6 ++-
 37 files changed, 190 insertions(+), 116 deletions(-)

More information about EpiDynamics at CRAN
Permanent link

Package acp updated to version 2.1 with previous version 2.0 dated 2015-05-22

Title: Autoregressive Conditional Poisson
Description: Analysis of count data exhibiting autoregressive properties, using the Autoregressive Conditional Poisson model (ACP(p,q)) proposed by Heinen (2003).
Author: Siakoulis Vasileios
Maintainer: Siakoulis Vasilios <Siakoulis.Vasilios@atticabank.gr>

Diff between acp versions 2.0 dated 2015-05-22 and 2.1 dated 2015-12-03

 DESCRIPTION |    8 +++----
 MD5         |    8 +++----
 NAMESPACE   |    5 +++-
 R/acp.R     |   63 +++++++++++++++++++++++++++++++++++++++++++++++++++---------
 man/acp.Rd  |    5 ++++
 5 files changed, 71 insertions(+), 18 deletions(-)

More information about acp at CRAN
Permanent link

Package RcppArmadillo updated to version 0.6.300.2.0 with previous version 0.6.200.2.0 dated 2015-10-31

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: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.6.200.2.0 dated 2015-10-31 and 0.6.300.2.0 dated 2015-12-03

 ChangeLog                                           |   25 
 DESCRIPTION                                         |    8 
 MD5                                                 |  124 +-
 inst/NEWS.Rd                                        |   17 
 inst/doc/RcppArmadillo-intro.pdf                    |binary
 inst/doc/RcppArmadillo-unitTests.pdf                |binary
 inst/include/RcppArmadilloAs.h                      |   88 ++
 inst/include/armadillo_bits/Base_bones.hpp          |    6 
 inst/include/armadillo_bits/Base_meat.hpp           |  100 +-
 inst/include/armadillo_bits/Cube_bones.hpp          |    8 
 inst/include/armadillo_bits/Cube_meat.hpp           |   31 
 inst/include/armadillo_bits/Mat_bones.hpp           |    8 
 inst/include/armadillo_bits/Mat_meat.hpp            |   35 
 inst/include/armadillo_bits/Proxy.hpp               |   39 
 inst/include/armadillo_bits/arma_forward.hpp        |    4 
 inst/include/armadillo_bits/arma_version.hpp        |    4 
 inst/include/armadillo_bits/auxlib_bones.hpp        |   41 
 inst/include/armadillo_bits/auxlib_meat.hpp         |  828 +++++++++++++++-----
 inst/include/armadillo_bits/compiler_setup.hpp      |    8 
 inst/include/armadillo_bits/def_lapack.hpp          |   99 ++
 inst/include/armadillo_bits/def_superlu.hpp         |    5 
 inst/include/armadillo_bits/diagview_meat.hpp       |   12 
 inst/include/armadillo_bits/diskio_bones.hpp        |    9 
 inst/include/armadillo_bits/diskio_meat.hpp         |  132 ---
 inst/include/armadillo_bits/fft_engine.hpp          |    2 
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 inst/include/armadillo_bits/fn_eig_gen.hpp          |   32 
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 inst/include/armadillo_bits/fn_solve.hpp            |  223 +++--
 inst/include/armadillo_bits/fn_spsolve.hpp          |   28 
 inst/include/armadillo_bits/glue_solve_bones.hpp    |   68 +
 inst/include/armadillo_bits/glue_solve_meat.hpp     |  184 +++-
 inst/include/armadillo_bits/glue_times_meat.hpp     |   27 
 inst/include/armadillo_bits/include_superlu.hpp     |   15 
 inst/include/armadillo_bits/memory.hpp              |   14 
 inst/include/armadillo_bits/op_inv_bones.hpp        |    4 
 inst/include/armadillo_bits/op_inv_meat.hpp         |    8 
 inst/include/armadillo_bits/op_symmat_meat.hpp      |    4 
 inst/include/armadillo_bits/op_trimat_meat.hpp      |    6 
 inst/include/armadillo_bits/sp_auxlib_bones.hpp     |   11 
 inst/include/armadillo_bits/sp_auxlib_meat.hpp      |  329 ++++++-
 inst/include/armadillo_bits/strip.hpp               |   11 
 inst/include/armadillo_bits/subview_bones.hpp       |    1 
 inst/include/armadillo_bits/subview_cube_bones.hpp  |    1 
 inst/include/armadillo_bits/subview_cube_meat.hpp   |   29 
 inst/include/armadillo_bits/subview_each_bones.hpp  |    8 
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 inst/include/armadillo_bits/subview_elem1_meat.hpp  |    2 
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 inst/include/armadillo_bits/subview_field_bones.hpp |    5 
 inst/include/armadillo_bits/subview_field_meat.hpp  |   63 +
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 inst/include/armadillo_bits/wall_clock_bones.hpp    |    4 
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 inst/include/armadillo_bits/wrapper_blas.hpp        |    4 
 inst/include/armadillo_bits/wrapper_lapack.hpp      |  197 ++++
 inst/include/armadillo_bits/wrapper_superlu.hpp     |   46 +
 inst/unitTests/cpp/cube.cpp                         |only
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 64 files changed, 2749 insertions(+), 969 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

Package pairwise updated to version 0.3.1 with previous version 0.2.5 dated 2014-05-28

Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>

Diff between pairwise versions 0.2.5 dated 2014-05-28 and 0.3.1 dated 2015-12-03

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More information about pairwise at CRAN
Permanent link

Package flowr updated to version 0.9.9.5 with previous version 0.9.8.2 dated 2015-10-03

Title: Streamlining Design and Deployment of Complex Workflows
Description: This framework allows you to design and implement complex pipelines, and deploy them on your institution's computing cluster. This has been built keeping in mind the needs of bioinformatics workflows. However, it is easily extendable to any field where a series of steps (shell commands) are to be executed in a (work)flow.
Author: Sahil Seth [aut, cre]
Maintainer: Sahil Seth <me@sahilseth.com>

Diff between flowr versions 0.9.8.2 dated 2015-10-03 and 0.9.9.5 dated 2015-12-03

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 flowr-0.9.9.5/flowr/NAMESPACE                                                          |    6 
 flowr-0.9.9.5/flowr/NEWS.md                                                            |   87 +
 flowr-0.9.9.5/flowr/R/check-args.R                                                     |    4 
 flowr-0.9.9.5/flowr/R/check.R                                                          |   24 
 flowr-0.9.9.5/flowr/R/class-def.R                                                      |   10 
 flowr-0.9.9.5/flowr/R/conf.R                                                           |   45 
 flowr-0.9.9.5/flowr/R/errors.R                                                         |    4 
 flowr-0.9.9.5/flowr/R/fetch.r                                                          |   32 
 flowr-0.9.9.5/flowr/R/kill-flow.R                                                      |    2 
 flowr-0.9.9.5/flowr/R/limit_runs.R                                                     |    1 
 flowr-0.9.9.5/flowr/R/parse-jobids.R                                                   |   11 
 flowr-0.9.9.5/flowr/R/plot.R                                                           |   21 
 flowr-0.9.9.5/flowr/R/render-dependency.R                                              |    9 
 flowr-0.9.9.5/flowr/R/rerun.R                                                          |  414 ++---
 flowr-0.9.9.5/flowr/R/run.R                                                            |   84 -
 flowr-0.9.9.5/flowr/R/setup.R                                                          |   27 
 flowr-0.9.9.5/flowr/R/status.R                                                         |   39 
 flowr-0.9.9.5/flowr/R/submit-flow.R                                                    |  240 +--
 flowr-0.9.9.5/flowr/R/submit-job.R                                                     |    6 
 flowr-0.9.9.5/flowr/R/submit-local.R                                                   |    2 
 flowr-0.9.9.5/flowr/R/to-flow.R                                                        |  780 +++++-----
 flowr-0.9.9.5/flowr/R/to-flowdef.R                                                     |  341 +++-
 flowr-0.9.9.5/flowr/R/to-flowdet.R                                                     |    2 
 flowr-0.9.9.5/flowr/R/to-flowmat.R                                                     |   49 
 flowr-0.9.9.5/flowr/R/verbose.R                                                        |    2 
 flowr-0.9.9.5/flowr/R/zz-db.R                                                          |    4 
 flowr-0.9.9.5/flowr/R/zz-parse-resources.R                                             |    8 
 flowr-0.9.9.5/flowr/R/zzz.R                                                            |    4 
 flowr-0.9.9.5/flowr/README.md                                                          |   57 
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 flowr-0.9.9.5/flowr/inst/conf/moab.sh                                                  |    3 
 flowr-0.9.9.5/flowr/inst/conf/sge.sh                                                   |    3 
 flowr-0.9.9.5/flowr/inst/conf/slurm.sh                                                 |    3 
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 flowr-0.9.9.5/flowr/man/error.Rd                                                       |    2 
 flowr-0.9.9.5/flowr/man/fetch.Rd                                                       |   38 
 flowr-0.9.9.5/flowr/man/flow.Rd                                                        |   12 
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 flowr-0.9.9.5/flowr/man/job.Rd                                                         |    2 
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 flowr-0.9.9.5/flowr/man/plot_flow.Rd                                                   |   10 
 flowr-0.9.9.5/flowr/man/queue.Rd                                                       |    2 
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 flowr-0.9.9.5/flowr/man/rerun.Rd                                                       |   26 
 flowr-0.9.9.5/flowr/man/run.Rd                                                         |   41 
 flowr-0.9.9.5/flowr/man/setup.Rd                                                       |   18 
 flowr-0.9.9.5/flowr/man/status.Rd                                                      |   18 
 flowr-0.9.9.5/flowr/man/submit_flow.Rd                                                 |   12 
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 flowr-0.9.9.5/flowr/man/test_queue.Rd                                                  |    4 
 flowr-0.9.9.5/flowr/man/to_flow.Rd                                                     |   76 
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 flowr-0.9.9.5/flowr/man/to_flowdet.Rd                                                  |    4 
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 flowr-0.9.9.5/flowr/tests/testthat.R                                                   |    2 
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More information about flowr at CRAN
Permanent link

Package ADPclust updated to version 0.6.5 with previous version 0.6.3 dated 2015-04-20

Title: Fast Clustering Using Adaptive Density Peak Detection
Description: An implementation of ADPclust clustering procedures (Fast Clustering Using Adaptive Density Peak Detection). The work is built and improved upon Rodriguez and Laio[2014]'s idea. ADPclust clusters data by finding density peaks in a density-distance plot generated from local multivariate Gaussian density estimation. It includes an automatic centroids selection and parameter optimization algorithm, which finds the number of clusters and cluster centroids by comparing average silhouettes on a grid of testing clustering results; It also includes an user interactive algorithm that allows the user to manually selects cluster centroids from a two dimensional "density-distance plot".
Author: Yifan "Ethan" Xu [aut, cre], Xiao-Feng Wang [aut]
Maintainer: Yifan "Ethan" Xu <ethan.yifanxu@gmail.com>

Diff between ADPclust versions 0.6.3 dated 2015-04-20 and 0.6.5 dated 2015-12-03

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Package RQuantLib updated to version 0.4.2 with previous version 0.4.1 dated 2015-09-11

Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R The 'QuantLib' project aims to provide a comprehensive software framework for quantitative finance. The goal is to provide a standard open source library for quantitative analysis, modeling, trading, and risk management of financial assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010)
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RQuantLib versions 0.4.1 dated 2015-09-11 and 0.4.2 dated 2015-12-03

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Package qtl updated to version 1.38-4 with previous version 1.37-11 dated 2015-08-25

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>

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New package CopulaDTA with initial version 0.0.1
Package: CopulaDTA
Type: Package
Title: Copula Based Bivariate Beta-Binomial Model for Diagnostic Test Accuracy Studies
Version: 0.0.1
Date: 2015-12-2
Authors@R: person("Victoria", "N Nyaga", email="victoria.nyaga@outlook.com", role=c("aut", "cre"))
Depends: R (>= 3.2.2), rstan (>= 2.8.2)
Imports: ggplot2 (>= 1.0.1), plyr (>= 1.8.3), stats (>= 3.2.2), reshape2 (>= 1.4.1), grDevices (>= 3.2.2)
Description: Modelling of sensitivity and specificity on their natural scale using copula based bivariate beta-binomial distribution to yield marginal mean sensitivity and specificity. The intrinsic negative correlation between sensitivity and specificity is modelled using a copula function. A forest plot can be obtained for categorical covariates or for the model with intercept only.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2015-12-03 12:40:08 UTC; Vnyawiranyaga
Author: Victoria N Nyaga [aut, cre]
Maintainer: Victoria N Nyaga <victoria.nyaga@outlook.com>
Repository: CRAN
Date/Publication: 2015-12-03 16:24:32

More information about CopulaDTA at CRAN
Permanent link

Package ChannelAttribution updated to version 1.3 with previous version 1.2 dated 2015-10-09

Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>

Diff between ChannelAttribution versions 1.2 dated 2015-10-09 and 1.3 dated 2015-12-03

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Package sglasso updated to version 1.2.2 with previous version 1.2.1 dated 2015-06-04

Title: Lasso Method for RCON(V,E) Models
Description: RCON(V, E) models (Højsgaard, et al., 2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. 'sglasso' package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>

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Package ryouready updated to version 0.4 with previous version 0.3 dated 2013-12-15

Title: Companion to the Forthcoming Book - R you Ready?
Description: Package contains some data and functions that are used in my forthcoming "R you ready?" book.
Author: Mark Heckmann [aut, cre]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>

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New package rangemodelR with initial version 0.1
Package: rangemodelR
Version: 0.1
Date: 2015-12-3
Title: Mid-Domain Effect and Species Richness Estimates
Author: Aniruddha Marathe <aniruddha.pravin.marathe@gmail.com>
Type: Package
Maintainer: Aniruddha Marathe <aniruddha.pravin.marathe@gmail.com>
Depends: R (>= 3.2.0)
Description: Generates expected values of species richness, with continuous or scattered ranges, for data across one or two dimensions.
License: GPL (>= 2)
Suggests: spdep,sp,ggplot2,maptools,plyr,reshape2
Imports: stats
NeedsCompilation: no
Packaged: 2015-12-03 09:28:16 UTC; aniruddha
Repository: CRAN
Date/Publication: 2015-12-03 13:28:29

More information about rangemodelR at CRAN
Permanent link

Package onewaytests updated to version 1.1 with previous version 1.0 dated 2015-08-24

Title: One-Way Independent Groups Design
Description: Two or more samples in one-way independent groups design are compared via different tests.
Author: Osman Dag, Anil Dolgun, N. Meric Konar
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>

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Package IntegratedJM updated to version 1.3 with previous version 1.2 dated 2015-11-12

Title: Joint Modelling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature
Description: Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Author: Rudradev Sengupta, Nolen Joy Perualila
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>

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Package jaatha updated to version 3.0.0 with previous version 2.7.0 dated 2014-11-26

Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to approximate maximum-likelihood estimates even when the likelihood function can not be evaluated directly. It can be applied whenever it is feasible to conduct many simulations, but works best when the data is approximately Poisson distributed. It was originally designed for demographic inference in evolutionary biology. It has optional support for conducting coalescent simulation using the 'coala' package.
Author: Paul Staab [aut, cre], Lisha Mathew [aut], Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>

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Package ACDm updated to version 1.0.3 with previous version 1.0.2 dated 2015-07-16

Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>

Diff between ACDm versions 1.0.2 dated 2015-07-16 and 1.0.3 dated 2015-12-03

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Package TMB updated to version 1.6.5 with previous version 1.6.2 dated 2015-10-19

Title: Template Model Builder: A General Random Effect Tool Inspired by ADMB
Description: With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines CppAD (C++ automatic differentiation), Eigen (templated matrix-vector library) and CHOLMOD (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph], Brad Bell [cph], Hans Skaug [ctb], Arni Magnusson [ctb], Casper Berg [ctb], Anders Nielsen [ctb], Martin Maechler [ctb], Theo Michelot [ctb], Mollie Brooks [ctb], Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>

Diff between TMB versions 1.6.2 dated 2015-10-19 and 1.6.5 dated 2015-12-03

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New package tggd with initial version 0.1.1
Package: tggd
Type: Package
Title: The Standard Distribution Functions for the Truncated Generalised Gamma Distribution
Version: 0.1.1
Date: 2015-12-03
Author: Aaron Robotham, Steven Murray
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Description: Density, distribution function, quantile function and random generation for the Truncated Generalised Gamma Distribution (also in log10(x) and ln(x) space).
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.00), gsl
NeedsCompilation: no
Packaged: 2015-12-03 02:56:23 UTC; aaron
Repository: CRAN
Date/Publication: 2015-12-03 13:05:16

More information about tggd at CRAN
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Package SAGA updated to version 2.0.0 with previous version 1.0 dated 2015-09-07

Title: Software for the Analysis of Genetic Architecture
Description: Implements an information theory approach to the analysis of line cross data providing model averaged results of parameter estimates and unconditional standard errors. Also includes functions to provide a visualization of models space, custom plots of multi-model inference results, and traditional line cross analysis plots.
Author: Heath Blackmon and Jeffery P. Demuth
Maintainer: Heath Blackmon <coleoguy@gmail.com>

Diff between SAGA versions 1.0 dated 2015-09-07 and 2.0.0 dated 2015-12-03

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Package rFerns updated to version 2.0.0 with previous version 1.1.0 dated 2014-11-30

Title: Random Ferns Classifier
Description: An R implementation of the random ferns classifier by Ozuysal et al., modified for generic and multi-label classification and featuring OOB error approximation and importance measure.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>

Diff between rFerns versions 1.1.0 dated 2014-11-30 and 2.0.0 dated 2015-12-03

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Package ppcor updated to version 1.1 with previous version 1.0 dated 2011-06-15

Title: Partial and Semi-Partial (Part) Correlation
Description: Calculates partial and semi-partial (part) correlations along with p-value.
Author: Seongho Kim
Maintainer: Seongho Kim <biostatistician.kim@gmail.com>

Diff between ppcor versions 1.0 dated 2011-06-15 and 1.1 dated 2015-12-03

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New package formattable with initial version 0.1.5
Package: formattable
Title: Formattable Data Structures
Version: 0.1.5
Authors@R: c( person("Kun", "Ren", role = c("aut", "cre"), email = "ken@renkun.me"), person("Kenton", "Russell", role = "aut", email = "kent.russell@timelyportfolio.com") )
Description: Provides functions to create formattable vectors and data frames. Formattable vectors are printed with text formatting, and formattable data frames are printed with multiple types of formatting in markdown to improve the readability of data presented in tabular form rendered as web pages.
Depends: R (>= 2.14.1)
Date: 2015-12-03
Imports: htmltools, htmlwidgets, markdown, knitr, shiny
License: MIT + file LICENSE
LazyData: true
URL: http://renkun.me/formattable, https://github.com/renkun-ken/formattable
BugReports: https://github.com/renkun-ken/formattable/issues
ByteCompile: TRUE
Suggests: testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2015-12-03 05:05:16 UTC; Kun
Author: Kun Ren [aut, cre], Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>
Repository: CRAN
Date/Publication: 2015-12-03 13:05:10

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Package JRF updated to version 0.1-2 with previous version 0.1-1 dated 2015-11-20

Title: Joint Random Forest (JRF) for the Simultaneous Estimation of Multiple Related Networks
Description: Simultaneous estimation of multiple related networks.
Author: Francesca Petralia Developer [aut, cre], Pei Wang Developer [aut], Zhidong Tu Developer [aut], Won-min Song Developer [aut], Adele Cutler Developer [ctb], Leo Breiman Developer [ctb], Andy Liaw Developer [ctb], Matthew Wiener Developer [ctb]
Maintainer: Francesca Petralia Developer <francesca.petralia@mssm.edu>

Diff between JRF versions 0.1-1 dated 2015-11-20 and 0.1-2 dated 2015-12-03

 DESCRIPTION       |    6 +++---
 MD5               |    6 +++---
 man/JRF.Rd        |   34 ++++++++++++++++++----------------
 man/importance.Rd |   11 ++++++-----
 4 files changed, 30 insertions(+), 27 deletions(-)

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Package FedData updated to version 2.0.2 with previous version 2.0.1 dated 2015-09-22

Title: Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package allows for retrieval of five datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; and the International Tree Ring Data Bank. Additional data sources are in the works, including global DEM resources (ETOPO1, ETOPO5, ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky <bocinsky@gmail.com> Dylan Beaudette <Dylan.Beaudette@ca.usda.gov>
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>

Diff between FedData versions 2.0.1 dated 2015-09-22 and 2.0.2 dated 2015-12-03

 DESCRIPTION                        |   28 ++
 MD5                                |   70 +++----
 NAMESPACE                          |    4 
 R/GHCN_FUNCTIONS.R                 |  361 ++++++++++++++++++++++++++++++++++---
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