Mon, 09 Feb 2015

Package VNM updated to version 4.0 with previous version 2.0 dated 2014-10-31

Title: Using V-algorithm and Newton-Raphson Method to Obtain Multiple-objective Optimal Design
Description: Using V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang

Diff between VNM versions 2.0 dated 2014-10-31 and 4.0 dated 2015-02-09

 DESCRIPTION            |   14 +++---
 MD5                    |   34 +++++++++-----
 NAMESPACE              |   14 +++++-
 R/AllClasses.R         |only
 R/Deff.R               |  109 +++++++++++++++++++++++++++++++++-------------
 R/MOPT.R               |  113 +++++++++++++++++++++++++++++++++++++-----------
 R/S.Weight.R           |   95 ++++++++++++++++++++++++++++------------
 R/ceff1.R              |  104 ++++++++++++++++++++++++++++++++------------
 R/ceff2.R              |  114 ++++++++++++++++++++++++++++++++++++-------------
 R/plot-methods.R       |only
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 man/ceff1.Rd           |   11 ++--
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 22 files changed, 464 insertions(+), 184 deletions(-)

More information about VNM at CRAN
Permanent link

New package SegCorr with initial version 1.0
Package: SegCorr
Type: Package
Title: Detecting Correlated Genomic Regions
Version: 1.0
Date: 2015-02-09
Author: Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, Francois Radvanyi, Stephane Robin, Jennifer Wong
Maintainer: Eleni Ioanna Delatola
Description: Performs correlation matrix segmentation and applies a test procedure to detect highly correlated regions in gene expression.
Depends: cghseg
License: GPL-2
Packaged: 2015-02-09 20:50:21 UTC; Eleanna
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-10 00:36:27

More information about SegCorr at CRAN
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Package psbcGroup updated to version 1.1 with previous version 1.0 dated 2013-04-05

Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and Grouping Priors
Description: The package provides algorithms for fitting penalized semiparametric Bayesian Cox (PSBC) models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee

Diff between psbcGroup versions 1.0 dated 2013-04-05 and 1.1 dated 2015-02-09

 DESCRIPTION      |   17 ++++++++---------
 MD5              |   18 +++++++++---------
 NAMESPACE        |    5 +++++
 R/psbcEN.R       |    1 -
 R/psbcFL.R       |    2 +-
 R/psbcGL.R       |    1 -
 man/psbcEN.Rd    |   22 +++++++++++++---------
 man/psbcFL.Rd    |   21 ++++++++++++---------
 man/psbcGL.Rd    |   25 +++++++++++++++----------
 man/psbcGroup.Rd |   15 ++++++++-------
 10 files changed, 71 insertions(+), 56 deletions(-)

More information about psbcGroup at CRAN
Permanent link

Package nat updated to version 1.6.4 with previous version 1.5.12 dated 2014-08-21

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite (see https://github.com/jefferis/nat.as) bundle of R code that we have been using for a number of years to analyse and visualise 3D biological image data, especially traced neurons. The nat package is considerably cleaner, properly documented and provides all of the core functionality of nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats and read surfaces in Amira's hxsurf format. Traced neurons can be imported from and written to SWC and Amira LineSet and SkeletonGraph formats. These data can then be visualised in 3D via rgl, manipulated including applying calculated registrations, e.g. using the CMTK registration suite, and analysed. The package also has a simple representation for neurons that have been subjected to a 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the nat.nblast extension package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis

Diff between nat versions 1.5.12 dated 2014-08-21 and 1.6.4 dated 2015-02-09

 nat-1.5.12/nat/man/amiralandmark-io.Rd                                            |only
 nat-1.5.12/nat/man/cmtklandmarks.Rd                                               |only
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 nat-1.6.4/nat/DESCRIPTION                                                         |   46 -
 nat-1.6.4/nat/MD5                                                                 |  346 +++++-----
 nat-1.6.4/nat/NAMESPACE                                                           |   38 -
 nat-1.6.4/nat/NEWS                                                                |   70 ++
 nat-1.6.4/nat/R/amiralandmarks-io.R                                               |  129 +++
 nat-1.6.4/nat/R/amiramesh-io.R                                                    |   72 +-
 nat-1.6.4/nat/R/cmtk-reformat.R                                                   |   58 +
 nat-1.6.4/nat/R/cmtk.R                                                            |   17 
 nat-1.6.4/nat/R/cmtk_io.R                                                         |   91 +-
 nat-1.6.4/nat/R/dotprops.R                                                        |   14 
 nat-1.6.4/nat/R/hxsurf.R                                                          |    5 
 nat-1.6.4/nat/R/im3d.R                                                            |   99 ++
 nat-1.6.4/nat/R/nat-package.R                                                     |    4 
 nat-1.6.4/nat/R/ndigest.R                                                         |   12 
 nat-1.6.4/nat/R/neuron-io-amira.R                                                 |   28 
 nat-1.6.4/nat/R/neuron-io-fiji.R                                                  |only
 nat-1.6.4/nat/R/neuron-io-neuroml.R                                               |only
 nat-1.6.4/nat/R/neuron-io.R                                                       |  284 ++++++--
 nat-1.6.4/nat/R/neuron-plot.R                                                     |   21 
 nat-1.6.4/nat/R/neuron.R                                                          |  228 +++---
 nat-1.6.4/nat/R/neuronlist.R                                                      |  225 +++++-
 nat-1.6.4/nat/R/neuronlist_sets.R                                                 |only
 nat-1.6.4/nat/R/ngraph.R                                                          |   85 +-
 nat-1.6.4/nat/R/nrrd-io.R                                                         |   20 
 nat-1.6.4/nat/R/seglist.R                                                         |   46 -
 nat-1.6.4/nat/R/vaa3draw-io.R                                                     |   40 -
 nat-1.6.4/nat/R/xform.R                                                           |   53 +
 nat-1.6.4/nat/R/xformimage.R                                                      |only
 nat-1.6.4/nat/R/xformpoints.R                                                     |    8 
 nat-1.6.4/nat/R/zzz.R                                                             |   39 +
 nat-1.6.4/nat/README.md                                                           |    5 
 nat-1.6.4/nat/man/Cell07PNs.Rd                                                    |    3 
 nat-1.6.4/nat/man/affmat2cmtkparams.Rd                                            |    3 
 nat-1.6.4/nat/man/all.equal.dotprops.Rd                                           |    3 
 nat-1.6.4/nat/man/all.equal.im3d.Rd                                               |   21 
 nat-1.6.4/nat/man/all.equal.neuron.Rd                                             |   31 
 nat-1.6.4/nat/man/amiramesh-io.Rd                                                 |    5 
 nat-1.6.4/nat/man/amiratype.Rd                                                    |    5 
 nat-1.6.4/nat/man/as.im3d.Rd                                                      |   36 -
 nat-1.6.4/nat/man/as.mesh3d.Rd                                                    |    3 
 nat-1.6.4/nat/man/as.neuronlist.Rd                                                |    5 
 nat-1.6.4/nat/man/as.neuronlist.neuronlistfh.Rd                                   |    3 
 nat-1.6.4/nat/man/boundingbox.Rd                                                  |   31 
 nat-1.6.4/nat/man/c.neuronlist.Rd                                                 |    3 
 nat-1.6.4/nat/man/clampmax.Rd                                                     |    3 
 nat-1.6.4/nat/man/cmtk.bindir.Rd                                                  |    5 
 nat-1.6.4/nat/man/cmtk.call.Rd                                                    |    5 
 nat-1.6.4/nat/man/cmtk.dof2mat.Rd                                                 |    3 
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 nat-1.6.4/nat/man/cmtk.mat2dof.Rd                                                 |    3 
 nat-1.6.4/nat/man/cmtk.reformatx.Rd                                               |   42 -
 nat-1.6.4/nat/man/cmtk.statistics.Rd                                              |    3 
 nat-1.6.4/nat/man/cmtk.targetvolume.Rd                                            |   18 
 nat-1.6.4/nat/man/cmtk.version.Rd                                                 |    3 
 nat-1.6.4/nat/man/cmtkparams2affmat.Rd                                            |   11 
 nat-1.6.4/nat/man/cmtkreg.Rd                                                      |    3 
 nat-1.6.4/nat/man/cmtkreglist.Rd                                                  |   10 
 nat-1.6.4/nat/man/coord2ind.Rd                                                    |    3 
 nat-1.6.4/nat/man/dotprops-arithmetic.Rd                                          |    3 
 nat-1.6.4/nat/man/dotprops.Rd                                                     |   21 
 nat-1.6.4/nat/man/fileformats.Rd                                                  |   71 +-
 nat-1.6.4/nat/man/find.neuron.Rd                                                  |    8 
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 nat-1.6.4/nat/man/flip.Rd                                                         |    3 
 nat-1.6.4/nat/man/graph.nodes.Rd                                                  |    3 
 nat-1.6.4/nat/man/im3d-coords.Rd                                                  |    6 
 nat-1.6.4/nat/man/im3d-io.Rd                                                      |   15 
 nat-1.6.4/nat/man/im3d.Rd                                                         |    6 
 nat-1.6.4/nat/man/image.im3d.Rd                                                   |   27 
 nat-1.6.4/nat/man/imexpand.grid.Rd                                                |    6 
 nat-1.6.4/nat/man/imscalebar.Rd                                                   |    3 
 nat-1.6.4/nat/man/imslice.Rd                                                      |    6 
 nat-1.6.4/nat/man/ind2coord.Rd                                                    |    3 
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 nat-1.6.4/nat/man/is.amiramesh.Rd                                                 |   17 
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 nat-1.6.4/nat/man/is.neuroml.Rd                                                   |only
 nat-1.6.4/nat/man/is.neuronlist.Rd                                                |    3 
 nat-1.6.4/nat/man/is.nrrd.Rd                                                      |   10 
 nat-1.6.4/nat/man/is.swc.Rd                                                       |only
 nat-1.6.4/nat/man/is.vaa3draw.Rd                                                  |   11 
 nat-1.6.4/nat/man/kcs20.Rd                                                        |    3 
 nat-1.6.4/nat/man/materials.Rd                                                    |    3 
 nat-1.6.4/nat/man/mirror.Rd                                                       |    3 
 nat-1.6.4/nat/man/nat-internal.Rd                                                 |    3 
 nat-1.6.4/nat/man/nat-package.Rd                                                  |   10 
 nat-1.6.4/nat/man/ndigest.Rd                                                      |   16 
 nat-1.6.4/nat/man/neuron-arithmetic.Rd                                            |    3 
 nat-1.6.4/nat/man/neuron.Rd                                                       |   13 
 nat-1.6.4/nat/man/neuronlist-arithmetic.Rd                                        |    3 
 nat-1.6.4/nat/man/neuronlist-dataframe-methods.Rd                                 |   15 
 nat-1.6.4/nat/man/neuronlist.Rd                                                   |    3 
 nat-1.6.4/nat/man/neuronlistfh.Rd                                                 |    9 
 nat-1.6.4/nat/man/ngraph.Rd                                                       |   81 +-
 nat-1.6.4/nat/man/nlapply.Rd                                                      |   10 
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 nat-1.6.4/nat/man/nopen3d.Rd                                                      |    3 
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 nat-1.6.4/nat/man/npop3d.Rd                                                       |    3 
 nat-1.6.4/nat/man/nrrd.voxdims.Rd                                                 |    3 
 nat-1.6.4/nat/man/origin.Rd                                                       |    6 
 nat-1.6.4/nat/man/pan3d.Rd                                                        |    3 
 nat-1.6.4/nat/man/plot.neuron.Rd                                                  |    3 
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 nat-1.6.4/nat/man/plot3d.boundingbox.Rd                                           |    3 
 nat-1.6.4/nat/man/plot3d.dotprops.Rd                                              |    3 
 nat-1.6.4/nat/man/plot3d.hxsurf.Rd                                                |    3 
 nat-1.6.4/nat/man/plot3d.neuron.Rd                                                |   10 
 nat-1.6.4/nat/man/plot3d.neuronlist.Rd                                            |   18 
 nat-1.6.4/nat/man/pointsinside.Rd                                                 |    3 
 nat-1.6.4/nat/man/potential_synapses.Rd                                           |   11 
 nat-1.6.4/nat/man/projection.Rd                                                   |    6 
 nat-1.6.4/nat/man/prune.Rd                                                        |    3 
 nat-1.6.4/nat/man/read.cmtk.Rd                                                    |    7 
 nat-1.6.4/nat/man/read.cmtkreg.Rd                                                 |   10 
 nat-1.6.4/nat/man/read.hxsurf.Rd                                                  |   10 
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 nat-1.6.4/nat/man/read.morphml.Rd                                                 |only
 nat-1.6.4/nat/man/read.neuron.Rd                                                  |   39 +
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 nat-1.6.4/nat/man/read.neuron.swc.Rd                                              |    6 
 nat-1.6.4/nat/man/read.neuronlistfh.Rd                                            |    3 
 nat-1.6.4/nat/man/read.neurons.Rd                                                 |   26 
 nat-1.6.4/nat/man/read.nrrd.Rd                                                    |    7 
 nat-1.6.4/nat/man/read.vaa3draw.Rd                                                |    3 
 nat-1.6.4/nat/man/remotesync.Rd                                                   |    7 
 nat-1.6.4/nat/man/resample.Rd                                                     |   20 
 nat-1.6.4/nat/man/rootpoints.Rd                                                   |    3 
 nat-1.6.4/nat/man/scale.dotprops.Rd                                               |    3 
 nat-1.6.4/nat/man/scale.neuron.Rd                                                 |    3 
 nat-1.6.4/nat/man/seglengths.Rd                                                   |    3 
 nat-1.6.4/nat/man/seglist.Rd                                                      |    3 
 nat-1.6.4/nat/man/seglist2swc.Rd                                                  |   39 -
 nat-1.6.4/nat/man/segmentgraph.Rd                                                 |    3 
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 nat-1.6.4/nat/man/spine.Rd                                                        |   16 
 nat-1.6.4/nat/man/sub-.neuronlistfh.Rd                                            |    3 
 nat-1.6.4/nat/man/sub2ind.Rd                                                      |    3 
 nat-1.6.4/nat/man/subset.dotprops.Rd                                              |    3 
 nat-1.6.4/nat/man/subset.hxsurf.Rd                                                |    3 
 nat-1.6.4/nat/man/subset.neuronlist.Rd                                            |    3 
 nat-1.6.4/nat/man/threshold.Rd                                                    |   10 
 nat-1.6.4/nat/man/union.Rd                                                        |only
 nat-1.6.4/nat/man/unmask.Rd                                                       |   12 
 nat-1.6.4/nat/man/voxdims.Rd                                                      |    6 
 nat-1.6.4/nat/man/write.amiramesh.Rd                                              |   13 
 nat-1.6.4/nat/man/write.cmtk.Rd                                                   |    7 
 nat-1.6.4/nat/man/write.cmtkreg.Rd                                                |    7 
 nat-1.6.4/nat/man/write.hxsurf.Rd                                                 |    5 
 nat-1.6.4/nat/man/write.neuron.Rd                                                 |   14 
 nat-1.6.4/nat/man/write.neuronlistfh.Rd                                           |    3 
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 nat-1.6.4/nat/man/write.nrrd.Rd                                                   |    3 
 nat-1.6.4/nat/man/xform.Rd                                                        |   29 
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 nat-1.6.4/nat/man/xformpoints.Rd                                                  |    3 
 nat-1.6.4/nat/man/xyzmatrix.Rd                                                    |    3 
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 nat-1.6.4/nat/tests/testthat/test-cmtk.R                                          |    1 
 nat-1.6.4/nat/tests/testthat/test-hxsurf.R                                        |    7 
 nat-1.6.4/nat/tests/testthat/test-im3d.R                                          |   16 
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 nat-1.6.4/nat/tests/testthat/test-ndigest.R                                       |    3 
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 nat-1.6.4/nat/tests/testthat/test-neuron.R                                        |   33 
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 nat-1.6.4/nat/tests/testthat/test-ngraph.R                                        |   23 
 nat-1.6.4/nat/tests/testthat/test-nrrd-io.R                                       |   10 
 nat-1.6.4/nat/tests/testthat/test-seglist.R                                       |    7 
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 190 files changed, 2452 insertions(+), 1044 deletions(-)

More information about nat at CRAN
Permanent link

Package letsR updated to version 2.0 with previous version 1.0 dated 2014-05-19

Title: Tools for Data Handling and Analysis in Macroecology
Description: Includes R functions for handling and analyzing geographic data, mainly species' geographic distributions (in ESRI shapefile format) and environmental variables (in raster format), as well as species' information related to their description (e.g. taxonomy and year of description) and conservation status (e.g. category of threat, population trend) as provided by the IUCN's RedList database. The package includes functions to create presence-absence matrices based on species distributions and user-defined grid systems, from which several other functions could be applied to generate, for example, species richness rasters and maps, and geographical midpoints of species. In addition, it provides a function to create spatial correlograms of variables, based on the Moran's I index, under the equiprobable or equidistant criterion to define distance classes.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela

Diff between letsR versions 1.0 dated 2014-05-19 and 2.0 dated 2015-02-09

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Package kSamples updated to version 1.0.1 with previous version 1.0 dated 2012-08-31

Title: K-Sample Rank Tests and their Combinations
Description: Compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, and Steel's multiple comparison test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test it also combines these tests across several blocks of samples. Also analyzed are 2 x t contingency tables and their blocked combinations using the Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous confidence bounds for shift parameters. A plotting function shows that asymptotic approximations for small sample sizes provide only very limited utility when comparing tail probabilities with those obtained via simulation or exact calculations.
Author: Fritz Scholz [aut, cre], Angie Zhu [aut]
Maintainer: Fritz Scholz

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Package HSROC updated to version 2.1.8 with previous version 2.1.7 dated 2013-08-22

Title: Meta-Analysis of Diagnostic Test Accuracy when Reference Test is Imperfect
Description: Implements a model for joint meta-analysis of sensitivity and specificity of the diagnostic test under evaluation, while taking into account the possibly imperfect sensitivity and specificity of the reference test. This hierarchical model accounts for both within and between study variability. Estimation is carried out using a Bayesian approach, implemented via a Gibbs sampler. The model can be applied in situations where more than one reference test is used in the selected studies.
Author: Ian Schiller and Nandini Dendukuri
Maintainer: Ian Schiller

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Package gridGraphics updated to version 0.1-3 with previous version 0.1-2 dated 2014-11-26

Title: Redraw Base Graphics Using grid Graphics
Description: Functions to convert a page of plots drawn with the graphics package into identical output drawn with the grid package. The result looks like the original graphics-based plot, but consists of grid grobs and viewports that can then be manipulated with grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell

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Package cmvnorm updated to version 1.0-1 with previous version 1.0 dated 2014-09-09

Title: The Complex Multivariate Gaussian Distribution
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin

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Package SemiParBIVProbit updated to version 3.3 with previous version 3.2-13.2 dated 2015-01-15

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

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Package Ckmeans.1d.dp updated to version 3.3.0 with previous version 3.02 dated 2014-03-30

Title: Optimal k-Means Clustering for One-Dimensional Data
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song

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Package snpEnrichment updated to version 1.6.3 with previous version 1.6.0 dated 2014-11-04

Title: SNPs Enrichment Analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre], Loic Yengo [ctb]
Maintainer: Mickael Canouil

Diff between snpEnrichment versions 1.6.0 dated 2014-11-04 and 1.6.3 dated 2015-02-09

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Package RPushbullet updated to version 0.2.0 with previous version 0.1.1 dated 2014-11-04

Title: R Interface to the Pushbullet Messaging Service
Description: An R interface to the Pushbullet messaging service which provides fast and efficient notifications (and file transfer) between computers, phones and tablets. An account has to be registered at the site http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

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Package openair updated to version 1.1-5 with previous version 1.1-3 dated 2015-01-27

Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution data. Data are typically hourly time series and both monitoring data and dispersion model output can be analysed. Many functions can also be applied to other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre], Karl Ropkins [aut]
Maintainer: David Carslaw

Diff between openair versions 1.1-3 dated 2015-01-27 and 1.1-5 dated 2015-02-09

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New package Rlibeemd with initial version 1.3.1
Package: Rlibeemd
Type: Package
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN)
Version: 1.3.1
Date: 2015-02-08
Authors@R: c(person(given = "Jouni", family = "Helske", role = c("aut","cre"), comment = "R interface",email = "jouni.helske@jyu.fi"), person(given = "Perttu", family = "Luukko", role = "aut", comment = "Original libeemd C library"))
Description: An R interface for C library libeemd for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the regular empirical mode decomposition (EMD).
License: GPL-3
NeedsCompilation: yes
SystemRequirements: GNU GSL
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Encoding: UTF-8
Packaged: 2015-02-09 14:29:43 UTC; jovetale
Author: Jouni Helske [aut, cre] (R interface), Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske
Repository: CRAN
Date/Publication: 2015-02-09 16:44:09

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Package gmm updated to version 1.5-1 with previous version 1.5-0 dated 2013-12-11

Title: Generalized Method of Moments and Generalized Empirical Likelihood
Description: It is a complete suite to estimate models based on moment conditions. It includes the two step Generalized method of moments (GMM) of Hansen(1982), the iterated GMM and continuous updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several methods that belong to the Generalized Empirical Likelihood (GEL) family of estimators, as presented by Smith(1997), Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse

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Package DirichletReg updated to version 0.6-2 with previous version 0.6-1 dated 2014-12-10

Title: Dirichlet Regression in R
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier

Diff between DirichletReg versions 0.6-1 dated 2014-12-10 and 0.6-2 dated 2015-02-09

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Package BayesFactor updated to version 0.9.10-2 with previous version 0.9.10-1 dated 2015-02-04

Title: Computation of Bayes Factors for Common Designs
Description: A suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.
Author: Richard D. Morey [aut, cre], Jeffrey N. Rouder [aut], Tahira Jamil [ctb]
Maintainer: Richard D. Morey

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Package vardpoor updated to version 0.2.6 with previous version 0.2.4 dated 2015-01-04

Title: Variance Estimation for Sample Surveys by the Ultimate Cluster Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks

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Package excursions updated to version 2.0.16 with previous version 2.0.6 dated 2015-02-02

Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin and Finn Lindgren
Maintainer: David Bolin

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Package rtfbs updated to version 0.3.4 with previous version 0.3.3 dated 2015-01-13

Title: Transcription Factor Binding Site Identification Tool
Description: RTFBS identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by G+C content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Maintainer: Melissa Hubisz

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Package LARF updated to version 1.3 with previous version 1.2 dated 2014-09-28

Title: Local Average Response Functions for Instrumental Variable Estimation of Treatment Effects
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An

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