Sat, 08 Nov 2014

Package spaMM updated to version 1.4.1 with previous version 1.4.0 dated 2014-11-07

Title: Mixed Models, Particularly Spatial GLMMs
Description: Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph]
Maintainer: François Rousset

Diff between spaMM versions 1.4.0 dated 2014-11-07 and 1.4.1 dated 2014-11-08

 spaMM-1.4.0/spaMM/tests/test-all.R                    |only
 spaMM-1.4.1/spaMM/DESCRIPTION                         |   10 +++----
 spaMM-1.4.1/spaMM/MD5                                 |   18 ++++++------
 spaMM-1.4.1/spaMM/R/HLCor.R                           |   14 +++++++---
 spaMM-1.4.1/spaMM/R/HLfit.R                           |    5 ++-
 spaMM-1.4.1/spaMM/R/corrHLfit.R                       |    2 -
 spaMM-1.4.1/spaMM/R/locoptim.R                        |   25 +++++++++---------
 spaMM-1.4.1/spaMM/R/summary.HL.R                      |    6 ++--
 spaMM-1.4.1/spaMM/tests/testthat/test-Nugget.R        |only
 spaMM-1.4.1/spaMM/tests/testthat/test-corMatern.R     |    3 --
 spaMM-1.4.1/spaMM/tests/testthat/test-inverse.Gamma.R |    2 +
 11 files changed, 49 insertions(+), 36 deletions(-)

More information about spaMM at CRAN
Permanent link

Package rugarch updated to version 1.3-4 with previous version 1.3-3 dated 2014-05-26

Title: Univariate GARCH models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Ghalanos
Maintainer: Alexios Ghalanos

Diff between rugarch versions 1.3-3 dated 2014-05-26 and 1.3-4 dated 2014-11-08

 .Rinstignore                                     |    4 -
 ChangeLog                                        |    9 +++
 DESCRIPTION                                      |   10 ++--
 MD5                                              |   55 +++++++++++------------
 R/arfima-main.R                                  |   16 +++++-
 R/arfima-methods.R                               |    8 ++-
 R/rugarch-aparch.R                               |    6 +-
 R/rugarch-csgarch.R                              |    6 +-
 R/rugarch-egarch.R                               |    6 +-
 R/rugarch-fgarch.R                               |    6 +-
 R/rugarch-gjrgarch.R                             |    6 +-
 R/rugarch-graphs.R                               |   49 +++++++++++++-------
 R/rugarch-helperfn.R                             |   32 ++++++++++---
 R/rugarch-igarch.R                               |    4 +
 R/rugarch-mcsgarch.R                             |   10 ++--
 R/rugarch-methods.R                              |   38 ++++++++++-----
 R/rugarch-numderiv.R                             |    8 +--
 R/rugarch-realgarch.R                            |    5 +-
 R/rugarch-rolling.R                              |    2 
 R/rugarch-sgarch.R                               |    6 +-
 R/rugarch-solvers.R                              |   10 ----
 README.md                                        |only
 build/vignette.rds                               |binary
 inst/doc/Introduction_to_the_rugarch_package.pdf |binary
 man/arfimafit-methods.Rd                         |    8 ++-
 man/rugarch-package.Rd                           |    6 +-
 man/ugarchfit-methods.Rd                         |    9 +++
 src/distributions.c                              |    4 +
 src/filters.c                                    |    8 +++
 src/garchmodels.c                                |    2 
 30 files changed, 217 insertions(+), 116 deletions(-)

More information about rugarch at CRAN
Permanent link

Package nCal updated to version 14.11-8 with previous version 14.10-31 dated 2014-11-02

Title: Nonlinear Calibration
Description: nCal is a package that performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong , Krisztian Sebestyen , Xuesong Yu
Maintainer: Youyi Fong

Diff between nCal versions 14.10-31 dated 2014-11-02 and 14.11-8 dated 2014-11-08

 DESCRIPTION                               |    6 +++---
 MD5                                       |   12 ++++++------
 inst/doc/nCal-vignette.pdf                |binary
 inst/unitTests/runit.bcrm.R               |   10 ++++++++--
 vignettes/figure/minimal-Example1bcrm.pdf |binary
 vignettes/figure/minimal-Example1drm.pdf  |binary
 vignettes/figure/minimal-Example2.pdf     |binary
 7 files changed, 17 insertions(+), 11 deletions(-)

More information about nCal at CRAN
Permanent link

Package extraTrees updated to version 1.0.4 with previous version 1.0.3 dated 2014-09-07

Title: Extremely Randomized Trees (ExtraTrees) method for classification and regression
Description: Classification and regression based on an ensemble of decision trees. The package also provides extensions of ExtraTrees to multi-task learning and quantile regression. Uses Java implementation of the method.
Author: Jaak Simm, Ildefons Magrans de Abril
Maintainer: Jaak Simm

Diff between extraTrees versions 1.0.3 dated 2014-09-07 and 1.0.4 dated 2014-11-08

 DESCRIPTION                                     |    8 ++---
 MD5                                             |   33 ++++++++++++------------
 NAMESPACE                                       |    2 -
 R/extraTrees.default.R                          |    7 +++++
 inst/CHANGELOG                                  |    4 ++
 inst/doc/extraTrees.pdf                         |binary
 inst/java/ExtraTrees.jar                        |binary
 inst/tests/testthat/test-classification.r       |   10 +++++++
 inst/tests/testthat/test-regression.r           |   10 +++++++
 java/src/org/extratrees/AbstractBinaryTree.java |    5 ++-
 java/src/org/extratrees/AbstractTrees.java      |   19 ++++++++-----
 java/src/org/extratrees/BinaryTree.java         |    6 +++-
 java/src/org/extratrees/ExtraTrees.java         |   16 ++++++++---
 java/src/org/extratrees/FactorBinaryTree.java   |    6 +++-
 java/src/org/extratrees/FactorExtraTrees.java   |   13 +++++++--
 man/extraTrees.Rd                               |    2 -
 man/prepareForSave.Rd                           |only
 man/selectTrees.Rd                              |    8 ++---
 18 files changed, 105 insertions(+), 44 deletions(-)

More information about extraTrees at CRAN
Permanent link

Package EntropyEstimation updated to version 1.1 with previous version 1.0 dated 2014-09-17

Title: Estimation of Entropy and Related Quantities
Description: Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Author: Lijuan Cao and Michael Grabchak
Maintainer: Michael Grabchak

Diff between EntropyEstimation versions 1.0 dated 2014-09-17 and 1.1 dated 2014-11-08

 DESCRIPTION                      |    9 ++---
 MD5                              |   24 ++++++++-----
 NAMESPACE                        |    2 -
 R/EntropEst.r                    |   55 +++++++++++++++++++++++++++++++
 man/EntropyEstimation-package.Rd |    6 +--
 man/GenSimp.sd.Rd                |only
 man/Hill.sd.Rd                   |only
 man/KL.Plugin.Rd                 |    2 -
 man/KL.sd.Rd                     |    2 -
 man/KL.z.Rd                      |    2 -
 man/MI.sd.Rd                     |    4 ++
 man/MI.z.Rd                      |    7 +++-
 man/Renyi.sd.Rd                  |only
 man/Tsallis.sd.Rd                |only
 src/EntropEst.c                  |   68 ++++++++++++++++++++++++++++++++++++++-
 15 files changed, 157 insertions(+), 24 deletions(-)

More information about EntropyEstimation at CRAN
Permanent link

Package TreePar updated to version 3.2 with previous version 3.1 dated 2014-09-23

Title: Estimating birth and death rates based on phylogenies
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreePar versions 3.1 dated 2014-09-23 and 3.2 dated 2014-11-08

 DESCRIPTION                |   10 +++++-----
 MD5                        |   16 +++++++++++-----
 NAMESPACE                  |    2 +-
 R/LikAge.R                 |only
 R/LikConstant.R            |    1 +
 R/LikConstantn.R           |    1 +
 R/bd.age.optim.matlab.R    |only
 R/create.mat.R             |only
 man/LikAge.Rd              |only
 man/TreePar-package.Rd     |    6 +++---
 man/bd.age.optim.matlab.Rd |only
 man/create.mat.Rd          |only
 12 files changed, 22 insertions(+), 14 deletions(-)

More information about TreePar at CRAN
Permanent link

New package sudokuAlt with initial version 0.1-2
Package: sudokuAlt
Type: Package
Title: Tools for Making, Displaying and Spoiling Sudoku Games
Version: 0.1-2
Date: 2014-11-08
Suggests: sudoku
Imports: graphics
Author: Bill Venables
Maintainer: Bill Venables
Description: Tools for making, retrieving, displaying and solving sudoku games. This package is an alternative to the earlier sudoku-solver package, 'sudoku'. The present package uses a slightly different algorithm, has a simpler coding and presents a few more sugar tools, such as plot and print methods.
License: GPL (>= 2)
Packaged: 2014-11-08 02:04:16 UTC; bill
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-08 17:10:19

More information about sudokuAlt at CRAN
Permanent link

Package opencpu updated to version 1.4.5 with previous version 1.4.4 dated 2014-08-20

Title: The OpenCPU system for embedded scientific computing and reproducible research.
Description: The OpenCPU system exposes an HTTP API for embedded scientific computing with R. This provides reliable and scalable foundations for integrating R based analysis and visualization modules into pipelines, web applications or big data infrastructures. The OpenCPU server can run either as a single-user development server within the interactive R session, or as a high performance multi-user cloud server that builds on Linux, Nginx and rApache. The current R package forms the core of the system. When loaded in R, it automatically initiates the single-user server and displays the web address in the console. For detailed information and documentation on the API, visit the OpenCPU website.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between opencpu versions 1.4.4 dated 2014-08-20 and 1.4.5 dated 2014-11-08

 DESCRIPTION                  |   12 ++--
 MD5                          |   28 +++++-----
 NAMESPACE                    |    3 -
 R/github_install.R           |   46 +++++++++-------
 R/httpget_session_tar.R      |    4 -
 R/httpget_webhook.R          |   39 ++++++++------
 R/parse_arg_prim.R           |   24 ++------
 R/parse_post.R               |   37 +++++++------
 R/request.R                  |    2 
 R/session.R                  |  117 +++++++++++++++++++++----------------------
 build/vignette.rds           |binary
 inst/doc/opencpu-paper.pdf   |binary
 inst/doc/opencpu-server.Rnw  |   32 ++++-------
 inst/doc/opencpu-server.pdf  |binary
 vignettes/opencpu-server.Rnw |   32 ++++-------
 15 files changed, 189 insertions(+), 187 deletions(-)

More information about opencpu at CRAN
Permanent link

New package OptionPricing with initial version 0.1
Package: OptionPricing
Type: Package
Title: Option Pricing with Efficient Simulation Algorithms
Version: 0.1
Date: 2014-11-07
Author: Kemal Dingec, Wolfgang Hormann
Maintainer: Wolfgang Hormann
Description: Efficient Monte Carlo Algorithms for the price and the sensitivities of Asian and European Options under Geometric Brownian Motion.
License: GPL-2 | GPL-3
Copyright: Wolfgang Hormann
Packaged: 2014-11-08 07:35:25 UTC; Wolfgang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-11-08 17:10:10

More information about OptionPricing at CRAN
Permanent link

Package geometry updated to version 0.3-5 with previous version 0.3-4 dated 2014-03-06

Title: Mesh generation and surface tesselation
Description: This package makes the qhull library (www.qhull.org) available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.
Author: C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Andreas Stahel [cph, aut], Andreas Stahel [cph, aut], David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt

Diff between geometry versions 0.3-4 dated 2014-03-06 and 0.3-5 dated 2014-11-08

 geometry-0.3-4/geometry/tests/compare-tsearch-tsearchn.R         |only
 geometry-0.3-4/geometry/tests/compare-tsearch-tsearchn.Rout.save |only
 geometry-0.3-4/geometry/tests/convhulln.R                        |only
 geometry-0.3-4/geometry/tests/convhulln.Rout.save                |only
 geometry-0.3-4/geometry/tests/delaunay.R                         |only
 geometry-0.3-4/geometry/tests/delaunay.Rout.save                 |only
 geometry-0.3-4/geometry/tests/parallel.R                         |only
 geometry-0.3-4/geometry/tests/parallel.Rout.save                 |only
 geometry-0.3-4/geometry/tests/tsearch.R                          |only
 geometry-0.3-4/geometry/tests/tsearch.Rout.save                  |only
 geometry-0.3-4/geometry/tests/tsearchn.R                         |only
 geometry-0.3-4/geometry/tests/tsearchn.Rout.save                 |only
 geometry-0.3-5/geometry/DESCRIPTION                              |   37 
 geometry-0.3-5/geometry/MD5                                      |  132 -
 geometry-0.3-5/geometry/NAMESPACE                                |    4 
 geometry-0.3-5/geometry/NEWS                                     |   58 
 geometry-0.3-5/geometry/R/convhulln.R                            |   18 
 geometry-0.3-5/geometry/R/delaunayn.R                            |   52 
 geometry-0.3-5/geometry/R/dotprod.R                              |    1 
 geometry-0.3-5/geometry/R/tetramesh.R                            |    6 
 geometry-0.3-5/geometry/R/tsearch.R                              |   32 
 geometry-0.3-5/geometry/inst/doc/html/index.html                 | 1195 ++++------
 geometry-0.3-5/geometry/inst/doc/html/qconvex.html               |  753 +++---
 geometry-0.3-5/geometry/inst/doc/html/qdelau_f.html              |  632 ++---
 geometry-0.3-5/geometry/inst/doc/html/qdelaun.html               |  736 ++----
 geometry-0.3-5/geometry/inst/doc/html/qh-code.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-eg.html                 |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-faq.html                |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-get.html                |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-impre.html              |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optc.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optf.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optg.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-opto.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optp.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optq.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-optt.html               |    2 
 geometry-0.3-5/geometry/inst/doc/html/qh-quick.html              |    2 
 geometry-0.3-5/geometry/inst/doc/html/qhalf.html                 |  700 ++---
 geometry-0.3-5/geometry/inst/doc/html/qhull.html                 |    2 
 geometry-0.3-5/geometry/inst/doc/html/qvoron_f.html              |    2 
 geometry-0.3-5/geometry/inst/doc/html/qvoronoi.html              |    2 
 geometry-0.3-5/geometry/inst/doc/html/rbox.html                  |    2 
 geometry-0.3-5/geometry/inst/doc/index.html                      |  518 ++--
 geometry-0.3-5/geometry/inst/extdata                             |only
 geometry-0.3-5/geometry/man/Unique.Rd                            |   28 
 geometry-0.3-5/geometry/man/bary2cart.Rd                         |   42 
 geometry-0.3-5/geometry/man/cart2bary.Rd                         |   91 
 geometry-0.3-5/geometry/man/convhulln.Rd                         |   69 
 geometry-0.3-5/geometry/man/delaunayn.Rd                         |  109 
 geometry-0.3-5/geometry/man/distmesh2d.Rd                        |  150 -
 geometry-0.3-5/geometry/man/distmeshnd.Rd                        |  138 -
 geometry-0.3-5/geometry/man/dot.Rd                               |   22 
 geometry-0.3-5/geometry/man/entry.value.Rd                       |   27 
 geometry-0.3-5/geometry/man/extprod3d.Rd                         |   25 
 geometry-0.3-5/geometry/man/matmax.Rd                            |   34 
 geometry-0.3-5/geometry/man/mesh.dcircle.Rd                      |   38 
 geometry-0.3-5/geometry/man/mesh.diff.Rd                         |   47 
 geometry-0.3-5/geometry/man/mesh.drectangle.Rd                   |   43 
 geometry-0.3-5/geometry/man/mesh.dsphere.Rd                      |   34 
 geometry-0.3-5/geometry/man/mesh.hunif.Rd                        |   24 
 geometry-0.3-5/geometry/man/polyarea.Rd                          |   30 
 geometry-0.3-5/geometry/man/surf.tri.Rd                          |   44 
 geometry-0.3-5/geometry/man/tetramesh.Rd                         |   42 
 geometry-0.3-5/geometry/man/trimesh.Rd                           |   44 
 geometry-0.3-5/geometry/man/tsearch.Rd                           |   50 
 geometry-0.3-5/geometry/man/tsearchn.Rd                          |   56 
 geometry-0.3-5/geometry/src/Rdelaunayn.c                         |   49 
 geometry-0.3-5/geometry/src/Rtsearch.c                           |    6 
 geometry-0.3-5/geometry/src/userprintf.c                         |    4 
 geometry-0.3-5/geometry/tests/testthat                           |only
 geometry-0.3-5/geometry/tests/testthat.R                         |only
 72 files changed, 3031 insertions(+), 3123 deletions(-)

More information about geometry at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.