Mon, 27 Apr 2015

New package SLOPE with initial version 0.1.1
Package: SLOPE
Type: Package
Title: Sorted L1 Penalized Estimation (SLOPE)
Version: 0.1.1
Date: 2015-04-27
Author: Malgorzata Bogdan, Ewout van den Berg, Chiara Sabatti, Weijie Su, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
Description: Efficient procedures for Sorted L1 Penalized Estimation (SLOPE). The sorted L1 norm is useful for statistical estimation and testing, particularly for variable selection in the linear model.
License: GPL-3
LinkingTo: Rcpp
Imports: Rcpp
Suggests: knitr, testthat, isotone, R.matlab
VignetteBuilder: knitr
Packaged: 2015-04-27 16:56:49 UTC; epatters
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-27 20:24:13

More information about SLOPE at CRAN
Permanent link

Package seqDesign updated to version 1.1 with previous version 1.0.2 dated 2014-10-08

Title: Simulation and Group Sequential Monitoring of Randomized Two-Stage Treatment Efficacy Trials with Time-to-Event Endpoints
Description: A modification of the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases) is implemented, with application generally to individual-randomized clinical trials with multiple active treatment groups and a shared control group, and a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment group for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial monitoring outcomes (e.g., stopping early for non-efficacy); unconditional power for comparing treatment efficacies; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with a clinical outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Maintainer: Michal Juraska

Diff between seqDesign versions 1.0.2 dated 2014-10-08 and 1.1 dated 2015-04-27

 seqDesign-1.0.2/seqDesign/inst/extdata/seqDesignReport.Rnw     |only
 seqDesign-1.1/seqDesign/DESCRIPTION                            |   16 
 seqDesign-1.1/seqDesign/MD5                                    |   31 
 seqDesign-1.1/seqDesign/NAMESPACE                              |    6 
 seqDesign-1.1/seqDesign/R/seqDesign.R                          | 6526 +++++-----
 seqDesign-1.1/seqDesign/build/vignette.rds                     |binary
 seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.R       |  101 
 seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.Rnw     |  211 
 seqDesign-1.1/seqDesign/inst/doc/seqDesignInstructions.pdf     |binary
 seqDesign-1.1/seqDesign/inst/extdata/seqDesignReportSample.Rnw |only
 seqDesign-1.1/seqDesign/inst/extdata/seqDesignReportSample.pdf |binary
 seqDesign-1.1/seqDesign/man/VEpowerPP.Rd                       |  169 
 seqDesign-1.1/seqDesign/man/censTrial.Rd                       |  153 
 seqDesign-1.1/seqDesign/man/getBlockSize.Rd                    |only
 seqDesign-1.1/seqDesign/man/monitorTrial.Rd                    |  233 
 seqDesign-1.1/seqDesign/man/rankTrial.Rd                       |  186 
 seqDesign-1.1/seqDesign/man/simTrial.Rd                        |  181 
 seqDesign-1.1/seqDesign/vignettes/seqDesignInstructions.Rnw    |  211 
 18 files changed, 4115 insertions(+), 3909 deletions(-)

More information about seqDesign at CRAN
Permanent link

Package qlcMatrix updated to version 0.9.4 with previous version 0.9.2 dated 2014-05-19

Title: Utility Sparse Matrix Functions for Quantitative Language Comparison
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw

Diff between qlcMatrix versions 0.9.2 dated 2014-05-19 and 0.9.4 dated 2015-04-27

 qlcMatrix-0.9.2/qlcMatrix/R/qlcMatrix.R            |only
 qlcMatrix-0.9.4/qlcMatrix/DESCRIPTION              |   17 +++---
 qlcMatrix-0.9.4/qlcMatrix/MD5                      |   55 ++++++++++++---------
 qlcMatrix-0.9.4/qlcMatrix/NAMESPACE                |    3 -
 qlcMatrix-0.9.4/qlcMatrix/R/assoc.R                |only
 qlcMatrix-0.9.4/qlcMatrix/R/base.R                 |only
 qlcMatrix-0.9.4/qlcMatrix/R/sim.R                  |only
 qlcMatrix-0.9.4/qlcMatrix/R/split.R                |only
 qlcMatrix-0.9.4/qlcMatrix/R/utils.R                |only
 qlcMatrix-0.9.4/qlcMatrix/README.md                |   10 +++
 qlcMatrix-0.9.4/qlcMatrix/build                    |only
 qlcMatrix-0.9.4/qlcMatrix/inst                     |only
 qlcMatrix-0.9.4/qlcMatrix/man/assocSparse.Rd       |    6 +-
 qlcMatrix-0.9.4/qlcMatrix/man/bibles.Rd            |    8 +--
 qlcMatrix-0.9.4/qlcMatrix/man/corSparse.Rd         |   22 ++++----
 qlcMatrix-0.9.4/qlcMatrix/man/cosNominal.Rd        |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/cosSparse.Rd         |   14 ++---
 qlcMatrix-0.9.4/qlcMatrix/man/huber.Rd             |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/pwMatrix.Rd          |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/qlcMatrix-package.Rd |    8 +--
 qlcMatrix-0.9.4/qlcMatrix/man/rowMax.Rd            |   10 +--
 qlcMatrix-0.9.4/qlcMatrix/man/sim.nominal.Rd       |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/sim.strings.Rd       |    8 +--
 qlcMatrix-0.9.4/qlcMatrix/man/sim.wordlist.Rd      |    4 -
 qlcMatrix-0.9.4/qlcMatrix/man/sim.words.Rd         |    4 -
 qlcMatrix-0.9.4/qlcMatrix/man/splitStrings.Rd      |    6 +-
 qlcMatrix-0.9.4/qlcMatrix/man/splitTable.Rd        |   10 ++-
 qlcMatrix-0.9.4/qlcMatrix/man/splitText.Rd         |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/splitWordlist.Rd     |    4 -
 qlcMatrix-0.9.4/qlcMatrix/man/unfold.Rd            |    2 
 qlcMatrix-0.9.4/qlcMatrix/man/wals.Rd              |    8 +--
 qlcMatrix-0.9.4/qlcMatrix/vignettes                |only
 32 files changed, 116 insertions(+), 93 deletions(-)

More information about qlcMatrix at CRAN
Permanent link

Package psych updated to version 1.5.4 with previous version 1.5.1 dated 2015-01-21

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multi-levels include within and between group statistics, including correlations and factor analysis. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle

Diff between psych versions 1.5.1 dated 2015-01-21 and 1.5.4 dated 2015-04-27

 psych-1.5.1/psych/R/CTA_lrn.R                |only
 psych-1.5.1/psych/R/cosiner.R                |only
 psych-1.5.1/psych/R/cta.new.R                |only
 psych-1.5.1/psych/R/nearcor.r                |only
 psych-1.5.4/psych/DESCRIPTION                |   10 
 psych-1.5.4/psych/MD5                        |  177 +++++-----
 psych-1.5.4/psych/NAMESPACE                  |   25 +
 psych-1.5.4/psych/R/ICLUST.R                 |   17 
 psych-1.5.4/psych/R/biplot.psych.R           |   14 
 psych-1.5.4/psych/R/cluster.plot.R           |   14 
 psych-1.5.4/psych/R/cor.plot.R               |    6 
 psych-1.5.4/psych/R/corr.test.R              |    7 
 psych-1.5.4/psych/R/cosinor.R                |    2 
 psych-1.5.4/psych/R/cta.15.R                 |only
 psych-1.5.4/psych/R/cta.R                    |    2 
 psych-1.5.4/psych/R/describe.R               |   12 
 psych-1.5.4/psych/R/df2latex.R               |  108 ++++--
 psych-1.5.4/psych/R/diagram.R                |   10 
 psych-1.5.4/psych/R/error.bars.by.R          |    8 
 psych-1.5.4/psych/R/fa.R                     |   27 +
 psych-1.5.4/psych/R/fa.diagram.R             |   17 
 psych-1.5.4/psych/R/fa.parallel.R            |  314 ++++++++++++------
 psych-1.5.4/psych/R/fa.parallel.poly.R       |    2 
 psych-1.5.4/psych/R/faBy.R                   |   52 ++
 psych-1.5.4/psych/R/factor.stats.R           |   83 +++-
 psych-1.5.4/psych/R/kappa.R                  |   29 +
 psych-1.5.4/psych/R/mat.regress.R            |  150 ++++----
 psych-1.5.4/psych/R/mediate.r                |  143 +++++---
 psych-1.5.4/psych/R/misc.R                   |   73 ++--
 psych-1.5.4/psych/R/mixed.cor.R              |   11 
 psych-1.5.4/psych/R/pairs.panels.R           |  469 ++++++++++++---------------
 psych-1.5.4/psych/R/phi.R                    |    3 
 psych-1.5.4/psych/R/principal.R              |    2 
 psych-1.5.4/psych/R/print.psych.R            |   71 +++-
 psych-1.5.4/psych/R/print.psych.fa.R         |    9 
 psych-1.5.4/psych/R/schmid.R                 |    2 
 psych-1.5.4/psych/R/score.items.R            |   12 
 psych-1.5.4/psych/R/scoreOverlap.r           |   61 ++-
 psych-1.5.4/psych/R/set.cor.R                |   37 +-
 psych-1.5.4/psych/R/sim.parallel.r           |   12 
 psych-1.5.4/psych/R/sim.structural.R         |   11 
 psych-1.5.4/psych/R/smc.R                    |   57 +++
 psych-1.5.4/psych/R/splitHalf.R              |   33 +
 psych-1.5.4/psych/R/statsBy.r                |   15 
 psych-1.5.4/psych/R/summary.psych.R          |   11 
 psych-1.5.4/psych/R/target.rot.R             |    1 
 psych-1.5.4/psych/R/test.all.R               |   21 +
 psych-1.5.4/psych/R/test.psych.r             |   40 ++
 psych-1.5.4/psych/inst/CITATION              |    4 
 psych-1.5.4/psych/inst/NEWS.Rd               |   63 +++
 psych-1.5.4/psych/inst/doc/overview.R        |    2 
 psych-1.5.4/psych/inst/doc/overview.Rnw      |    4 
 psych-1.5.4/psych/inst/doc/overview.pdf      |binary
 psych-1.5.4/psych/inst/doc/psych_for_sem.pdf |binary
 psych-1.5.4/psych/man/ICLUST.Rd              |    8 
 psych-1.5.4/psych/man/ICLUST.graph.Rd        |    6 
 psych-1.5.4/psych/man/ICLUST.rgraph.Rd       |    6 
 psych-1.5.4/psych/man/VSS.Rd                 |    6 
 psych-1.5.4/psych/man/alpha.Rd               |    2 
 psych-1.5.4/psych/man/best.scales.Rd         |   36 --
 psych-1.5.4/psych/man/blot.Rd                |    2 
 psych-1.5.4/psych/man/cluster.loadings.Rd    |    2 
 psych-1.5.4/psych/man/cluster.plot.Rd        |    2 
 psych-1.5.4/psych/man/cor.plot.Rd            |    6 
 psych-1.5.4/psych/man/corr.test.Rd           |    7 
 psych-1.5.4/psych/man/cosinor.Rd             |  162 +++++++--
 psych-1.5.4/psych/man/cta.Rd                 |   37 +-
 psych-1.5.4/psych/man/describe.Rd            |    8 
 psych-1.5.4/psych/man/df2latex.Rd            |   39 +-
 psych-1.5.4/psych/man/diagram.Rd             |    2 
 psych-1.5.4/psych/man/epi.Rd                 |    5 
 psych-1.5.4/psych/man/error.bars.by.Rd       |   15 
 psych-1.5.4/psych/man/fa.Rd                  |   44 +-
 psych-1.5.4/psych/man/fa.diagram.Rd          |    6 
 psych-1.5.4/psych/man/fa.parallel.Rd         |   38 +-
 psych-1.5.4/psych/man/guttman.Rd             |   10 
 psych-1.5.4/psych/man/kappa.Rd               |    4 
 psych-1.5.4/psych/man/mediate.Rd             |   27 +
 psych-1.5.4/psych/man/misc.Rd                |   17 
 psych-1.5.4/psych/man/mixed.cor.Rd           |    4 
 psych-1.5.4/psych/man/msq.Rd                 |   61 ++-
 psych-1.5.4/psych/man/omega.Rd               |   51 +-
 psych-1.5.4/psych/man/pairs.panels.Rd        |   10 
 psych-1.5.4/psych/man/score.items.Rd         |   13 
 psych-1.5.4/psych/man/set.cor.Rd             |    5 
 psych-1.5.4/psych/man/sim.item.Rd            |    2 
 psych-1.5.4/psych/man/sim.structural.Rd      |    9 
 psych-1.5.4/psych/man/simulation.circ.Rd     |    2 
 psych-1.5.4/psych/man/smc.Rd                 |    4 
 psych-1.5.4/psych/man/statsBy.Rd             |   17 
 psych-1.5.4/psych/man/test.psych.Rd          |    8 
 psych-1.5.4/psych/vignettes/overview.Rnw     |    4 
 92 files changed, 1916 insertions(+), 1024 deletions(-)

More information about psych at CRAN
Permanent link

Package NeuralNetTools updated to version 1.3.1 with previous version 1.0.1 dated 2015-01-28

Title: Visualization and Analysis Tools for Neural Networks
Description: Visualization and analysis tools to aid in the interpretation of neural network models. Functions are available for plotting, quantifying variable importance, conducting a sensitivity analysis, and obtaining a simple list of model weights.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck

Diff between NeuralNetTools versions 1.0.1 dated 2015-01-28 and 1.3.1 dated 2015-04-27

 DESCRIPTION              |   10 -
 MD5                      |   30 +++--
 NAMESPACE                |   10 +
 R/NeuralNetTools_gar.R   |  266 +++++++++++++++++++++++------------------------
 R/NeuralNetTools_lek.R   |    2 
 R/NeuralNetTools_old.R   |only
 R/NeuralNetTools_plot.R  |   12 +-
 R/NeuralNetTools_utils.R |   75 ++++++++++++-
 README.md                |   93 +++++++++++++++-
 inst                     |only
 man/garson.Rd            |   51 +++++----
 man/lekprofile.Rd        |    4 
 man/neuraldat.Rd         |    2 
 man/neuralskips.Rd       |only
 man/neuralweights.Rd     |    6 -
 man/olden.Rd             |only
 man/plotnet.Rd           |    4 
 man/pred_sens.Rd         |    2 
 18 files changed, 379 insertions(+), 188 deletions(-)

More information about NeuralNetTools at CRAN
Permanent link

New package lfactors with initial version 0.4.0
Package: lfactors
Version: 0.4.0
Date: 2015-04-22
Title: Factors with Levels
Authors@R: c(person("Paul", "Bailey", role=c("aut", "cre"), email="pbailey@air.org"))
Author: Paul Bailey [aut, cre]
Maintainer: Paul Bailey
Depends: R (>= 3.1.0), methods
Description: Provides an extension to factors called 'lfactor' that are similar to factors but allow users to refer to 'lfactor' levels by either the level or the label.
License: GPL-2
NeedsCompilation: no
Packaged: 2015-04-27 14:10:00 UTC; pbailey
Repository: CRAN
Date/Publication: 2015-04-27 18:40:22

More information about lfactors at CRAN
Permanent link

New package fracprolif with initial version 1.0.6
Package: fracprolif
Type: Package
Title: Fraction Proliferation via a Quiescent Growth Model
Version: 1.0.6
Date: 2015-04-21
Author: Shawn Garbett, Darren Tyson
Maintainer: Shawn Garbett
Description: Functions for fitting data to a quiescent growth model, i.e. a growth process that involves members of the population who stop dividing or propagating.
License: GPL-2 | file LICENSE
LazyLoad: yes
Depends: emg (>= 1.0.5), numDeriv, methods, stats4
Packaged: 2015-04-23 14:09:19 UTC; sgarbett
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-27 18:58:56

More information about fracprolif at CRAN
Permanent link

Package sysfonts updated to version 0.5 with previous version 0.4 dated 2015-01-12

Title: Loading System Fonts into R
Description: Using FreeType to load system fonts and Google Fonts (https://www.google.com/fonts) into R. It is supposed to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between sysfonts versions 0.4 dated 2015-01-12 and 0.5 dated 2015-04-27

 DESCRIPTION             |   14 +++++++-------
 MD5                     |    7 ++++---
 NEWS                    |   10 ++++++++++
 R/google.R              |   29 ++++++++++++++++++++++++-----
 inst/fonts/webfonts.bz2 |only
 5 files changed, 45 insertions(+), 15 deletions(-)

More information about sysfonts at CRAN
Permanent link

Package SPOT updated to version 1.0.5543 with previous version 1.0.4184 dated 2013-06-26

Title: Sequential Parameter Optimization Toolbox
Description: The Sequential Parameter Optimization Toolbox provides a set of tools for Parameter-tuning, based on modelling techniques, DoE and statistical methods.
Author: Thomas Bartz-Beielstein [aut], Martin Zaefferer [cre, ctb], Joerg Ziegenhirt [ctb], Wolfgang Konen [ctb], Oliver Flasch [ctb], Patrick Koch [ctb], Martina Friese [ctb]
Maintainer: Martin Zaefferer

Diff between SPOT versions 1.0.4184 dated 2013-06-26 and 1.0.5543 dated 2015-04-27

 SPOT-1.0.4184/SPOT/R/spotComparison.R                      |only
 SPOT-1.0.4184/SPOT/R/spotExplainInterfaces.R               |only
 SPOT-1.0.4184/SPOT/man/spotAlgStart....Rd                  |only
 SPOT-1.0.4184/SPOT/man/spotCompare.Rd                      |only
 SPOT-1.0.4184/SPOT/man/spotCreateDesign....Rd              |only
 SPOT-1.0.4184/SPOT/man/spotHelpInterfaces....Rd            |only
 SPOT-1.0.4184/SPOT/man/spotOcbaTest.Rd                     |only
 SPOT-1.0.4184/SPOT/man/spotPlotPower.Rd                    |only
 SPOT-1.0.4184/SPOT/man/spotPlotSeverity.Rd                 |only
 SPOT-1.0.4184/SPOT/man/spotPower.Rd                        |only
 SPOT-1.0.4184/SPOT/man/spotPredict....Rd                   |only
 SPOT-1.0.4184/SPOT/man/spotPrepareSystem.Rd                |only
 SPOT-1.0.4184/SPOT/man/spotSeverity.Rd                     |only
 SPOT-1.0.5543/SPOT/DESCRIPTION                             |   86 -
 SPOT-1.0.5543/SPOT/MD5                                     |  630 ++++++-------
 SPOT-1.0.5543/SPOT/NAMESPACE                               |   41 
 SPOT-1.0.5543/SPOT/NEWS                                    |   41 
 SPOT-1.0.5543/SPOT/R/sms_emoa.r                            |  142 +-
 SPOT-1.0.5543/SPOT/R/spot.R                                |  101 +-
 SPOT-1.0.5543/SPOT/R/spotAlgStartEs.R                      |   74 -
 SPOT-1.0.5543/SPOT/R/spotAlgStartEsGlg.R                   |   12 
 SPOT-1.0.5543/SPOT/R/spotAlgStartRgp.R                     |    8 
 SPOT-1.0.5543/SPOT/R/spotAlgStartSmsEmoaGlg.R              |    4 
 SPOT-1.0.5543/SPOT/R/spotCreateDesignBasicDoe.R            |    4 
 SPOT-1.0.5543/SPOT/R/spotCreateDesignFactors.R             |    9 
 SPOT-1.0.5543/SPOT/R/spotCreateDesignFrF2.R                |   14 
 SPOT-1.0.5543/SPOT/R/spotCreateDesignLhd.R                 |   94 +
 SPOT-1.0.5543/SPOT/R/spotCreateDesignLhs.R                 |    2 
 SPOT-1.0.5543/SPOT/R/spotCreateDesignLhsOpt.R              |    2 
 SPOT-1.0.5543/SPOT/R/spotEnsembleFunctions.R               |   28 
 SPOT-1.0.5543/SPOT/R/spotEnsembleSingleBLAbern.R           |    2 
 SPOT-1.0.5543/SPOT/R/spotExpectedImprovement.R             |   28 
 SPOT-1.0.5543/SPOT/R/spotFuncStartBranin.R                 |    3 
 SPOT-1.0.5543/SPOT/R/spotFuncStartMexicanHat.R             |    3 
 SPOT-1.0.5543/SPOT/R/spotFuncStartRastrigin.R              |    3 
 SPOT-1.0.5543/SPOT/R/spotFuncStartRosenbrock.R             |    4 
 SPOT-1.0.5543/SPOT/R/spotFuncStartSixHump.R                |   51 -
 SPOT-1.0.5543/SPOT/R/spotFuncStartSphere.R                 |    5 
 SPOT-1.0.5543/SPOT/R/spotFuncTools.R                       |  202 ++--
 SPOT-1.0.5543/SPOT/R/spotGenerateSequentialDesign.R        |   45 
 SPOT-1.0.5543/SPOT/R/spotGetOptions.R                      |   35 
 SPOT-1.0.5543/SPOT/R/spotHelpFunctions.R                   |    4 
 SPOT-1.0.5543/SPOT/R/spotMcoSort.R                         |   20 
 SPOT-1.0.5543/SPOT/R/spotModelOptim.R                      |   51 -
 SPOT-1.0.5543/SPOT/R/spotModelParetoOptim.R                |   54 -
 SPOT-1.0.5543/SPOT/R/spotModelSelection.R                  |   12 
 SPOT-1.0.5543/SPOT/R/spotOcba.R                            |  178 +--
 SPOT-1.0.5543/SPOT/R/spotOptimEs.R                         |   26 
 SPOT-1.0.5543/SPOT/R/spotOptimizationFunctions.R           |   52 -
 SPOT-1.0.5543/SPOT/R/spotPlot.R                            |    9 
 SPOT-1.0.5543/SPOT/R/spotPredictCoForrester.R              |  364 +++----
 SPOT-1.0.5543/SPOT/R/spotPredictDace.R                     |  234 +---
 SPOT-1.0.5543/SPOT/R/spotPredictDice.R                     |   10 
 SPOT-1.0.5543/SPOT/R/spotPredictEarth.R                    |   13 
 SPOT-1.0.5543/SPOT/R/spotPredictEnsembleMultiAlternate.R   |    3 
 SPOT-1.0.5543/SPOT/R/spotPredictEnsembleMultiRank.R        |    5 
 SPOT-1.0.5543/SPOT/R/spotPredictEsvm.R                     |   14 
 SPOT-1.0.5543/SPOT/R/spotPredictForrester.R                |  439 ++++-----
 SPOT-1.0.5543/SPOT/R/spotPredictGausspr.R                  |    6 
 SPOT-1.0.5543/SPOT/R/spotPredictHelpFunctions.R            |   22 
 SPOT-1.0.5543/SPOT/R/spotPredictKrig.R                     |    5 
 SPOT-1.0.5543/SPOT/R/spotPredictKsvm.R                     |   19 
 SPOT-1.0.5543/SPOT/R/spotPredictLm.R                       |   17 
 SPOT-1.0.5543/SPOT/R/spotPredictLmFactor.R                 |   24 
 SPOT-1.0.5543/SPOT/R/spotPredictMCO.R                      |   11 
 SPOT-1.0.5543/SPOT/R/spotPredictMLP.R                      |   26 
 SPOT-1.0.5543/SPOT/R/spotPredictMlegp.R                    |   24 
 SPOT-1.0.5543/SPOT/R/spotPredictNeuralnet.R                |only
 SPOT-1.0.5543/SPOT/R/spotPredictQrnn.R                     |   10 
 SPOT-1.0.5543/SPOT/R/spotPredictRandomForest.R             |    2 
 SPOT-1.0.5543/SPOT/R/spotPredictTgp.R                      |    7 
 SPOT-1.0.5543/SPOT/R/spotPredictTree.R                     |    7 
 SPOT-1.0.5543/SPOT/R/spotPrepareData.R                     |   14 
 SPOT-1.0.5543/SPOT/R/spotRepairMissingValues.R             |only
 SPOT-1.0.5543/SPOT/R/spotRepeats.R                         |   66 -
 SPOT-1.0.5543/SPOT/R/spotReport3d.R                        |   17 
 SPOT-1.0.5543/SPOT/R/spotReportContour.R                   |    7 
 SPOT-1.0.5543/SPOT/R/spotReportDefault.R                   |    4 
 SPOT-1.0.5543/SPOT/R/spotReportEarth.R                     |    4 
 SPOT-1.0.5543/SPOT/R/spotReportMAMP.R                      |   86 -
 SPOT-1.0.5543/SPOT/R/spotReportSAMP.R                      |   30 
 SPOT-1.0.5543/SPOT/R/spotReportSens.R                      |    7 
 SPOT-1.0.5543/SPOT/R/spotStatistics.R                      |    4 
 SPOT-1.0.5543/SPOT/R/spotSurf.R                            |   40 
 SPOT-1.0.5543/SPOT/R/spotTargetFunctions.R                 |   16 
 SPOT-1.0.5543/SPOT/demo/00Index                            |    1 
 SPOT-1.0.5543/SPOT/demo/spotDemo23RgpKtfg.R                |only
 SPOT-1.0.5543/SPOT/inst/demo23RgpKtfg                      |only
 SPOT-1.0.5543/SPOT/inst/doc/SPOT.pdf                       |binary
 SPOT-1.0.5543/SPOT/inst/doc/index.html                     |    2 
 SPOT-1.0.5543/SPOT/java                                    |only
 SPOT-1.0.5543/SPOT/man/SPOT-package.Rd                     |   55 -
 SPOT-1.0.5543/SPOT/man/Testfunctions.Rd                    |   76 -
 SPOT-1.0.5543/SPOT/man/corrcubic.Rd                        |   40 
 SPOT-1.0.5543/SPOT/man/correxp.Rd                          |   40 
 SPOT-1.0.5543/SPOT/man/correxpg.Rd                         |   41 
 SPOT-1.0.5543/SPOT/man/corrgauss.Rd                        |   40 
 SPOT-1.0.5543/SPOT/man/corrkriging.Rd                      |   38 
 SPOT-1.0.5543/SPOT/man/corrlin.Rd                          |   40 
 SPOT-1.0.5543/SPOT/man/corrnoisygauss.Rd                   |   38 
 SPOT-1.0.5543/SPOT/man/corrnoisykriging.Rd                 |   38 
 SPOT-1.0.5543/SPOT/man/corrspherical.Rd                    |   40 
 SPOT-1.0.5543/SPOT/man/corrspline.Rd                       |   40 
 SPOT-1.0.5543/SPOT/man/daceBuilder.Rd                      |  110 --
 SPOT-1.0.5543/SPOT/man/daceEvalFit.Rd                      |   18 
 SPOT-1.0.5543/SPOT/man/daceFixTheta.Rd                     |   44 
 SPOT-1.0.5543/SPOT/man/daceGetFit.Rd                       |   52 -
 SPOT-1.0.5543/SPOT/man/daceLikelihood.Rd                   |   20 
 SPOT-1.0.5543/SPOT/man/daceObjfunc.Rd                      |   49 -
 SPOT-1.0.5543/SPOT/man/dacePredictor.Rd                    |   67 -
 SPOT-1.0.5543/SPOT/man/dacePrepareFit.Rd                   |   44 
 SPOT-1.0.5543/SPOT/man/daceStartParameters.Rd              |   42 
 SPOT-1.0.5543/SPOT/man/forrBuilder.Rd                      |  119 --
 SPOT-1.0.5543/SPOT/man/forrCoBuilder.Rd                    |  137 +-
 SPOT-1.0.5543/SPOT/man/forrCoLikelihood.Rd                 |   40 
 SPOT-1.0.5543/SPOT/man/forrCoModel.Rd                      |   21 
 SPOT-1.0.5543/SPOT/man/forrCoRegPredictor.Rd               |   31 
 SPOT-1.0.5543/SPOT/man/forrIF.Rd                           |   10 
 SPOT-1.0.5543/SPOT/man/forrRegLikelihood.Rd                |   28 
 SPOT-1.0.5543/SPOT/man/forrRegPredictor.Rd                 |   41 
 SPOT-1.0.5543/SPOT/man/forrReintPredictor.Rd               |   41 
 SPOT-1.0.5543/SPOT/man/predict.forr.Rd                     |only
 SPOT-1.0.5543/SPOT/man/print.Rd                            |   28 
 SPOT-1.0.5543/SPOT/man/regpoly0.Rd                         |   28 
 SPOT-1.0.5543/SPOT/man/regpoly1.Rd                         |   31 
 SPOT-1.0.5543/SPOT/man/regpoly2.Rd                         |   30 
 SPOT-1.0.5543/SPOT/man/repmat.Rd                           |   15 
 SPOT-1.0.5543/SPOT/man/spot.Rd                             |   82 -
 SPOT-1.0.5543/SPOT/man/spotAlgEs.Rd                        |  105 --
 SPOT-1.0.5543/SPOT/man/spotAlgEsDominantReco.Rd            |   22 
 SPOT-1.0.5543/SPOT/man/spotAlgEsGetSuccessRate.Rd          |   16 
 SPOT-1.0.5543/SPOT/man/spotAlgEsHps.Rd                     |   17 
 SPOT-1.0.5543/SPOT/man/spotAlgEsIndividualInitial.Rd       |   37 
 SPOT-1.0.5543/SPOT/man/spotAlgEsInitParentPop.Rd           |   37 
 SPOT-1.0.5543/SPOT/man/spotAlgEsInterReco.Rd               |   22 
 SPOT-1.0.5543/SPOT/man/spotAlgEsInterRecoBeSw02.Rd         |   18 
 SPOT-1.0.5543/SPOT/man/spotAlgEsMarriage.Rd                |   16 
 SPOT-1.0.5543/SPOT/man/spotAlgEsMarriageWithReplace.Rd     |   17 
 SPOT-1.0.5543/SPOT/man/spotAlgEsObjMutation.Rd             |   10 
 SPOT-1.0.5543/SPOT/man/spotAlgEsQuickTest.Rd               |   31 
 SPOT-1.0.5543/SPOT/man/spotAlgEsSelection.Rd               |   19 
 SPOT-1.0.5543/SPOT/man/spotAlgEsStratMutation.Rd           |   25 
 SPOT-1.0.5543/SPOT/man/spotAlgEsTermination.Rd             |   34 
 SPOT-1.0.5543/SPOT/man/spotAlgStartEs.Rd                   |   42 
 SPOT-1.0.5543/SPOT/man/spotAlgStartEsGlg.Rd                |   43 
 SPOT-1.0.5543/SPOT/man/spotAlgStartEsVar.Rd                |   48 
 SPOT-1.0.5543/SPOT/man/spotAlgStartRgp.Rd                  |   40 
 SPOT-1.0.5543/SPOT/man/spotAlgStartSann.Rd                 |   46 
 SPOT-1.0.5543/SPOT/man/spotAlgStartSannVar.Rd              |   52 -
 SPOT-1.0.5543/SPOT/man/spotAlgStartSmsEmoaGlg.Rd           |   43 
 SPOT-1.0.5543/SPOT/man/spotCalcNoise.Rd                    |   24 
 SPOT-1.0.5543/SPOT/man/spotCallCoFunction.Rd               |   26 
 SPOT-1.0.5543/SPOT/man/spotCodeFormulas.Rd                 |   20 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignBasicDoe.Rd         |   39 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignFactors.Rd          |   29 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignFrF2.Rd             |   33 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignLhd.Rd              |   37 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignLhs.Rd              |   29 
 SPOT-1.0.5543/SPOT/man/spotCreateDesignLhsOpt.Rd           |   29 
 SPOT-1.0.5543/SPOT/man/spotEnsembleMinimum.Rd              |   11 
 SPOT-1.0.5543/SPOT/man/spotEnsembleModelBuilding.Rd        |   25 
 SPOT-1.0.5543/SPOT/man/spotEnsembleModelEvaluate.Rd        |   21 
 SPOT-1.0.5543/SPOT/man/spotEnsembleMultiAlternate.Rd       |   84 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleMultiAverage.Rd         |   90 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleMultiChoose.Rd          |   89 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleMultiRank.Rd            |   74 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleMultiRankWeighted.Rd    |   72 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleBLAbern.Rd        |   78 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleBLAnorm.Rd        |   78 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleEpsGreedy.Rd      |   84 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSinglePOKER.Rd          |   91 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleRoundSearch.Rd    |   79 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleSoftMax.Rd        |   94 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleSingleUCB1.Rd           |   83 -
 SPOT-1.0.5543/SPOT/man/spotEnsembleStatsMin.Rd             |   12 
 SPOT-1.0.5543/SPOT/man/spotEnsembleStatsSd.Rd              |   12 
 SPOT-1.0.5543/SPOT/man/spotEnsembleSubdesigns.Rd           |   26 
 SPOT-1.0.5543/SPOT/man/spotEnsembleSummedRank.Rd           |   14 
 SPOT-1.0.5543/SPOT/man/spotEnsembleSummedRankWeighted.Rd   |   16 
 SPOT-1.0.5543/SPOT/man/spotExiPsi.Rd                       |   14 
 SPOT-1.0.5543/SPOT/man/spotFeedback.Rd                     |   84 -
 SPOT-1.0.5543/SPOT/man/spotForceFactorDesign.Rd            |   20 
 SPOT-1.0.5543/SPOT/man/spotForceFactorX.Rd                 |   18 
 SPOT-1.0.5543/SPOT/man/spotFuncStartBranin.Rd              |   36 
 SPOT-1.0.5543/SPOT/man/spotFuncStartDisBranin.Rd           |   36 
 SPOT-1.0.5543/SPOT/man/spotFuncStartMexicanHat.Rd          |   36 
 SPOT-1.0.5543/SPOT/man/spotFuncStartRastrigin.Rd           |   38 
 SPOT-1.0.5543/SPOT/man/spotFuncStartRosenbrock.Rd          |   36 
 SPOT-1.0.5543/SPOT/man/spotFuncStartSixHump.Rd             |   38 
 SPOT-1.0.5543/SPOT/man/spotFuncStartSphere.Rd              |   36 
 SPOT-1.0.5543/SPOT/man/spotGenerateSequentialDesign.Rd     |   31 
 SPOT-1.0.5543/SPOT/man/spotGetAllRepeats.Rd                |   12 
 SPOT-1.0.5543/SPOT/man/spotGetMergedDataMatrixB.Rd         |   31 
 SPOT-1.0.5543/SPOT/man/spotGetOptions.Rd                   |  263 +----
 SPOT-1.0.5543/SPOT/man/spotGetRawDataMatrixB.Rd            |   32 
 SPOT-1.0.5543/SPOT/man/spotGetRawResData.Rd                |   26 
 SPOT-1.0.5543/SPOT/man/spotGetRepeats.Rd                   |   16 
 SPOT-1.0.5543/SPOT/man/spotGlgCore.Rd                      |   34 
 SPOT-1.0.5543/SPOT/man/spotGlgCreate.Rd                    |   65 -
 SPOT-1.0.5543/SPOT/man/spotGlgCreateN.Rd                   |   68 -
 SPOT-1.0.5543/SPOT/man/spotGlgCreateRot.Rd                 |   63 -
 SPOT-1.0.5543/SPOT/man/spotGlgCreateRotSearched.Rd         |   64 -
 SPOT-1.0.5543/SPOT/man/spotGlgEval.Rd                      |   35 
 SPOT-1.0.5543/SPOT/man/spotGlgEvalN.Rd                     |   33 
 SPOT-1.0.5543/SPOT/man/spotGlgEvalRot.Rd                   |   34 
 SPOT-1.0.5543/SPOT/man/spotGlgInit.Rd                      |   72 -
 SPOT-1.0.5543/SPOT/man/spotGlgInitN.Rd                     |   74 -
 SPOT-1.0.5543/SPOT/man/spotGui.Rd                          |   14 
 SPOT-1.0.5543/SPOT/man/spotHelpBslash.Rd                   |   13 
 SPOT-1.0.5543/SPOT/man/spotHlpF.norm.Rd                    |   13 
 SPOT-1.0.5543/SPOT/man/spotHlpF.norminv.Rd                 |   14 
 SPOT-1.0.5543/SPOT/man/spotInfillExpImp.Rd                 |   19 
 SPOT-1.0.5543/SPOT/man/spotInfillHyperVolume.Rd            |   22 
 SPOT-1.0.5543/SPOT/man/spotInfillLcbHyperVolume.Rd         |   41 
 SPOT-1.0.5543/SPOT/man/spotInfillLcbMulti.Rd               |   19 
 SPOT-1.0.5543/SPOT/man/spotInfillLcbSingle.Rd              |   14 
 SPOT-1.0.5543/SPOT/man/spotInfillProbImp.Rd                |   20 
 SPOT-1.0.5543/SPOT/man/spotInfillSD.Rd                     |   17 
 SPOT-1.0.5543/SPOT/man/spotInfillSExI2d.Rd                 |   36 
 SPOT-1.0.5543/SPOT/man/spotInitializePredictor.Rd          |   38 
 SPOT-1.0.5543/SPOT/man/spotInstAndLoadPackages.Rd          |   32 
 SPOT-1.0.5543/SPOT/man/spotInvChisq.Rd                     |   14 
 SPOT-1.0.5543/SPOT/man/spotMcoCrowdTournament.Rd           |   23 
 SPOT-1.0.5543/SPOT/man/spotMcoSelectionHypervol.Rd         |   50 -
 SPOT-1.0.5543/SPOT/man/spotMcoSort.Rd                      |   29 
 SPOT-1.0.5543/SPOT/man/spotMcoTournament.Rd                |   22 
 SPOT-1.0.5543/SPOT/man/spotMetaFlattenFbsRow.Rd            |   17 
 SPOT-1.0.5543/SPOT/man/spotModel.func.Rd                   |   35 
 SPOT-1.0.5543/SPOT/man/spotModel.predict.Rd                |   26 
 SPOT-1.0.5543/SPOT/man/spotModel.train.Rd                  |   36 
 SPOT-1.0.5543/SPOT/man/spotModelDescentLm.Rd               |   24 
 SPOT-1.0.5543/SPOT/man/spotModelOptim.Rd                   |  101 --
 SPOT-1.0.5543/SPOT/man/spotModelParetoOptim.Rd             |   43 
 SPOT-1.0.5543/SPOT/man/spotNormDesign.Rd                   |   34 
 SPOT-1.0.5543/SPOT/man/spotNormalizeMatrix.Rd              |   23 
 SPOT-1.0.5543/SPOT/man/spotNormalizeMatrix2.Rd             |   27 
 SPOT-1.0.5543/SPOT/man/spotOcba.Rd                         |   26 
 SPOT-1.0.5543/SPOT/man/spotOptim.Rd                        |   85 -
 SPOT-1.0.5543/SPOT/man/spotOptimEs.Rd                      |  119 +-
 SPOT-1.0.5543/SPOT/man/spotOptimInterface.Rd               |   54 -
 SPOT-1.0.5543/SPOT/man/spotOptimLHS.Rd                     |   55 -
 SPOT-1.0.5543/SPOT/man/spotOptimizationInterface.Rd        |  137 +-
 SPOT-1.0.5543/SPOT/man/spotOptimizationInterfaceMco.Rd     |   81 -
 SPOT-1.0.5543/SPOT/man/spotParetoOptMulti.Rd               |   10 
 SPOT-1.0.5543/SPOT/man/spotPenalizeMissingValues.Rd        |only
 SPOT-1.0.5543/SPOT/man/spotPlotBst.Rd                      |   19 
 SPOT-1.0.5543/SPOT/man/spotPredictCoForrester.Rd           |   97 --
 SPOT-1.0.5543/SPOT/man/spotPredictDace.Rd                  |   91 -
 SPOT-1.0.5543/SPOT/man/spotPredictDice.Rd                  |   39 
 SPOT-1.0.5543/SPOT/man/spotPredictEarth.Rd                 |   60 -
 SPOT-1.0.5543/SPOT/man/spotPredictEsvm.Rd                  |   36 
 SPOT-1.0.5543/SPOT/man/spotPredictForrester.Rd             |   85 -
 SPOT-1.0.5543/SPOT/man/spotPredictGausspr.Rd               |   35 
 SPOT-1.0.5543/SPOT/man/spotPredictKrig.Rd                  |   34 
 SPOT-1.0.5543/SPOT/man/spotPredictKsvm.Rd                  |   36 
 SPOT-1.0.5543/SPOT/man/spotPredictLm.Rd                    |   46 
 SPOT-1.0.5543/SPOT/man/spotPredictLmFactor.Rd              |   55 -
 SPOT-1.0.5543/SPOT/man/spotPredictMCO.Rd                   |   65 -
 SPOT-1.0.5543/SPOT/man/spotPredictMLP.Rd                   |   35 
 SPOT-1.0.5543/SPOT/man/spotPredictMlegp.Rd                 |   59 -
 SPOT-1.0.5543/SPOT/man/spotPredictNeuralnet.Rd             |only
 SPOT-1.0.5543/SPOT/man/spotPredictOptMulti.Rd              |   10 
 SPOT-1.0.5543/SPOT/man/spotPredictQrnn.Rd                  |   35 
 SPOT-1.0.5543/SPOT/man/spotPredictRandomForest.Rd          |   58 -
 SPOT-1.0.5543/SPOT/man/spotPredictRandomForestMlegp.Rd     |   38 
 SPOT-1.0.5543/SPOT/man/spotPredictTest.Rd                  |   37 
 SPOT-1.0.5543/SPOT/man/spotPredictTgp.Rd                   |   37 
 SPOT-1.0.5543/SPOT/man/spotPredictTree.Rd                  |   37 
 SPOT-1.0.5543/SPOT/man/spotPrepare.Rd                      |   39 
 SPOT-1.0.5543/SPOT/man/spotPrepareData.Rd                  |   46 
 SPOT-1.0.5543/SPOT/man/spotPrepareDataAsMatrixC.Rd         |   28 
 SPOT-1.0.5543/SPOT/man/spotPrepareResult.Rd                |only
 SPOT-1.0.5543/SPOT/man/spotPrint.Rd                        |   19 
 SPOT-1.0.5543/SPOT/man/spotROI.Rd                          |   31 
 SPOT-1.0.5543/SPOT/man/spotReadBstFile.Rd                  |   26 
 SPOT-1.0.5543/SPOT/man/spotReadRoi.Rd                      |   18 
 SPOT-1.0.5543/SPOT/man/spotRepairMissingValues.Rd          |only
 SPOT-1.0.5543/SPOT/man/spotRepairMissingValuesCoKriging.Rd |only
 SPOT-1.0.5543/SPOT/man/spotRepeats.Rd                      |   17 
 SPOT-1.0.5543/SPOT/man/spotRepeatsOcba.Rd                  |   18 
 SPOT-1.0.5543/SPOT/man/spotReport3d.Rd                     |   50 -
 SPOT-1.0.5543/SPOT/man/spotReport3dMulti.Rd                |   42 
 SPOT-1.0.5543/SPOT/man/spotReportContour.Rd                |   50 -
 SPOT-1.0.5543/SPOT/man/spotReportContourMulti.Rd           |   29 
 SPOT-1.0.5543/SPOT/man/spotReportDefault.Rd                |   40 
 SPOT-1.0.5543/SPOT/man/spotReportEarth.Rd                  |   16 
 SPOT-1.0.5543/SPOT/man/spotReportMAMP.Rd                   |   20 
 SPOT-1.0.5543/SPOT/man/spotReportMetaDefault.Rd            |   28 
 SPOT-1.0.5543/SPOT/man/spotReportSAMP.Rd                   |   20 
 SPOT-1.0.5543/SPOT/man/spotReportSens.Rd                   |   20 
 SPOT-1.0.5543/SPOT/man/spotReportSensY.Rd                  |   19 
 SPOT-1.0.5543/SPOT/man/spotReverseNormalizeMatrix.Rd       |   24 
 SPOT-1.0.5543/SPOT/man/spotRgpTargetFunction.Rd            |   27 
 SPOT-1.0.5543/SPOT/man/spotSExI2d.Rd                       |   47 
 SPOT-1.0.5543/SPOT/man/spotSelectionCriteria.Rd            |   53 -
 SPOT-1.0.5543/SPOT/man/spotSeqDesignIncreaseMultTwo.Rd     |   20 
 SPOT-1.0.5543/SPOT/man/spotSeqDesignIncreasePlusOne.Rd     |   20 
 SPOT-1.0.5543/SPOT/man/spotSmsEmoa.Rd                      |   43 
 SPOT-1.0.5543/SPOT/man/spotSmsEmoaKriging.Rd               |   38 
 SPOT-1.0.5543/SPOT/man/spotStepAutoOpt.Rd                  |   36 
 SPOT-1.0.5543/SPOT/man/spotStepInitial.Rd                  |   42 
 SPOT-1.0.5543/SPOT/man/spotStepMetaOpt.Rd                  |   26 
 SPOT-1.0.5543/SPOT/man/spotStepReport.Rd                   |   26 
 SPOT-1.0.5543/SPOT/man/spotStepRunAlg.Rd                   |   47 
 SPOT-1.0.5543/SPOT/man/spotStepSequential.Rd               |   30 
 SPOT-1.0.5543/SPOT/man/spotSurf3d.Rd                       |   36 
 SPOT-1.0.5543/SPOT/man/spotSurfContour.Rd                  |   64 -
 SPOT-1.0.5543/SPOT/man/spotVersion.Rd                      |   11 
 SPOT-1.0.5543/SPOT/man/spotWriteAroi.Rd                    |   22 
 SPOT-1.0.5543/SPOT/man/spotWriteBest.Rd                    |   33 
 SPOT-1.0.5543/SPOT/man/spotWriteDes.Rd                     |   24 
 SPOT-1.0.5543/SPOT/man/spotWriteLines.Rd                   |   23 
 SPOT-1.0.5543/SPOT/man/spotWriteRes.Rd                     |only
 SPOT-1.0.5543/SPOT/man/spotWriteRoiFileForRepeats.Rd       |   15 
 SPOT-1.0.5543/SPOT/vignettes/SPOT.Rnw                      |    2 
 315 files changed, 5270 insertions(+), 7219 deletions(-)

More information about SPOT at CRAN
Permanent link

Package showtext updated to version 0.4-1 with previous version 0.3 dated 2015-03-11

Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supporting most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as Ghostscript is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu

Diff between showtext versions 0.3 dated 2015-03-11 and 0.4-1 dated 2015-04-27

 DESCRIPTION           |   12 +-
 MD5                   |   36 +++---
 NAMESPACE             |    2 
 R/showtext.R          |  261 ++++++++++++++++++++++++++++++++++++++---------
 R/zzz.R               |   15 ++
 README.md             |  272 +++++++++++++++++++++++++++++++++++---------------
 inst/NEWS.Rd          |   21 +++
 man/showtext.auto.Rd  |only
 man/showtext.begin.Rd |   83 ++++++---------
 man/showtext.end.Rd   |    6 -
 man/showtext.opts.Rd  |only
 src/devfuns.c         |   79 ++++++++++----
 src/devfuns.h         |only
 src/fonts.c           |only
 src/fonts.h           |   21 +++
 src/outline.c         |   35 ------
 src/outline.h         |   66 ++++--------
 src/raster.c          |only
 src/raster.h          |only
 src/showtext.c        |   17 +--
 src/util.c            |  140 +++++--------------------
 src/util.h            |   27 ++++
 22 files changed, 674 insertions(+), 419 deletions(-)

More information about showtext at CRAN
Permanent link

New package RcppTOML with initial version 0.0.3
Package: RcppTOML
Type: Package
Title: Rcpp Bindings to Parser for Tom's Obvious Markup Language
Version: 0.0.3
Date: 2015-04-27
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
Description: The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format suitable for both human editing as well as the obvious uses of a machine-readable format. This package uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
OS_type: unix
SystemRequirements: A C++11 compiler. Version 4.6.* of g++ (as currently in Rtools) is insufficient; versions 4.8.*, 4.9.* or latter will be fine.
License: GPL (>= 2)
Imports: Rcpp (>= 0.11.5)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2015-04-27 11:16:11.67427 UTC; edd
Repository: CRAN
Date/Publication: 2015-04-27 16:07:39

More information about RcppTOML at CRAN
Permanent link

Package EffectTreat updated to version 0.1-11 with previous version 0.1-1 dated 2014-12-11

Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst

Diff between EffectTreat versions 0.1-1 dated 2014-12-11 and 0.1-11 dated 2015-04-27

 DESCRIPTION         |   10 +++++-----
 MD5                 |    8 ++++----
 NAMESPACE           |    9 +++++++++
 NEWS                |    3 +++
 man/Example.Data.Rd |    2 +-
 5 files changed, 22 insertions(+), 10 deletions(-)

More information about EffectTreat at CRAN
Permanent link

Package dynBiplotGUI updated to version 1.1.3 with previous version 1.1.2 dated 2014-12-10

Title: Full Interactive GUI for Dynamic Biplot in R
Description: A GUI to solve dynamic biplots and classical biplot. Try matrices of 2-way and 3-way. The GUI can be run in multiple languages.
Author: Jaime Egido [aut, cre]
Maintainer: Jaime Egido

Diff between dynBiplotGUI versions 1.1.2 dated 2014-12-10 and 1.1.3 dated 2015-04-27

 ChangeLog                   |   15 +
 DESCRIPTION                 |   10 
 MD5                         |   16 -
 R/dynBiplot.R               |  529 ++++++++++++++++++++------------------------
 inst/lang/Language.csv      |    4 
 man/dynBiplot.Rd            |    8 
 man/dynBiplotGUI-package.Rd |    6 
 man/panelFormat_en.Rd       |    1 
 man/panelFormat_es.Rd       |    1 
 9 files changed, 293 insertions(+), 297 deletions(-)

More information about dynBiplotGUI at CRAN
Permanent link

Package coxinterval updated to version 1.1 with previous version 1.0 dated 2014-07-20

Title: Cox-Type Models for Interval-Censored Data
Description: Fits Cox-type models based on interval-censored data from a survival or illness-death process.
Author: Audrey Boruvka and Richard J. Cook
Maintainer: Audrey Boruvka

Diff between coxinterval versions 1.0 dated 2014-07-20 and 1.1 dated 2015-04-27

 coxinterval-1.0/coxinterval/R/coxaalenic.R                |only
 coxinterval-1.0/coxinterval/R/coxaalenic.control.R        |only
 coxinterval-1.0/coxinterval/R/coxaalenic.ineq.R           |only
 coxinterval-1.0/coxinterval/R/coxic.R                     |only
 coxinterval-1.0/coxinterval/R/coxic.control.R             |only
 coxinterval-1.0/coxinterval/R/coxic.data.R                |only
 coxinterval-1.0/coxinterval/R/na.coxic.R                  |only
 coxinterval-1.0/coxinterval/man/coxaalenic.Rd             |only
 coxinterval-1.0/coxinterval/man/coxaalenic.control.Rd     |only
 coxinterval-1.0/coxinterval/man/coxic.Rd                  |only
 coxinterval-1.0/coxinterval/man/coxic.control.Rd          |only
 coxinterval-1.0/coxinterval/src/coxaalenic.c              |only
 coxinterval-1.0/coxinterval/src/coxic.c                   |only
 coxinterval-1.1/coxinterval/DESCRIPTION                   |   21 ++-
 coxinterval-1.1/coxinterval/INSTALL                       |   38 ++++--
 coxinterval-1.1/coxinterval/MD5                           |   77 +++++++-------
 coxinterval-1.1/coxinterval/NAMESPACE                     |   23 ++--
 coxinterval-1.1/coxinterval/NEWS                          |only
 coxinterval-1.1/coxinterval/R/const2lin.R                 |    3 
 coxinterval-1.1/coxinterval/R/coxaalen.R                  |only
 coxinterval-1.1/coxinterval/R/coxaalen.control.R          |only
 coxinterval-1.1/coxinterval/R/coxaalen.ineq.R             |only
 coxinterval-1.1/coxinterval/R/coxdual.R                   |only
 coxinterval-1.1/coxinterval/R/coxdual.control.R           |only
 coxinterval-1.1/coxinterval/R/coxdual.data.R              |only
 coxinterval-1.1/coxinterval/R/jump2step.R                 |    3 
 coxinterval-1.1/coxinterval/R/lin2const.R                 |    3 
 coxinterval-1.1/coxinterval/R/maximalint.R                |   15 --
 coxinterval-1.1/coxinterval/R/na.coxdual.R                |only
 coxinterval-1.1/coxinterval/R/print.coxinterval.R         |    9 +
 coxinterval-1.1/coxinterval/R/print.summary.coxinterval.R |    6 -
 coxinterval-1.1/coxinterval/R/step2jump.R                 |    3 
 coxinterval-1.1/coxinterval/R/step2stepfun.R              |only
 coxinterval-1.1/coxinterval/R/summary.coxinterval.R       |    8 -
 coxinterval-1.1/coxinterval/man/const2lin.Rd              |only
 coxinterval-1.1/coxinterval/man/cosmesis.Rd               |    1 
 coxinterval-1.1/coxinterval/man/coxaalen.Rd               |only
 coxinterval-1.1/coxinterval/man/coxaalen.control.Rd       |only
 coxinterval-1.1/coxinterval/man/coxdual.Rd                |only
 coxinterval-1.1/coxinterval/man/coxdual.control.Rd        |only
 coxinterval-1.1/coxinterval/man/dualic.Rd                 |   10 -
 coxinterval-1.1/coxinterval/man/dualrc.Rd                 |    6 -
 coxinterval-1.1/coxinterval/man/jump2step.Rd              |only
 coxinterval-1.1/coxinterval/man/lin2const.Rd              |only
 coxinterval-1.1/coxinterval/man/linapprox.Rd              |only
 coxinterval-1.1/coxinterval/man/maximalint.Rd             |only
 coxinterval-1.1/coxinterval/man/print.coxinterval.Rd      |    2 
 coxinterval-1.1/coxinterval/man/step2jump.Rd              |only
 coxinterval-1.1/coxinterval/man/step2stepfun.Rd           |only
 coxinterval-1.1/coxinterval/man/summary.coxinterval.Rd    |   10 -
 coxinterval-1.1/coxinterval/man/trans.Rd                  |    6 -
 coxinterval-1.1/coxinterval/src/Makevars                  |    8 -
 coxinterval-1.1/coxinterval/src/Makevars.win              |   16 +-
 coxinterval-1.1/coxinterval/src/coxaalen.c                |only
 coxinterval-1.1/coxinterval/src/coxdual.c                 |only
 coxinterval-1.1/coxinterval/src/coxinterval.h             |    3 
 coxinterval-1.1/coxinterval/src/rcplex.c                  |    1 
 57 files changed, 142 insertions(+), 130 deletions(-)

More information about coxinterval at CRAN
Permanent link

Package zoeppritz updated to version 1.0-5 with previous version 1.0-4 dated 2013-03-13

Title: Seismic Reflection and Scattering Coefficients
Description: Calculate and plot scattering matrix coefficients for plane waves at interface.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between zoeppritz versions 1.0-4 dated 2013-03-13 and 1.0-5 dated 2015-04-27

 DESCRIPTION       |   19 +++++++++----------
 MD5               |    4 ++--
 man/pzoeppritz.Rd |   16 +++++++++++-----
 3 files changed, 22 insertions(+), 17 deletions(-)

More information about zoeppritz at CRAN
Permanent link

Package StatDA updated to version 1.6.9 with previous version 1.6.7 dated 2013-08-22

Title: Statistical Analysis for Environmental Data
Description: This package offers different possibilities to make statistical analysis for Environmental Data.
Author: Peter Filzmoser
Maintainer: Peter Filzmoser

Diff between StatDA versions 1.6.7 dated 2013-08-22 and 1.6.9 dated 2015-04-27

 DESCRIPTION                |    8 +++---
 MD5                        |   54 +++++++++++++++++++++++----------------------
 R/SymbLegend.R             |    6 +++--
 build                      |only
 data/AuNEW.rda             |binary
 data/AuOLD.rda             |binary
 data/CHorANADUP.rda        |binary
 data/CHorFieldDUP.rda      |binary
 data/CHorSTANDARD.rda      |binary
 data/bhorizon.rda          |binary
 data/bordersKola.rda       |binary
 data/chorizon.rda          |binary
 data/kola.background.rda   |binary
 data/monch.rda             |binary
 data/moss.rda              |binary
 data/nizap.rda             |binary
 data/ohorizon.rda          |binary
 data/res.eyefit.As_C.rda   |binary
 data/res.eyefit.As_C_m.rda |binary
 data/res.eyefit.AuNEW.rda  |binary
 data/res.eyefit.Ca_C.rda   |binary
 data/res.eyefit.Ca_O.rda   |binary
 data/res.eyefit.Hg_O.rda   |binary
 data/res.eyefit.Pb_O1.rda  |binary
 data/res.eyefit.Pb_O2.rda  |binary
 data/timetrend.rda         |binary
 data/topsoil.rda           |binary
 inst/doc/StatDA.R          |only
 man/plotelement.Rd         |    2 -
 29 files changed, 37 insertions(+), 33 deletions(-)

More information about StatDA at CRAN
Permanent link

Package RTOMO updated to version 1.1-3 with previous version 1.1-2 dated 2014-01-06

Title: Visualization for Seismic Tomography
Description: Aimed at seismic tomography, the package plots tomographic images, and allows one to interact and query three-dimensional tomographic models. Vertical cross-sectional cuts can be extracted by mouse click. Geographic information can be added easily.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between RTOMO versions 1.1-2 dated 2014-01-06 and 1.1-3 dated 2015-04-27

 RTOMO-1.1-2/RTOMO/R/TOMO.colors.R      |only
 RTOMO-1.1-2/RTOMO/man/TOMO.colors.Rd   |only
 RTOMO-1.1-3/RTOMO/DESCRIPTION          |   12 ++++-----
 RTOMO-1.1-3/RTOMO/MD5                  |   40 ++++++++++++++++++---------------
 RTOMO-1.1-3/RTOMO/R/FANCY.TOMO.R       |    2 -
 RTOMO-1.1-3/RTOMO/R/HOZscale.R         |only
 RTOMO-1.1-3/RTOMO/R/PLOT.TOMOXSEC.R    |    6 ++--
 RTOMO-1.1-3/RTOMO/R/SHOWTOMO.R         |    4 +--
 RTOMO-1.1-3/RTOMO/R/TOMO3D.drive.R     |    8 +++---
 RTOMO-1.1-3/RTOMO/R/TOMOXSEC.R         |    2 -
 RTOMO-1.1-3/RTOMO/R/XSEC.drive.R       |    4 +--
 RTOMO-1.1-3/RTOMO/R/get2Drayblox.R     |    4 +--
 RTOMO-1.1-3/RTOMO/R/jstats.R           |only
 RTOMO-1.1-3/RTOMO/R/makeMOD.R          |    2 -
 RTOMO-1.1-3/RTOMO/R/meshgrid.R         |only
 RTOMO-1.1-3/RTOMO/R/pltomo.R           |    2 -
 RTOMO-1.1-3/RTOMO/R/tomo.colors.R      |only
 RTOMO-1.1-3/RTOMO/man/HOZscale.Rd      |only
 RTOMO-1.1-3/RTOMO/man/PLOT.TOMOXSEC.Rd |    2 -
 RTOMO-1.1-3/RTOMO/man/RTOMO-package.Rd |    2 -
 RTOMO-1.1-3/RTOMO/man/TOMOXSEC.Rd      |    2 -
 RTOMO-1.1-3/RTOMO/man/XSEC.drive.Rd    |    2 -
 RTOMO-1.1-3/RTOMO/man/jstats.Rd        |only
 RTOMO-1.1-3/RTOMO/man/meshgrid.Rd      |only
 RTOMO-1.1-3/RTOMO/man/pltomo.Rd        |    2 -
 RTOMO-1.1-3/RTOMO/man/tomo.colors.Rd   |only
 26 files changed, 51 insertions(+), 45 deletions(-)

More information about RTOMO at CRAN
Permanent link

Package Rquake updated to version 2.3-1 with previous version 2.2 dated 2014-01-06

Title: Seismic Hypocenter Determination
Description: Hypocenter estimation and analysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from RSEIS and GEOmap to help researchers pick, locate, and store hypocenters for detailed seismic investigation.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between Rquake versions 2.2 dated 2014-01-06 and 2.3-1 dated 2015-04-27

 DESCRIPTION        |   12 +++----
 MD5                |   14 ++++----
 NAMESPACE          |    3 +
 R/RElocateEQ.R     |   37 +++++++++++-----------
 R/ROTcovQUAKE.R    |only
 R/plotJACKLLZ.R    |   89 +++++++++++++++++++++++++++++++++++++++--------------
 man/RElocateEQ.Rd  |    4 +-
 man/ROTcovQUAKE.Rd |only
 man/plotJACKLLZ.Rd |   15 +++++++-
 9 files changed, 117 insertions(+), 57 deletions(-)

More information about Rquake at CRAN
Permanent link

Package Kernelheaping updated to version 0.5 with previous version 0.2 dated 2015-01-27

Title: Kernel Density Estimation for Heaped Data
Description: In self-reported data the user often encounters heaped data, i.e. data which are rounded to a different degree of coarseness. While this is mostly a minor problem in parametric density estimation the bias can be very large for non-parametric methods such as kernel density estimation. This package implements a partly Bayesian algorithm treating the true unknown values as additional parameters and estimates the rounding parameters to give a corrected kernel density estimate. It supports various standard bandwidth selection methods. Additionally varying rounding probabilities (with the true value) and asymmetric rounding is estimable as well.
Author: Marcus Gross
Maintainer: Marcus Gross

Diff between Kernelheaping versions 0.2 dated 2015-01-27 and 0.5 dated 2015-04-27

 Kernelheaping-0.2/Kernelheaping/man/Rprx2.Rd                    |only
 Kernelheaping-0.5/Kernelheaping/DESCRIPTION                     |   12 
 Kernelheaping-0.5/Kernelheaping/MD5                             |   17 
 Kernelheaping-0.5/Kernelheaping/NAMESPACE                       |    4 
 Kernelheaping-0.5/Kernelheaping/R/Kernelheaping.R               |    2 
 Kernelheaping-0.5/Kernelheaping/R/functions.R                   |  274 ++++++----
 Kernelheaping-0.5/Kernelheaping/man/Rprx.Rd                     |only
 Kernelheaping-0.5/Kernelheaping/man/createSim.Kernelheaping.Rd  |    4 
 Kernelheaping-0.5/Kernelheaping/man/dheaping.Rd                 |   27 
 Kernelheaping-0.5/Kernelheaping/man/sim.Kernelheaping.Rd        |   32 +
 Kernelheaping-0.5/Kernelheaping/man/simSummary.Kernelheaping.Rd |only
 11 files changed, 239 insertions(+), 133 deletions(-)

More information about Kernelheaping at CRAN
Permanent link

Package hermite updated to version 1.1.0 with previous version 1.0.2 dated 2015-03-20

Title: Generalized Hermite Distribution
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and María Oliveira
Maintainer: David Moriña Soler

Diff between hermite versions 1.0.2 dated 2015-03-20 and 1.1.0 dated 2015-04-27

 DESCRIPTION                   |    8 ++++----
 MD5                           |   24 +++++++++++++-----------
 NAMESPACE                     |    3 +++
 R/glm.hermite.R               |   13 +++++++++++++
 R/print.summary.glm.hermite.R |only
 R/qhermite.R                  |   30 +++++++++++++++++++-----------
 R/summary.glm.hermite.R       |only
 man/dhermite.Rd               |    4 ++--
 man/glm.hermite.Rd            |    7 +++++--
 man/hermite-internal.Rd       |    4 ++++
 man/hermite-package.Rd        |   12 +++++++-----
 man/phermite.Rd               |    4 ++--
 man/qhermite.Rd               |   10 +++-------
 man/rhermite.Rd               |    4 +++-
 14 files changed, 78 insertions(+), 45 deletions(-)

More information about hermite at CRAN
Permanent link

Package geophys updated to version 1.3-8 with previous version 1.3-6 dated 2014-01-13

Title: Geophysics, Continuum Mechanics, Mogi Models, Gravity
Description: Codes for analyzing various problems of Geophysics, Continuum Mechanics and Mogi Models.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between geophys versions 1.3-6 dated 2014-01-13 and 1.3-8 dated 2015-04-27

 DESCRIPTION      |   12 ++++++------
 MD5              |   14 +++++++-------
 R/mogi1.R        |   14 +++++++-------
 R/mogiM.R        |   18 +++++++++---------
 R/okada85.R      |   10 +++++-----
 demo/Fry.R       |    2 +-
 demo/Sdemo.R     |   12 ++++++------
 man/Maxstress.Rd |    2 ++
 8 files changed, 43 insertions(+), 41 deletions(-)

More information about geophys at CRAN
Permanent link

Package adegraphics updated to version 1.0-2 with previous version 1.0-1 dated 2015-04-14

Title: An S4 Lattice-Based Package for the Representation of Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray and Aurélie Siberchicot , with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot

Diff between adegraphics versions 1.0-1 dated 2015-04-14 and 1.0-2 dated 2015-04-27

 DESCRIPTION                |   15 ++++++---------
 MD5                        |   14 +++++++-------
 NAMESPACE                  |    2 +-
 R/ADEg.S2.R                |    2 +-
 R/ade4-plot.R              |    2 +-
 R/panelfunctions.R         |    2 +-
 inst/doc/adegraphics.pdf   |binary
 man/adegraphics-package.Rd |    4 ++--
 8 files changed, 19 insertions(+), 22 deletions(-)

More information about adegraphics at CRAN
Permanent link

Package support.CEs updated to version 0.3-3 with previous version 0.3-2 dated 2014-06-22

Title: Basic Functions for Supporting an Implementation of Choice Experiments
Description: Provides seven basic functions that support an implementation of choice experiments.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki

Diff between support.CEs versions 0.3-2 dated 2014-06-22 and 0.3-3 dated 2015-04-27

 DESCRIPTION                |   20 +++++++++-----------
 MD5                        |    6 +++---
 NEWS                       |    3 +++
 man/support.CEs-package.Rd |    2 --
 4 files changed, 15 insertions(+), 16 deletions(-)

More information about support.CEs at CRAN
Permanent link

Package support.BWS updated to version 0.1-3 with previous version 0.1-2 dated 2014-06-22

Title: Basic Functions for Supporting an Implementation of Best-Worst Scaling
Description: Provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki

Diff between support.BWS versions 0.1-2 dated 2014-06-22 and 0.1-3 dated 2015-04-27

 DESCRIPTION                |   16 ++++++++--------
 MD5                        |    6 +++---
 NEWS                       |    3 +++
 man/support.BWS-package.Rd |    2 --
 4 files changed, 14 insertions(+), 13 deletions(-)

More information about support.BWS at CRAN
Permanent link

Package mded updated to version 0.1-2 with previous version 0.1-1 dated 2014-06-22

Title: Measuring the Difference Between Two Empirical Distributions
Description: Provides a function for measuring the difference between two independent or non-independent empirical distributions and returning a significance level of the difference.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki

Diff between mded versions 0.1-1 dated 2014-06-22 and 0.1-2 dated 2015-04-27

 DESCRIPTION         |   14 +++++++-------
 MD5                 |    6 +++---
 NEWS                |    3 +++
 man/mded-package.Rd |    2 --
 4 files changed, 13 insertions(+), 12 deletions(-)

More information about mded at CRAN
Permanent link

New package VCA with initial version 1.1.1
Package: VCA
Version: 1.1.1
Date: 2015-04-16
Title: Variance Component Analysis
Author: Andre Schuetzenmeister
Maintainer: Andre Schuetzenmeister
Depends: R (>= 3.0.0), stats
Imports: Matrix, numDeriv
Description: ANOVA-type estimation (prediction) of random effects and variance components in linear mixed models, is implemented. Random models, a sub-set of mixed models, can be fit applying a Variance Component Analysis (VCA). This is a special type of analysis frequently used in verifying the precision performance of diagnostics. The Satterthwaite approximation of the total degrees of freedom is implemented. There are several functions for extracting, random effects, fixed effects, variance-covariance matrices of random and fixed effects. Residuals can be extracted as raw, standardized and studentized residuals. Additionally, a variability chart is implemented for visualizing the variability in sub-classes emerging from an experimental design ('varPlot').
License: GPL (>= 3)
Collate: 'plot.R' 'vca.R'
NeedsCompilation: yes
Packaged: 2015-04-16 10:21:45 UTC; schueta6
Repository: CRAN
Date/Publication: 2015-04-27 09:02:57

More information about VCA at CRAN
Permanent link

Package migui updated to version 1.1 with previous version 0.00-09 dated 2011-11-21

Title: Graphical User Interface to the 'mi' Package
Description: This GUI for the mi package walks the user through the steps of multiple imputation and the analysis of completed data.
Author: Bob Carpenter [ctb], Ben Goodrich [cre, aut], Yu-Sung Su [ctb]
Maintainer: Ben Goodrich

Diff between migui versions 0.00-09 dated 2011-11-21 and 1.1 dated 2015-04-27

 migui-0.00-09/migui/LICENSE                                |only
 migui-0.00-09/migui/R/analysis.poolRegressionEstimates.R   |only
 migui-0.00-09/migui/R/analysis.saveImputedData.R           |only
 migui-0.00-09/migui/R/file.saveWorkspace.R                 |only
 migui-0.00-09/migui/R/help.menu.R                          |only
 migui-0.00-09/migui/R/imputation.checkModelFit.R           |only
 migui-0.00-09/migui/R/imputation.runImputation.R           |only
 migui-0.00-09/migui/R/load.first.R                         |only
 migui-0.00-09/migui/R/setup.displayMissingDataPattern.R    |only
 migui-0.00-09/migui/R/setup.importDataFrom.R               |only
 migui-0.00-09/migui/R/setup.loadSession.R                  |only
 migui-0.00-09/migui/R/setup.preprocessData.R               |only
 migui-0.00-09/migui/R/setup.specifyImputationInformation.R |only
 migui-0.00-09/migui/R/utils.R                              |only
 migui-1.1/migui/DESCRIPTION                                |   29 
 migui-1.1/migui/MD5                                        |   23 
 migui-1.1/migui/NAMESPACE                                  |    8 
 migui-1.1/migui/R/migui.R                                  | 1268 +++++++++++--
 migui-1.1/migui/R/zzz.R                                    |only
 migui-1.1/migui/man/migui.Rd                               |   73 
 20 files changed, 1197 insertions(+), 204 deletions(-)

More information about migui at CRAN
Permanent link

Package geoRglm updated to version 0.9-8 with previous version 0.9-4 dated 2013-12-13

Title: A Package for Generalised Linear Spatial Models
Description: Functions for inference in generalised linear spatial models. The posterior and predictive inference is based on Markov chain Monte Carlo methods. Package geoRglm is an extension to the package geoR, which must be installed first.
Author: Ole F. Christensen [aut, cre], Paulo J. Ribeiro Jr [aut]
Maintainer: Ole F. Christensen

Diff between geoRglm versions 0.9-4 dated 2013-12-13 and 0.9-8 dated 2015-04-27

 geoRglm-0.9-4/geoRglm/INDEX                     |only
 geoRglm-0.9-8/geoRglm/DESCRIPTION               |   24 +++--
 geoRglm-0.9-8/geoRglm/MD5                       |   47 +++++-----
 geoRglm-0.9-8/geoRglm/NAMESPACE                 |    5 -
 geoRglm-0.9-8/geoRglm/R/bayes.R                 |   14 +--
 geoRglm-0.9-8/geoRglm/R/binom.bayes.R           |    6 -
 geoRglm-0.9-8/geoRglm/R/binom.pred.R            |    4 
 geoRglm-0.9-8/geoRglm/R/extensions.R            |    8 -
 geoRglm-0.9-8/geoRglm/R/glsm.krige.R            |    2 
 geoRglm-0.9-8/geoRglm/R/mcmc.R                  |    9 --
 geoRglm-0.9-8/geoRglm/R/nonpar.R                |    2 
 geoRglm-0.9-8/geoRglm/R/pois.bayes.R            |   12 +-
 geoRglm-0.9-8/geoRglm/R/pois.pred.R             |    6 -
 geoRglm-0.9-8/geoRglm/R/zzz.R                   |   18 ++--
 geoRglm-0.9-8/geoRglm/build/vignette.rds        |binary
 geoRglm-0.9-8/geoRglm/data/b50.rda              |binary
 geoRglm-0.9-8/geoRglm/data/b64.rda              |binary
 geoRglm-0.9-8/geoRglm/data/p50.rda              |binary
 geoRglm-0.9-8/geoRglm/data/rongelap.rda         |binary
 geoRglm-0.9-8/geoRglm/inst/doc/geoRglmintro.pdf |binary
 geoRglm-0.9-8/geoRglm/man/binom.krige.bayes.Rd  |  108 +++++++++++++-----------
 geoRglm-0.9-8/geoRglm/man/glsm.mcmc.Rd          |    1 
 geoRglm-0.9-8/geoRglm/man/output.glm.control.Rd |   14 +--
 geoRglm-0.9-8/geoRglm/man/pois.krige.bayes.Rd   |   44 ++++-----
 geoRglm-0.9-8/geoRglm/src/geoRglm.c             |   50 +++++------
 25 files changed, 197 insertions(+), 177 deletions(-)

More information about geoRglm at CRAN
Permanent link

Package faoutlier updated to version 0.5 with previous version 0.4 dated 2014-05-24

Title: Influential Case Detection Methods for Factor Analysis and Structural Equation Models
Description: Tools for detecting and summarize influential cases that can affect exploratory and confirmatory factor analysis models as well as structural equation models more generally.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers

Diff between faoutlier versions 0.4 dated 2014-05-24 and 0.5 dated 2015-04-27

 DESCRIPTION                          |   18 +-
 MD5                                  |   54 ++++----
 NAMESPACE                            |    9 +
 NEWS                                 |    8 +
 R/GOF.R                              |only
 R/LD.R                               |  123 +++++++++++--------
 R/faoutlier.R                        |    5 
 R/forward.search.R                   |  223 +++++++++++++++++------------------
 R/gCD.R                              |  106 ++++++++--------
 R/obs.resid.R                        |  108 ++++++++--------
 R/robustMD.R                         |   47 +++----
 R/setClusters.R                      |    6 
 inst                                 |only
 man/GOF.Rd                           |only
 man/LD.Rd                            |   32 +++--
 man/faoutlier.Rd                     |    3 
 man/forward.search.Rd                |   26 ++--
 man/gCD.Rd                           |   15 +-
 man/holzinger.Rd                     |    3 
 man/holzinger.outlier.Rd             |    3 
 man/obs.resid.Rd                     |    9 -
 man/robustMD.Rd                      |   11 -
 man/setCluster.Rd                    |    3 
 tests/testthat/test-GOF.R            |only
 tests/testthat/test-LD.R             |   46 ++-----
 tests/testthat/test-forward.search.R |    8 -
 tests/testthat/test-gCD.R            |   26 ++--
 tests/testthat/test-obs.resid.R      |   21 ---
 28 files changed, 482 insertions(+), 431 deletions(-)

More information about faoutlier at CRAN
Permanent link

Sun, 26 Apr 2015

Package dfmta updated to version 1.3-1 with previous version 1.2 dated 2015-04-21

Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere

Diff between dfmta versions 1.2 dated 2015-04-21 and 1.3-1 dated 2015-04-26

 DESCRIPTION        |   12 ++++++------
 MD5                |    8 ++++----
 configure          |   18 +++++++++---------
 man/mtaBin_next.Rd |    2 +-
 src/dfmta.cpp      |    7 +++----
 5 files changed, 23 insertions(+), 24 deletions(-)

More information about dfmta at CRAN
Permanent link

Package dfcomb updated to version 2.1-1 with previous version 2.1 dated 2015-04-21

Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere

Diff between dfcomb versions 2.1 dated 2015-04-21 and 2.1-1 dated 2015-04-26

 DESCRIPTION     |    6 +++---
 MD5             |    6 +++---
 configure       |   18 +++++++++---------
 src/plateau.cpp |    1 +
 4 files changed, 16 insertions(+), 15 deletions(-)

More information about dfcomb at CRAN
Permanent link

New package h5 with initial version 0.9
Package: h5
Type: Package
Title: Interface to the 'HDF5' Library
Version: 0.9
Date: 2015-04-22
Authors@R: c(person("Mario", "Annau", role = c("aut", "cre"), email = "mario.annau@gmail.com"))
Copyright: See COPYRIGHTS file.
Description: S4 Interface to the 'HDF5' library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The 'HDF5' format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.
License: BSD_2_clause + file LICENSE
BugReports: https://github.com/mannau/h5/issues
SystemRequirements: libhdf5 (>= 1.8.4) with C++ interface enabled (--enable-cxx=yes)
Depends: R (>= 3.1)
Imports: Rcpp (>= 0.11.5), methods
LinkingTo: Rcpp
Suggests: testthat, roxygen2, RCurl
Collate: 'H5Location-Attribute.R' 'Attribute.R' 'CommonFG.R' 'CommonFG-DataSet.R' 'CommonFG-Group.R' 'DataSet.R' 'DataSpace.R' 'Dataset-Extend.R' 'Dataset-Subset.R' 'H5File.R' 'H5Group.R' 'Helpers.R' 'RcppExports.R' 'h5-package.R'
NeedsCompilation: yes
Packaged: 2015-04-26 17:45:02 UTC; mario
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau
Repository: CRAN
Date/Publication: 2015-04-26 22:45:59

More information about h5 at CRAN
Permanent link

Package Rwave updated to version 2.4 with previous version 2.2 dated 2014-05-08

Title: Time-Frequency Analysis of 1-D Signals
Description: A set of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani, Academic Press, 1998.
Author: S original by Rene Carmona and Bruno Torresani ; R port by Brandon Whitcher ; upgrade by Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between Rwave versions 2.2 dated 2014-05-08 and 2.4 dated 2015-04-26

 DESCRIPTION            |   12 +++++-----
 MD5                    |   54 ++++++++++++++++++++++++-------------------------
 src/choldc.c           |   28 ++++++++++++-------------
 src/compinteg.c        |   12 +++++-----
 src/crazy_family.c     |    4 +--
 src/cwt_maxima.c       |    3 --
 src/cwt_morlet.c       |    6 ++---
 src/cwt_thierry.c      |    4 +--
 src/dau.c              |    5 ++--
 src/dau_wave.c         |    2 -
 src/dualwavelet.c      |    8 +++----
 src/dwfilter.c         |   10 ++++-----
 src/dwkernel.c         |    2 -
 src/gabor.c            |    8 +++----
 src/gkernel.c          |    8 +++----
 src/hessian_climbers.c |    2 -
 src/mreconst.c         |    8 +++----
 src/pca_climbers.c     |   10 ++++-----
 src/pca_family.c       |    8 +++----
 src/ridge_annealing.c  |    2 -
 src/ridge_coronoid.c   |    2 -
 src/ridge_snakenoid.c  |    6 ++---
 src/rwkernel.c         |   18 ++++++++--------
 src/snake_annealing.c  |    4 +--
 src/splridge.c         |    2 -
 src/splsnake.c         |    2 -
 src/svd.c              |    2 -
 src/wv.c               |    4 +--
 28 files changed, 118 insertions(+), 118 deletions(-)

More information about Rwave at CRAN
Permanent link

Package RPMG updated to version 2.1-7 with previous version 2.1-5 dated 2014-01-03

Title: Graphical User Interface (GUI) for Interactive R Analysis Sessions
Description: Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between RPMG versions 2.1-5 dated 2014-01-03 and 2.1-7 dated 2015-04-26

 DESCRIPTION         |   16 ++++----
 MD5                 |   15 ++++----
 R/jpng.R            |   96 +++++++++++++++++++++++++++++++++++++++-------------
 man/SELOPT.Rd       |    2 -
 man/SHOWPAL.Rd      |    2 -
 man/aGETXprofile.Rd |    3 +
 man/chooser.Rd      |    4 +-
 man/jpng.Rd         |only
 man/jpostscript.Rd  |    2 -
 9 files changed, 95 insertions(+), 45 deletions(-)

More information about RPMG at CRAN
Permanent link

Package R.utils updated to version 2.0.1 with previous version 2.0.0 dated 2015-03-01

Title: Various Programming Utilities
Description: Utility functions useful when programming and developing R packages.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.utils versions 2.0.0 dated 2015-03-01 and 2.0.1 dated 2015-04-26

 DESCRIPTION            |    8 -
 MD5                    |   18 +-
 NEWS                   |   21 ++-
 R/addFinalizerToLast.R |    5 
 R/compressFile.R       |    2 
 R/toCamelCase.R        |    2 
 R/withSeed.R           |  144 ++++++++++-----------
 R/withSink.R           |  334 ++++++++++++++++++++++++-------------------------
 tests/toCamelCase.R    |   13 +
 tests/withLocale.R     |  118 ++++++++---------
 10 files changed, 344 insertions(+), 321 deletions(-)

More information about R.utils at CRAN
Permanent link

New package haplotypes with initial version 1.0
Package: haplotypes
Title: Haplotype Inference and Statistical Analysis of Genetic Variation
Version: 1.0
Date: 2015-04-24
Author: Caner Aktas
Maintainer: Caner Aktas
Description: Provides S4 classes and methods for reading and manipulating aligned DNA sequences, supporting an indel coding methods (only simple indel coding method is available in the current version), showing base substitutions and indels, calculating absolute pairwise distances between DNA sequences, and inferring haplotypes from DNA sequences or user provided absolute character difference matrix. This package also includes S4 classes and methods for estimating genealogical relationships among haplotypes using statistical parsimony.
License: GPL-2
URL: http://cran.r-project.org, https://biolsystematics.wordpress.com/r/
Depends: R (>= 3.1.1), methods, network
Suggests: sna
NeedsCompilation: no
Packaged: 2015-04-25 18:32:05 UTC; cnr
Repository: CRAN
Date/Publication: 2015-04-26 09:49:28

More information about haplotypes at CRAN
Permanent link

Sat, 25 Apr 2015

Package trajectories updated to version 0.1-2 with previous version 0.1-1 dated 2014-08-28

Title: Classes and Methods for Trajectory Data
Description: Classes and methods for trajectory data, with nested classes for individual trips, and collections for different entities. Methods include selection, generalization, aggregation, intersection, and plotting.
Author: Edzer Pebesma [cre, aut], Benedikt Klus [aut]
Maintainer: Edzer Pebesma

Diff between trajectories versions 0.1-1 dated 2014-08-28 and 0.1-2 dated 2015-04-25

 DESCRIPTION            |   10 ++++-----
 MD5                    |   10 ++++-----
 R/Tracks-methods.R     |   52 +++++++++++++++++++++++++++++--------------------
 R/stplot.R             |    4 +--
 build/vignette.rds     |binary
 tests/tracks.Rout.save |   34 ++++++++++++++++----------------
 6 files changed, 60 insertions(+), 50 deletions(-)

More information about trajectories at CRAN
Permanent link

Package pcaL1 updated to version 1.3 with previous version 1.2.1 dated 2013-12-23

Title: Three L1-Norm PCA Methods
Description: Three implementations of principal component analysis methods using the L1 norm. The package depends on COIN-OR Clp version >= 1.12.0. The methods implemented are PCA-L1 (Kwak 2008), L1-PCA (Ke and Kanade 2003, 2005), and L1-PCA* (Brooks, Dula, and Boone 2013).
Author: Sapan Jot and Paul Brooks
Maintainer: Paul Brooks

Diff between pcaL1 versions 1.2.1 dated 2013-12-23 and 1.3 dated 2015-04-25

 ChangeLog            |   10 +
 DESCRIPTION          |   17 +-
 INSTALL              |   36 +++-
 MD5                  |   28 +--
 NAMESPACE            |    3 
 NEWS                 |    6 
 R/l1pca.R            |   14 +
 R/pcal1.R            |   13 +
 configure            |  383 ++++++++++++++++++---------------------------------
 configure.ac         |   46 ++----
 man/l1pcastar.Rd     |    6 
 man/pcaL1-package.Rd |    8 -
 src/pcal1.c          |   21 +-
 src/pcal1_R.c        |    8 -
 src/type.h           |    1 
 15 files changed, 266 insertions(+), 334 deletions(-)

More information about pcaL1 at CRAN
Permanent link

Package lifecontingencies updated to version 1.1.6 with previous version 1.1.5 dated 2015-01-03

Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table, actuarial tables (also multiple decrement tables). Moreover, functions to easily perform demographic, financial and actuarial mathematics on life contingencies insurances calculations are contained therein.
Author: Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb] and Kevin J. Owens [ctb]
Maintainer: Giorgio Alfredo Spedicato

Diff between lifecontingencies versions 1.1.5 dated 2015-01-03 and 1.1.6 dated 2015-04-25

 lifecontingencies-1.1.5/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package-deathsIPS55Mfig.pdf |only
 lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-003.pdf                                     |only
 lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-ktProjectionPlot.pdf                        |only
 lifecontingencies-1.1.5/lifecontingencies/vignettes/mortality_projection-leeCarterResults.pdf                        |only
 lifecontingencies-1.1.6/lifecontingencies/ChangeLog                                                                  |    8 +
 lifecontingencies-1.1.6/lifecontingencies/DESCRIPTION                                                                |   25 ++--
 lifecontingencies-1.1.6/lifecontingencies/MD5                                                                        |   58 +++++-----
 lifecontingencies-1.1.6/lifecontingencies/NAMESPACE                                                                  |    2 
 lifecontingencies-1.1.6/lifecontingencies/NEWS                                                                       |   10 -
 lifecontingencies-1.1.6/lifecontingencies/R/0_lifetableAndActuarialtableClassesAndMethods.R                          |    7 +
 lifecontingencies-1.1.6/lifecontingencies/R/4_financialFunctions.R                                                   |   19 +--
 lifecontingencies-1.1.6/lifecontingencies/R/6_randomGenerationFunctions.R                                            |    2 
 lifecontingencies-1.1.6/lifecontingencies/R/RcppExports.R                                                            |only
 lifecontingencies-1.1.6/lifecontingencies/R/zzz.R                                                                    |    8 +
 lifecontingencies-1.1.6/lifecontingencies/README.md                                                                  |only
 lifecontingencies-1.1.6/lifecontingencies/build/vignette.rds                                                         |binary
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.Rnw                  |    4 
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf                  |binary
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.R                                        |only
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.Rmd                                      |only
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/introToLifecontingencies.pdf                                      |only
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/mortality_projection.pdf                                          |binary
 lifecontingencies-1.1.6/lifecontingencies/inst/doc/multiple_decrements_with_lifecontingencies_package.pdf            |binary
 lifecontingencies-1.1.6/lifecontingencies/man/demoFrance.Rd                                                          |    6 -
 lifecontingencies-1.1.6/lifecontingencies/man/demoIta.Rd                                                             |    1 
 lifecontingencies-1.1.6/lifecontingencies/man/lifecontingencies-package.Rd                                           |    4 
 lifecontingencies-1.1.6/lifecontingencies/man/soa08.Rd                                                               |    3 
 lifecontingencies-1.1.6/lifecontingencies/man/soa08Act.Rd                                                            |    5 
 lifecontingencies-1.1.6/lifecontingencies/man/soaLt.Rd                                                               |    3 
 lifecontingencies-1.1.6/lifecontingencies/src                                                                        |only
 lifecontingencies-1.1.6/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.Rnw                 |    4 
 lifecontingencies-1.1.6/lifecontingencies/vignettes/introToLifecontingencies.Rmd                                     |only
 lifecontingencies-1.1.6/lifecontingencies/vignettes/introToLifecontingencies_files                                   |only
 lifecontingencies-1.1.6/lifecontingencies/vignettes/lifecontingenciesBiblio.bib                                      |   40 +++++-
 34 files changed, 122 insertions(+), 87 deletions(-)

More information about lifecontingencies at CRAN
Permanent link

Fri, 24 Apr 2015

Package rfordummies updated to version 0.1.1 with previous version 0.0-2 dated 2014-08-18

Title: Code Examples to Accompany the Book "R for Dummies"
Description: Contains all the code examples in the book "R for Dummies" (1st edition). You can view the table of contents as well as the sample code for each chapter.
Author: Andrie de Vries [aut, cre], Joris Meys [aut]
Maintainer: Andrie de Vries

Diff between rfordummies versions 0.0-2 dated 2014-08-18 and 0.1.1 dated 2015-04-24

 DESCRIPTION         |   16 +++++++--------
 MD5                 |   54 ++++++++++++++++++++++++++--------------------------
 NAMESPACE           |    3 +-
 R/chapters.R        |    2 -
 R/saveElements.R    |only
 man/ch01.Rd         |    3 +-
 man/ch02.Rd         |    3 +-
 man/ch03.Rd         |    3 +-
 man/ch04.Rd         |    3 +-
 man/ch05.Rd         |    3 +-
 man/ch06.Rd         |    3 +-
 man/ch07.Rd         |    3 +-
 man/ch08.Rd         |    3 +-
 man/ch09.Rd         |    3 +-
 man/ch10.Rd         |    3 +-
 man/ch11.Rd         |    3 +-
 man/ch12.Rd         |    3 +-
 man/ch13.Rd         |    3 +-
 man/ch14.Rd         |    3 +-
 man/ch15.Rd         |    3 +-
 man/ch16.Rd         |    3 +-
 man/ch17.Rd         |    3 +-
 man/ch18.Rd         |    3 +-
 man/ch19.Rd         |    3 +-
 man/ch20.Rd         |    3 +-
 man/elements.Rd     |    3 +-
 man/rfordummies.Rd  |    3 +-
 man/saveElements.Rd |only
 man/toc.Rd          |    3 +-
 29 files changed, 85 insertions(+), 59 deletions(-)

More information about rfordummies at CRAN
Permanent link

Package spacetime updated to version 1.1-4 with previous version 1.1-3 dated 2015-01-22

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal combining or aggregating, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma

Diff between spacetime versions 1.1-3 dated 2015-01-22 and 1.1-4 dated 2015-04-24

 DESCRIPTION           |   12 
 MD5                   |   66 +--
 NAMESPACE             |    4 
 R/Class-ST.R          |    4 
 R/Class-STSDF.R       |    2 
 R/STFDF-methods.R     |   13 
 R/STSDF-methods.R     |    7 
 R/stplot.R            |   65 ++-
 build/vignette.rds    |binary
 data/air.rda          |binary
 data/datalist         |    2 
 data/fires.rda        |binary
 demo/CressieWikle.R   |    2 
 demo/aggregate.R      |    2 
 demo/edc.R            |    4 
 demo/sos4R.R          |    2 
 inst/ChangeLog        |  258 ++++++++++++++
 inst/doc/jss816.R     |   91 ++---
 inst/doc/jss816.Rnw   |    7 
 inst/doc/jss816.pdf   |  891 +++++++++++++++++++++++++-------------------------
 inst/doc/stgvis.html  |  217 ++++++------
 inst/doc/sto.R        |   33 -
 inst/doc/sto.Rnw      |   17 
 inst/doc/sto.pdf      |binary
 inst/doc/stpg.pdf     |binary
 inst/doc/stsubs.pdf   |binary
 man/air.Rd            |    4 
 man/fires.Rd          |    5 
 man/stconstruct.Rd    |    3 
 man/stplot.Rd         |    4 
 tests/basic.Rout.save |   70 +--
 tests/rw.Rout.save    |    4 
 vignettes/jss816.Rnw  |    7 
 vignettes/sto.Rnw     |   17 
 34 files changed, 1033 insertions(+), 780 deletions(-)

More information about spacetime at CRAN
Permanent link

Package sp updated to version 1.1-0 with previous version 1.0-17 dated 2015-01-08

Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb], Robert Hijmans [ctb], Michael Sumner [ctb], Don MacQueen [ctb], Josh O'Brien [ctb]
Maintainer: Edzer Pebesma

Diff between sp versions 1.0-17 dated 2015-01-08 and 1.1-0 dated 2015-04-24

 sp-1.0-17/sp/R/overlay.R                           |only
 sp-1.1-0/sp/ChangeLog                              |only
 sp-1.1-0/sp/DESCRIPTION                            |   46 +-
 sp-1.1-0/sp/MD5                                    |  150 +++----
 sp-1.1-0/sp/NAMESPACE                              |    4 
 sp-1.1-0/sp/R/CRS-methods.R                        |   15 
 sp-1.1-0/sp/R/Class-CRS.R                          |   14 
 sp-1.1-0/sp/R/Class-GridTopology.R                 |    9 
 sp-1.1-0/sp/R/Class-Spatial.R                      |   11 
 sp-1.1-0/sp/R/Class-SpatialGrid.R                  |   18 
 sp-1.1-0/sp/R/Class-SpatialGridDataFrame.R         |   12 
 sp-1.1-0/sp/R/Class-SpatialLines.R                 |   16 
 sp-1.1-0/sp/R/Class-SpatialLinesDataFrame.R        |    4 
 sp-1.1-0/sp/R/Class-SpatialPoints.R                |   15 
 sp-1.1-0/sp/R/Class-SpatialPointsDataFrame.R       |   17 
 sp-1.1-0/sp/R/Class-SpatialPolygons.R              |   16 
 sp-1.1-0/sp/R/Class-SpatialPolygonsDataFrame.R     |    9 
 sp-1.1-0/sp/R/Spatial-methods.R                    |   40 +-
 sp-1.1-0/sp/R/SpatialGrid-methods.R                |  118 +++++-
 sp-1.1-0/sp/R/SpatialGridDataFrame-methods.R       |   36 +
 sp-1.1-0/sp/R/SpatialLines-methods.R               |   23 -
 sp-1.1-0/sp/R/SpatialPoints-methods.R              |   30 -
 sp-1.1-0/sp/R/SpatialPointsDataFrame-methods.R     |   40 +-
 sp-1.1-0/sp/R/SpatialPolygons-methods.R            |   42 +-
 sp-1.1-0/sp/R/SpatialPolygonsDataFrame-methods.R   |   21 -
 sp-1.1-0/sp/R/aggregate.R                          |   35 +
 sp-1.1-0/sp/R/bubble.R                             |    3 
 sp-1.1-0/sp/R/over.R                               |    8 
 sp-1.1-0/sp/R/projected.R                          |   12 
 sp-1.1-0/sp/R/rbind.R                              |    9 
 sp-1.1-0/sp/R/spplot.R                             |  156 ++++----
 sp-1.1-0/sp/R/spsample.R                           |   24 -
 sp-1.1-0/sp/R/subset.R                             |   21 -
 sp-1.1-0/sp/build/vignette.rds                     |binary
 sp-1.1-0/sp/demo/depend.R                          |   12 
 sp-1.1-0/sp/demo/gallery.R                         |    2 
 sp-1.1-0/sp/inst/ChangeLog                         |  408 +++++++++++++++++++++
 sp-1.1-0/sp/inst/doc/csdacm.pdf                    |binary
 sp-1.1-0/sp/inst/doc/intro_sp.pdf                  |binary
 sp-1.1-0/sp/inst/doc/over.R                        |   14 
 sp-1.1-0/sp/inst/doc/over.Rnw                      |   13 
 sp-1.1-0/sp/inst/doc/over.pdf                      |binary
 sp-1.1-0/sp/inst/include/sp.h                      |   37 +
 sp-1.1-0/sp/inst/include/sp_xports.c               |  217 ++++++-----
 sp-1.1-0/sp/man/CRS-class.Rd                       |    2 
 sp-1.1-0/sp/man/Spatial-class.Rd                   |   22 +
 sp-1.1-0/sp/man/SpatialLines-class.Rd              |   20 +
 sp-1.1-0/sp/man/SpatialPixels-class.Rd             |    4 
 sp-1.1-0/sp/man/SpatialPoints-class.Rd             |   20 +
 sp-1.1-0/sp/man/SpatialPoints.Rd                   |   34 +
 sp-1.1-0/sp/man/SpatialPolygons-class.Rd           |    2 
 sp-1.1-0/sp/man/addattr.Rd                         |    3 
 sp-1.1-0/sp/man/aggregate.Rd                       |   50 ++
 sp-1.1-0/sp/man/as.SpatialPolygons.GridTopology.Rd |    3 
 sp-1.1-0/sp/man/degaxis.Rd                         |    2 
 sp-1.1-0/sp/man/is.projected.Rd                    |    7 
 sp-1.1-0/sp/man/meuse.Rd                           |    2 
 sp-1.1-0/sp/man/nowrapSpatialLines.Rd              |    2 
 sp-1.1-0/sp/man/over.Rd                            |   13 
 sp-1.1-0/sp/man/panel.Rd                           |    2 
 sp-1.1-0/sp/man/recenter-methods.Rd                |   10 
 sp-1.1-0/sp/man/sp-deprecated.Rd                   |   43 --
 sp-1.1-0/sp/man/spDistsN1.Rd                       |    2 
 sp-1.1-0/sp/man/spTransform.Rd                     |   16 
 sp-1.1-0/sp/man/spplot.Rd                          |   97 +++-
 sp-1.1-0/sp/man/spsample.Rd                        |   11 
 sp-1.1-0/sp/src/init.c                             |    1 
 sp-1.1-0/sp/src/pip.c                              |   16 
 sp-1.1-0/sp/src/pip2.c                             |   20 -
 sp-1.1-0/sp/src/sp.h                               |   34 -
 sp-1.1-0/sp/src/sp_xports.c                        |  217 ++++++-----
 sp-1.1-0/sp/tests/fail1.R                          |    4 
 sp-1.1-0/sp/tests/fail1.Rout.save                  |   26 -
 sp-1.1-0/sp/tests/grid.Rout.save                   |   27 -
 sp-1.1-0/sp/tests/pass1.R                          |   89 ++++
 sp-1.1-0/sp/tests/pass1.Rout.save                  |  343 +++++++++++++++++
 sp-1.1-0/sp/vignettes/over.Rnw                     |   13 
 77 files changed, 2032 insertions(+), 802 deletions(-)

More information about sp at CRAN
Permanent link

Package RCurl updated to version 1.95-4.6 with previous version 1.95-4.5 dated 2014-12-06

Title: General network (HTTP/FTP/...) client interface for R
Description: The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang

Diff between RCurl versions 1.95-4.5 dated 2014-12-06 and 1.95-4.6 dated 2015-04-24

 DESCRIPTION                 |   12 +++++-------
 MD5                         |    6 +++---
 R/dynamic.R                 |    2 +-
 data/mimeTypeExtensions.rda |binary
 4 files changed, 9 insertions(+), 11 deletions(-)

More information about RCurl at CRAN
Permanent link

Package maptools updated to version 0.8-36 with previous version 0.8-34 dated 2015-02-03

Title: Tools for Reading and Handling Spatial Objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut], Nicholas Lewin-Koh [aut], Edzer Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb], Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan [ctb], German Carrillo [ctb], Stéphane Dray [ctb], David Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb], Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb], Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai [ctb], Edzer Pebesma [ctb], Oscar Perpiñán Lamigueiro [ctb], Tom Short [ctb], Greg Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf Turner [ctb]
Maintainer: Roger Bivand

Diff between maptools versions 0.8-34 dated 2015-02-03 and 0.8-36 dated 2015-04-24

 ChangeLog                     | 1680 ++++++++----------------------------------
 DESCRIPTION                   |   14 
 MD5                           |   28 
 R/checkHoles.R                |   10 
 R/sp2pbs.R                    |    8 
 build/vignette.rds            |binary
 data/wrld_simpl.rda           |binary
 inst/ChangeLog                | 1680 ++++++++----------------------------------
 inst/doc/combine_maptools.pdf |binary
 man/GE_SpatialGrid.Rd         |    4 
 man/SpatialLines2PolySet.Rd   |    4 
 man/kmlLine.Rd                |    2 
 man/kmlLines.Rd               |    2 
 man/kmlOverlay.Rd             |   16 
 man/nowrapRecenter.Rd         |    7 
 15 files changed, 717 insertions(+), 2738 deletions(-)

More information about maptools at CRAN
Permanent link

Package TSMySQL (with last version 2013.9-1) was removed from CRAN

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

2013-09-29 2013.9-1
2012-10-02 2012.8-1
2012-05-03 2012.4-1
2012-03-29 2012.3-1
2011-11-02 2011.11-1
2011-09-14 2011.8-2
2011-08-14 2011.8-1
2011-07-25 2011.7-1
2011-03-23 2011.3-1
2010-12-22 2010.12-1
2010-05-31 2010.5-1
2010-04-11 2010.3-1
2009-12-16 2009.10-1
2009-10-27 2009.5-1
2009-03-25 2009.3-2
2009-03-22 2009.3-1
2008-11-03 2008.11-1
2008-08-06 2008.8-1
2008-05-08 2008.5-1
2007-11-05 2007.10-1

Permanent link
Package DiceKriging updated to version 1.5.5 with previous version 1.5.4 dated 2015-01-05

Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant

Diff between DiceKriging versions 1.5.4 dated 2015-01-05 and 1.5.5 dated 2015-04-24

 CHANGELOG                        |    7 +-
 DESCRIPTION                      |   10 +-
 MD5                              |   24 +++----
 NAMESPACE                        |   10 ++
 R/allGenerics.R                  |   11 +--
 R/covStruct_Base_TensorProduct.R |  131 +++++++++++++++++++--------------------
 R/covStruct_User.R               |    4 -
 R/kmEstimate.R                   |   10 +-
 R/logLikGrad.R                   |    3 
 R/scalingFun.R                   |    2 
 man/DiceKriging-package.Rd       |    6 -
 man/coef.Rd                      |    8 +-
 man/covTensorProduct-class.Rd    |    4 -
 13 files changed, 125 insertions(+), 105 deletions(-)

More information about DiceKriging at CRAN
Permanent link

New package RJafroc with initial version 0.0.1
Package: RJafroc
Type: Package
Title: Analysis of Data Acquired Using the Receiver Operating Characteristic Paradigm and Its Extensions
Version: 0.0.1
Date: 2015-04-21
Authors@R: c(person("Xuetong", "Zhai", role = c("aut", "cre"), email = "xuetong.zhai@gmail.com"), person("Dev", "Chakraborty", role = c("aut", "ths"), email = "dpc10ster@gmail.com"))
Maintainer: Xuetong Zhai
Depends: tools, xlsx, ggplot2, stringr, utils
Suggests: knitr
VignetteBuilder: knitr
Description: A common task in medical imaging is assessing whether a new imaging system or device is an improvement over an existing one. Observer performance methodology, such as receiver operating characteristic analysis, is widely used for this purpose. Receiver operating characteristic studies are often required for regulatory approval of new devices. The purpose of this work is to software for the analysis of data acquired using the receiver operating characteristic paradigm and its location specific extensions. It is an enhanced implementation of existing Windows software (http://www.devchakraborty.com). In this paradigm the radiologist rates each image for confidence in presence of disease. The images are typically split equally between actually non-diseased and diseased. A common figure of merit is the area under the receiver operating characteristic curve, which has the physical interpretation as the probability that a diseased image is rated higher than a non-diseased one. In receiver operating characteristic studies a number of radiologists (readers) rate images in two or more treatments, and the object of the analysis is to determine the significance of the inter-treatment difference between reader-averaged figures of merit. In the free-response paradigm the reader marks the locations of suspicious regions and rates each region for confidence in presence of disease, and credit for detection is only given if a true lesion is correctly localized. In the region of interest paradigm each image is divided into a number of regions and the reader rates each region. Each paradigm requires definition of a valid figure of merit that rewards correct decisions and penalizes incorrect ones and specialized significance testing procedures are applied. The package reads data in all currently used data formats including Excel. Significance testing uses two models in widespread use, a jackknife pseudo-value based model and an analysis of variance model with correlated errors. Included are tools for (1) calculating a variety of free-response figures of merit; (2) sample size estimation for planning a future study based on pilot data; (3) viewing empirical operating characteristics in receiver operating characteristic and free-response paradigms; (4) producing formatted report files; and (5) saving a data file in appropriate format for analysis with alternate software.
License: GPL-3
LazyData: true
URL: http://www.devchakraborty.com
Packaged: 2015-04-23 03:52:09 UTC; XuetongZhai
Author: Xuetong Zhai [aut, cre], Dev Chakraborty [aut, ths]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-24 08:18:56

More information about RJafroc at CRAN
Permanent link

Package tsDyn updated to version 0.9-43 with previous version 0.9-41 dated 2014-08-26

Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut], Jose Luis Aznarte [ctb], Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler

Diff between tsDyn versions 0.9-41 dated 2014-08-26 and 0.9-43 dated 2015-04-24

 tsDyn-0.9-41/tsDyn/man/predict.Rd                     |only
 tsDyn-0.9-41/tsDyn/tests/lstar.Rout.save              |only
 tsDyn-0.9-43/tsDyn/DESCRIPTION                        |   18 -
 tsDyn-0.9-43/tsDyn/MD5                                |  130 +++++-----
 tsDyn-0.9-43/tsDyn/NAMESPACE                          |    1 
 tsDyn-0.9-43/tsDyn/R/TVAR.sim.R                       |  131 +++++------
 tsDyn-0.9-43/tsDyn/R/TVECM.R                          |    2 
 tsDyn-0.9-43/tsDyn/R/TVECM.sim.R                      |   17 +
 tsDyn-0.9-43/tsDyn/R/VAR.sim.R                        |only
 tsDyn-0.9-43/tsDyn/R/predict.R                        |   78 ++++++
 tsDyn-0.9-43/tsDyn/R/predict.VAR.R                    |only
 tsDyn-0.9-43/tsDyn/R/selectLSTAR.R                    |    2 
 tsDyn-0.9-43/tsDyn/R/star.R                           |    2 
 tsDyn-0.9-43/tsDyn/R/vec2var.tsDyn.R                  |   40 ---
 tsDyn-0.9-43/tsDyn/build/vignette.rds                 |binary
 tsDyn-0.9-43/tsDyn/data/barry.rda                     |binary
 tsDyn-0.9-43/tsDyn/data/zeroyld.rda                   |binary
 tsDyn-0.9-43/tsDyn/inst/ChangeLog                     |    8 
 tsDyn-0.9-43/tsDyn/inst/doc/ThCointOverview.pdf       |binary
 tsDyn-0.9-43/tsDyn/inst/doc/tsDyn.pdf                 |binary
 tsDyn-0.9-43/tsDyn/man/BBCTest.Rd                     |    3 
 tsDyn-0.9-43/tsDyn/man/MAPE.Rd                        |    3 
 tsDyn-0.9-43/tsDyn/man/MakeThSpec.Rd                  |    7 
 tsDyn-0.9-43/tsDyn/man/TVAR.LRtest.Rd                 |    3 
 tsDyn-0.9-43/tsDyn/man/TVAR.Rd                        |    3 
 tsDyn-0.9-43/tsDyn/man/TVAR.boot.Rd                   |    9 
 tsDyn-0.9-43/tsDyn/man/TVAR.sim.Rd                    |    8 
 tsDyn-0.9-43/tsDyn/man/TVECM.Rd                       |    3 
 tsDyn-0.9-43/tsDyn/man/TVECM.SeoTest.Rd               |    3 
 tsDyn-0.9-43/tsDyn/man/TVECM.sim.Rd                   |   31 +-
 tsDyn-0.9-43/tsDyn/man/VAR.boot.Rd                    |only
 tsDyn-0.9-43/tsDyn/man/VARrep.Rd                      |    3 
 tsDyn-0.9-43/tsDyn/man/VECM.Rd                        |    9 
 tsDyn-0.9-43/tsDyn/man/VECM_symbolic.Rd               |    3 
 tsDyn-0.9-43/tsDyn/man/accuracy_stat.Rd               |    3 
 tsDyn-0.9-43/tsDyn/man/addRegime.Rd                   |    3 
 tsDyn-0.9-43/tsDyn/man/autopairs.Rd                   |    3 
 tsDyn-0.9-43/tsDyn/man/autotriples.Rd                 |    3 
 tsDyn-0.9-43/tsDyn/man/autotriples.rgl.Rd             |    3 
 tsDyn-0.9-43/tsDyn/man/availableModels.Rd             |    3 
 tsDyn-0.9-43/tsDyn/man/coefB.Rd                       |    7 
 tsDyn-0.9-43/tsDyn/man/computeGradient.Rd             |    3 
 tsDyn-0.9-43/tsDyn/man/delta.Rd                       |    3 
 tsDyn-0.9-43/tsDyn/man/delta.lin.Rd                   |    3 
 tsDyn-0.9-43/tsDyn/man/fitted.nlVar.Rd                |    3 
 tsDyn-0.9-43/tsDyn/man/getTh.Rd                       |    3 
 tsDyn-0.9-43/tsDyn/man/isLinear.Rd                    |    3 
 tsDyn-0.9-43/tsDyn/man/lags.select.Rd                 |    3 
 tsDyn-0.9-43/tsDyn/man/lineVar.Rd                     |    9 
 tsDyn-0.9-43/tsDyn/man/logLik.VECM.Rd                 |    3 
 tsDyn-0.9-43/tsDyn/man/logLik.nlVar.Rd                |    3 
 tsDyn-0.9-43/tsDyn/man/mse.Rd                         |    3 
 tsDyn-0.9-43/tsDyn/man/nlar.Rd                        |    3 
 tsDyn-0.9-43/tsDyn/man/oneStep.Rd                     |    3 
 tsDyn-0.9-43/tsDyn/man/predict.VAR.Rd                 |only
 tsDyn-0.9-43/tsDyn/man/predict.nlar.Rd                |only
 tsDyn-0.9-43/tsDyn/man/predict_rolling.Rd             |    3 
 tsDyn-0.9-43/tsDyn/man/rank.select.Rd                 |    7 
 tsDyn-0.9-43/tsDyn/man/rank.test.Rd                   |    7 
 tsDyn-0.9-43/tsDyn/man/regime.Rd                      |    3 
 tsDyn-0.9-43/tsDyn/man/setar.sim.Rd                   |   15 -
 tsDyn-0.9-43/tsDyn/man/sigmoid.Rd                     |    3 
 tsDyn-0.9-43/tsDyn/man/toLatex.setar.Rd               |    3 
 tsDyn-0.9-43/tsDyn/tests/TVECM.sim.Rout.save          |   38 +--
 tsDyn-0.9-43/tsDyn/tests/VAR.R                        |   23 +
 tsDyn-0.9-43/tsDyn/tests/VAR.Rout.save                |  213 +++++++++++-------
 tsDyn-0.9-43/tsDyn/tests/VECM.Rout.save               |  162 ++++++-------
 tsDyn-0.9-43/tsDyn/tests/compare_tsDyn_vars.R         |    2 
 tsDyn-0.9-43/tsDyn/tests/compare_tsDyn_vars.Rout.save |   13 -
 tsDyn-0.9-43/tsDyn/tests/lstar.Rout.save_bkp          |only
 70 files changed, 622 insertions(+), 457 deletions(-)

More information about tsDyn at CRAN
Permanent link

New package RRTCS with initial version 0.0.1
Package: RRTCS
Type: Package
Title: Randomized Response Techniques for Complex Surveys
Version: 0.0.1
Date: 2015-04-22
Author: Beatriz Cobo Rodríguez, María del Mar Rueda García, Antonio Arcos Cebrián
Maintainer: Beatriz Cobo Rodríguez
Description: Point and interval estimation of linear parameters with data obtained from complex surveys (including stratified and clustered samples) when randomization techniques are used. The randomized response technique was developed to obtain estimates that are more valid when studying sensitive topics. Estimators and variances for 14 randomized response methods for qualitative variables and 7 randomized response methods for quantitative variables are also implemented. In addition, some data sets from surveys with these randomization methods are included in the package.
License: GPL (>= 2)
Encoding: UTF-8
Imports: sampling, samplingVarEst
Packaged: 2015-04-23 18:21:36 UTC; Usuario
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-24 06:50:24

More information about RRTCS at CRAN
Permanent link

Package PBSmapping updated to version 2.69.76 with previous version 2.68.68 dated 2015-01-14

Title: Mapping Fisheries Data and Spatial Analysis Tools
Description: This software has evolved from fisheries research conducted at the Pacific Biological Station (PBS) in `Nanaimo', British Columbia, Canada. It extends the R language to include two-dimensional plotting features similar to those commonly available in a Geographic Information System (GIS). Embedded C code speeds algorithms from computational geometry, such as finding polygons that contain specified point events or converting between longitude-latitude and Universal Transverse Mercator (UTM) coordinates. Additionally, we include `C++' code developed by Angus Johnson for the `Clipper' library. Also included are data for a global shoreline and other data sets in the public domain. The R directory `.../library/PBSmapping/doc' offers a complete user's guide, which should be consulted to use package functions effectively.
Author: Jon T. Schnute [aut], Nicholas Boers [aut], Rowan Haigh [aut, cre], Alex Couture-Beil [ctb], Denis Chabot [ctb], Chris Grandin [ctb], Angus Johnson [ctb], Paul Wessel [ctb], Franklin Antonio [ctb], Nicholas J. Lewin-Koh [ctb], Roger Bivand [ctb]
Maintainer: Rowan Haigh

Diff between PBSmapping versions 2.68.68 dated 2015-01-14 and 2.69.76 dated 2015-04-24

 PBSmapping-2.68.68/PBSmapping/man/nepacLLhigh.Rd         |only
 PBSmapping-2.68.68/PBSmapping/man/worldLL.Rd             |only
 PBSmapping-2.68.68/PBSmapping/man/worldLLhigh.Rd         |only
 PBSmapping-2.69.76/PBSmapping/DESCRIPTION                |   45 
 PBSmapping-2.69.76/PBSmapping/MD5                        |   41 
 PBSmapping-2.69.76/PBSmapping/NAMESPACE                  |    9 
 PBSmapping-2.69.76/PBSmapping/R/PBSfigs.r                |    4 
 PBSmapping-2.69.76/PBSmapping/R/PBSmapping.r             |  273 
 PBSmapping-2.69.76/PBSmapping/data/nepacLL.rda           |binary
 PBSmapping-2.69.76/PBSmapping/data/surveyData.rda        |binary
 PBSmapping-2.69.76/PBSmapping/inst/doc/ChangeLog.txt     |  181 
 PBSmapping-2.69.76/PBSmapping/inst/doc/PBSmapping-UG.pdf |binary
 PBSmapping-2.69.76/PBSmapping/inst/doc/index.html        |    2 
 PBSmapping-2.69.76/PBSmapping/man/EventData.Rd           |   67 
 PBSmapping-2.69.76/PBSmapping/man/LocationSet.Rd         |   34 
 PBSmapping-2.69.76/PBSmapping/man/PolyData.Rd            |   33 
 PBSmapping-2.69.76/PBSmapping/man/PolySet.Rd             |   31 
 PBSmapping-2.69.76/PBSmapping/man/importGSHHS.Rd         |  143 
 PBSmapping-2.69.76/PBSmapping/man/joinPolys.Rd           |   55 
 PBSmapping-2.69.76/PBSmapping/man/nepacLL.Rd             |   63 
 PBSmapping-2.69.76/PBSmapping/src/clipper.cpp            | 4772 ++++++++-------
 PBSmapping-2.69.76/PBSmapping/src/clipper.h              |  358 -
 PBSmapping-2.69.76/PBSmapping/src/clipperWrapper.cpp     |  198 
 23 files changed, 3767 insertions(+), 2542 deletions(-)

More information about PBSmapping at CRAN
Permanent link

Package mma updated to version 2.0-0 with previous version 1.0-1 dated 2015-04-10

Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis. The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu

Diff between mma versions 1.0-1 dated 2015-04-10 and 2.0-0 dated 2015-04-24

 DESCRIPTION           |    8 +-
 MD5                   |   14 ++---
 R/mma.r               |  135 ++++++++++++++++++++++++++++++++++++++++----------
 man/boot.med.binx.Rd  |    3 -
 man/boot.med.contx.Rd |    1 
 man/mma.Rd            |    1 
 man/plot.mma.Rd       |   18 ++++--
 man/summary.mma.Rd    |    7 +-
 8 files changed, 140 insertions(+), 47 deletions(-)

More information about mma at CRAN
Permanent link

Thu, 23 Apr 2015

Package knitr updated to version 1.10 with previous version 1.9 dated 2015-01-20

Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Author: Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Ashley Manton [ctb], Brian Diggs [ctb], Cassio Pereira [ctb], David Robinson [ctb], Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty), Doug Hemken [ctb], Duncan Murdoch [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Gregoire Detrez [ctb], Hadley Wickham [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jeff Arnold [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Michael Friendly [ctb], Michel Kuhlmann [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Noam Ross [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Romain Francois [ctb], Scott Kostyshak [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Yihui Xie [aut, cre]
Maintainer: Yihui Xie

Diff between knitr versions 1.9 dated 2015-01-20 and 1.10 dated 2015-04-23

 DESCRIPTION                           |   61 ++++--------
 MD5                                   |  171 +++++++++++++++++-----------------
 NAMESPACE                             |    9 -
 R/block.R                             |   59 ++++++-----
 R/cache.R                             |    7 -
 R/citation.R                          |   64 +++++-------
 R/defaults.R                          |   12 +-
 R/engine.R                            |   83 +++++++++++-----
 R/header.R                            |   31 ++----
 R/highlight.R                         |   18 +--
 R/hooks-asciidoc.R                    |    2 
 R/hooks-extra.R                       |   10 +
 R/hooks-html.R                        |   26 ++---
 R/hooks-latex.R                       |   12 +-
 R/hooks-md.R                          |   24 +++-
 R/hooks-textile.R                     |    2 
 R/output.R                            |  108 +++++++++++++--------
 R/package.R                           |    8 -
 R/pandoc.R                            |    2 
 R/params.R                            |only
 R/parser.R                            |  106 ++++++++++++++++-----
 R/pattern.R                           |    3 
 R/plot.R                              |   46 +++------
 R/rocco.R                             |    2 
 R/spin.R                              |    8 -
 R/table.R                             |   40 +++++--
 R/template.R                          |    9 -
 R/themes-eclipse.R                    |    4 
 R/themes.R                            |    8 -
 R/utils-base64.R                      |   18 +--
 R/utils-conversion.R                  |    3 
 R/utils-rd2html.R                     |   10 -
 R/utils-sweave.R                      |    2 
 R/utils-vignettes.R                   |   45 +++++++-
 R/utils.R                             |   67 ++++++++++---
 build/knitr.pdf                       |binary
 build/vignette.rds                    |binary
 inst/doc/knit_expand.html             |    4 
 inst/doc/knit_print.html              |    9 -
 inst/doc/knitr-html.html              |   12 +-
 inst/doc/knitr-intro.Rmd              |    4 
 inst/doc/knitr-intro.html             |   18 +--
 inst/doc/knitr-markdown.Rmd           |    4 
 inst/doc/knitr-markdown.html          |    8 +
 inst/doc/knitr-refcard.pdf            |binary
 inst/examples/knitr-beamer.Rnw        |    6 -
 inst/examples/knitr-graphics.Rnw      |   27 +----
 inst/examples/knitr-listings.Rnw      |    2 
 inst/examples/knitr-manual.Rnw        |   46 +++------
 inst/examples/knitr-minimal.Rnw       |    2 
 inst/examples/knitr-packages.bib      |   33 +++---
 inst/examples/knitr-spin.R            |    6 -
 inst/examples/knitr-spin.Rmd          |    4 
 inst/examples/knitr-subfloats.Rnw     |    2 
 inst/examples/knitr-themes.Rnw        |   22 +---
 inst/examples/knitr-twocolumn.Rnw     |    2 
 inst/misc/knitr.css                   |   12 +-
 inst/misc/stitch-test.R               |    4 
 inst/misc/tweak_bib.csv               |only
 inst/misc/vignette.css                |   17 +--
 man/all_labels.Rd                     |   29 +++++
 man/all_patterns.Rd                   |    4 
 man/current_input.Rd                  |    6 -
 man/eclipse_theme.Rd                  |    4 
 man/knit.Rd                           |   44 ++++----
 man/knit_child.Rd                     |    4 
 man/knit_params.Rd                    |only
 man/knit_print.Rd                     |    4 
 man/knit_rd.Rd                        |    2 
 man/knit_theme.Rd                     |    6 -
 man/knitr-package.Rd                  |    4 
 man/rand_seed.Rd                      |    2 
 man/read_rforge.Rd                    |    1 
 man/set_alias.Rd                      |    2 
 man/stitch.Rd                         |    5 
 man/vignette_engines.Rd               |   21 +++-
 man/write_bib.Rd                      |    6 -
 tests/testit/test-cache.R             |    6 -
 tests/testit/test-citation.R          |only
 tests/testit/test-closure.R           |   12 +-
 tests/testit/test-hooks.R             |    2 
 tests/testit/test-params.R            |only
 tests/testit/test-parser.R            |   32 ++++--
 tests/testit/test-plot.R              |   34 ++++--
 tests/testit/test-table.R             |   20 ++-
 tests/testit/test-utils.R             |   11 +-
 vignettes/assets/template-refcard.tex |    2 
 vignettes/knitr-intro.Rmd             |    4 
 vignettes/knitr-markdown.Rmd          |    4 
 89 files changed, 928 insertions(+), 667 deletions(-)

More information about knitr at CRAN
Permanent link

Package monitoR updated to version 1.0.3 with previous version 1.0.2 dated 2014-05-14

Title: Acoustic Template Detection in R
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner and Jon Katz , with code for the Fourier transform from the seewave package (by Jerome Sueur, Thierry Aubin, and Caroline Simonis), and code for the readMP3 function from the tuneR package (by Uwe Ligges).
Maintainer: Sasha D. Hafner

Diff between monitoR versions 1.0.2 dated 2014-05-14 and 1.0.3 dated 2015-04-23

 ChangeLog                        |  159 +++++++++++++++++++++++++++++++++++
 DESCRIPTION                      |   12 +-
 MD5                              |  132 ++++++++++++++---------------
 NAMESPACE                        |    2 
 R/binMatch.R                     |   54 ++++++------
 R/bindEvents.R                   |    6 -
 R/corMatch.R                     |   55 +++++-------
 R/dbDownloadCardRecorderID.R     |   47 +++++++---
 R/dbDownloadResult.R             |   18 +---
 R/dbDownloadSurvey.R             |   81 ++++++++++++------
 R/dbDownloadTemplate.R           |   76 +++++++++-------
 R/dbSchema.R                     |   19 ++--
 R/dbUploadAnno.R                 |   13 +-
 R/dbUploadResult.R               |   17 +--
 R/dbUploadSurvey.R               |   15 +--
 R/dbUploadTemplate.R             |   17 +--
 R/eventEval.R                    |   10 --
 R/fileCopyRename.R               |    5 -
 R/findPeaks.R                    |    5 -
 R/getClip.R                      |   19 ++--
 R/makeBinTemplate.R              |   75 ++++++----------
 R/makeCorTemplate.R              |   42 +++++----
 R/readBinTemplates.R             |    5 -
 R/readCorTemplates.R             |    5 -
 R/showPeaks.R                    |   52 +++++++++--
 R/stft.R                         |   13 +-
 R/templatePath.R                 |only
 R/viewSpec.R                     |   29 ++++--
 R/writeBinTemplates.R            |    5 -
 R/writeCorTemplates.R            |    5 -
 build/vignette.rds               |binary
 data/btnw.rda                    |binary
 data/oven.rda                    |binary
 data/survey.rda                  |binary
 data/survey_anno.rda             |binary
 inst/doc/monitoR_QuickStart.R    |  175 ++++++++++++++-------------------------
 inst/doc/monitoR_QuickStart.Rnw  |   39 +++++---
 inst/doc/monitoR_QuickStart.pdf  |binary
 man/changeSampRate.Rd            |    2 
 man/collapseClips.Rd             |   10 --
 man/combineTemplates.Rd          |   46 ++++++----
 man/compareTemplates.Rd          |   32 ++++---
 man/dbDownload.Rd                |   10 +-
 man/dbDownloadTemplate.Rd        |   22 ++--
 man/dbUploadResult.Rd            |   24 ++++-
 man/dbUploadTemplate.Rd          |    6 -
 man/eventEval.Rd                 |   31 ++++--
 man/fileCopyRename.Rd            |   13 +-
 man/findPeaks.Rd                 |   43 ++++++---
 man/getDetections.Rd             |   37 +++++---
 man/makeTemplate.Rd              |   71 +++++++++------
 man/monitoR-package.Rd           |   32 ++++---
 man/mp3Subsamp.Rd                |    2 
 man/plot-methods.Rd              |   50 ++++++-----
 man/readTemplates.Rd             |   31 ++++--
 man/show-methods.Rd              |   26 ++++-
 man/showPeaks.Rd                 |   51 ++++++++---
 man/specCols.Rd                  |   20 ++--
 man/survey_anno.Rd               |    8 +
 man/templateComment.Rd           |   54 ++++++------
 man/templateCutoff.Rd            |   32 ++++---
 man/templateMatching.Rd          |   12 +-
 man/templateNames.Rd             |   31 ++++--
 man/templatePath.Rd              |only
 man/timeAlign.Rd                 |   17 ++-
 man/viewSpec.Rd                  |   25 +++--
 man/writeTemplates.Rd            |   29 ++++--
 vignettes/monitoR_QuickStart.Rnw |   39 +++++---
 68 files changed, 1209 insertions(+), 804 deletions(-)

More information about monitoR at CRAN
Permanent link

Package geoR updated to version 1.7-5.1 with previous version 1.7-4.1 dated 2014-09-14

Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including traditional, likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr and Peter J. Diggle
Maintainer: Paulo J. Ribeiro Jr

Diff between geoR versions 1.7-4.1 dated 2014-09-14 and 1.7-5.1 dated 2015-04-23

 geoR-1.7-4.1/geoR/R/likOLD.R                   |only
 geoR-1.7-4.1/geoR/inst/CITATION                |only
 geoR-1.7-5.1/geoR/DESCRIPTION                  |   25 +++----
 geoR-1.7-5.1/geoR/MD5                          |   79 ++++++++++++-------------
 geoR-1.7-5.1/geoR/NAMESPACE                    |   28 ++++++--
 geoR-1.7-5.1/geoR/R/Cwrappers.R                |    1 
 geoR-1.7-5.1/geoR/R/auxiliar.R                 |   11 +--
 geoR-1.7-5.1/geoR/R/corcov.R                   |    2 
 geoR-1.7-5.1/geoR/R/eyefit.R                   |    2 
 geoR-1.7-5.1/geoR/R/geobayes.R                 |    6 -
 geoR-1.7-5.1/geoR/R/geodata.R                  |    4 -
 geoR-1.7-5.1/geoR/R/profiles.R                 |   69 +++++++++++++++++++++
 geoR-1.7-5.1/geoR/R/simul.R                    |    3 
 geoR-1.7-5.1/geoR/data/Ksat.rda                |binary
 geoR-1.7-5.1/geoR/data/SIC.rda                 |binary
 geoR-1.7-5.1/geoR/data/ca20.rda                |binary
 geoR-1.7-5.1/geoR/data/camg.rda                |binary
 geoR-1.7-5.1/geoR/data/elevation.rda           |binary
 geoR-1.7-5.1/geoR/data/gambia.rda              |binary
 geoR-1.7-5.1/geoR/data/head.rda                |binary
 geoR-1.7-5.1/geoR/data/hoef.rda                |binary
 geoR-1.7-5.1/geoR/data/isaaks.rda              |binary
 geoR-1.7-5.1/geoR/data/kattegat.rda            |binary
 geoR-1.7-5.1/geoR/data/landim1.rda             |binary
 geoR-1.7-5.1/geoR/data/parana.rda              |binary
 geoR-1.7-5.1/geoR/data/s100.rda                |binary
 geoR-1.7-5.1/geoR/data/s121.rda                |binary
 geoR-1.7-5.1/geoR/data/s256i.rda               |binary
 geoR-1.7-5.1/geoR/data/soil250.rda             |binary
 geoR-1.7-5.1/geoR/data/soja98.rda              |binary
 geoR-1.7-5.1/geoR/data/tce.rda                 |binary
 geoR-1.7-5.1/geoR/data/wo.rda                  |binary
 geoR-1.7-5.1/geoR/data/wolfcamp.rda            |binary
 geoR-1.7-5.1/geoR/data/wrc.rda                 |binary
 geoR-1.7-5.1/geoR/inst/CHANGES                 |   13 +++-
 geoR-1.7-5.1/geoR/inst/doc/CHANGES             |only
 geoR-1.7-5.1/geoR/man/SIC.Rd                   |    2 
 geoR-1.7-5.1/geoR/man/coords2coords.Rd         |    6 +
 geoR-1.7-5.1/geoR/man/grf.Rd                   |    3 
 geoR-1.7-5.1/geoR/man/sample.prior.Rd          |    5 +
 geoR-1.7-5.1/geoR/man/statistics.predictive.Rd |    2 
 geoR-1.7-5.1/geoR/man/subarea.Rd               |    8 +-
 42 files changed, 184 insertions(+), 85 deletions(-)

More information about geoR at CRAN
Permanent link

Package drgee updated to version 1.1.0 with previous version 1.0.1 dated 2014-01-27

Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association between an exposure and an outcome, given covariates. Three methods are implemented: O-estimation, where a nuisance model for the association between the covariates and the outcome is used; E-estimation where a nuisance model for the association between the covariates and the exposure is used, and doubly robust (DR) estimation where both nuisance models are used. In DR-estimation, the estimates will be consistent when at least one of the nuisance models is correctly specified, not necessarily both.
Author: Johan Zetterqvist , Arvid Sjölander with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist

Diff between drgee versions 1.0.1 dated 2014-01-27 and 1.1.0 dated 2015-04-23

 drgee-1.0.1/drgee/R/ebeFit.R           |only
 drgee-1.0.1/drgee/R/obeFit.R           |only
 drgee-1.0.1/drgee/man/drFit.Rd         |only
 drgee-1.0.1/drgee/man/ebeFit.Rd        |only
 drgee-1.0.1/drgee/man/geeFit.Rd        |only
 drgee-1.0.1/drgee/man/obeFit.Rd        |only
 drgee-1.1.0/drgee/DESCRIPTION          |   29 -
 drgee-1.1.0/drgee/MD5                  |   42 +-
 drgee-1.1.0/drgee/NAMESPACE            |   12 
 drgee-1.1.0/drgee/NEWS                 |   27 +
 drgee-1.1.0/drgee/R/clogitRes.R        |only
 drgee-1.1.0/drgee/R/drFit.R            |  191 -----------
 drgee-1.1.0/drgee/R/dreFit.R           |only
 drgee-1.1.0/drgee/R/dreFitCond.R       |only
 drgee-1.1.0/drgee/R/drgee.R            |  199 +++++++-----
 drgee-1.1.0/drgee/R/drgeeData.R        |  538 +++++++++++++++++++++++++--------
 drgee-1.1.0/drgee/R/eFit.R             |only
 drgee-1.1.0/drgee/R/findRoots.R        |   23 -
 drgee-1.1.0/drgee/R/gee.R              |only
 drgee-1.1.0/drgee/R/geeFit.R           |   51 +--
 drgee-1.1.0/drgee/R/geeFitCond.R       |only
 drgee-1.1.0/drgee/R/oFit.R             |only
 drgee-1.1.0/drgee/R/robVcov.R          |   29 -
 drgee-1.1.0/drgee/man/drgee-package.Rd |   38 +-
 drgee-1.1.0/drgee/man/drgee.Rd         |  335 +++++++++++---------
 drgee-1.1.0/drgee/man/drgeeData.Rd     |  112 ++++--
 drgee-1.1.0/drgee/man/findRoots.Rd     |   16 
 drgee-1.1.0/drgee/man/gee.Rd           |only
 drgee-1.1.0/drgee/man/robVcov.Rd       |   16 
 29 files changed, 971 insertions(+), 687 deletions(-)

More information about drgee at CRAN
Permanent link

Package plotKML updated to version 0.5-1 with previous version 0.5-0 dated 2015-01-28

Title: Visualization of Spatial and Spatio-temporal Objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl

Diff between plotKML versions 0.5-0 dated 2015-01-28 and 0.5-1 dated 2015-04-23

 DESCRIPTION                 |   10 ++++----
 MD5                         |   34 ++++++++++++++++--------------
 R/AAA-md.R                  |    6 +++++
 R/AAAA.R                    |   10 ++++----
 R/aesthetics.R              |    3 --
 R/kml.tiles.R               |only
 R/legend.bar.R              |    2 -
 R/plot.SpatialPredictions.R |   25 +++++++++++++++-------
 R/plotKML.GDALobj.R         |   25 ++++++++++++----------
 R/spMetadata.R              |   14 ++++++++++++
 build/vignette.rds          |binary
 inst/INSPIRE_ISO19139.xml   |   23 +++++++++++++++++++-
 inst/doc/jss1079.pdf        |binary
 man/baranja.Rd              |   49 ++++++++++++++++++++++++++------------------
 man/kml.Rd                  |    4 ++-
 man/kml.tiles.Rd            |only
 man/plotKML.GDALobj.Rd      |   12 ++++++----
 man/plotKML.Rd              |    9 ++++++++
 man/plotKML.env.Rd          |   12 +++++-----
 19 files changed, 158 insertions(+), 80 deletions(-)

More information about plotKML at CRAN
Permanent link

Package LinRegInteractive updated to version 0.3-1 with previous version 0.3-0 dated 2014-11-12

Title: Interactive Interpretation of Linear Regression Models
Description: Interactive visualization of effects, response functions and marginal effects for different kinds of regression models. In this version linear regression models, generalized linear models, generalized additive models and linear mixed-effects models are supported. Major features are the interactive approach and the handling of the effects of categorical covariates: if two or more factors are used as covariates every combination of the levels of each factor is treated separately. The automatic calculation of marginal effects and a number of possibilities to customize the graphical output are useful features as well.
Author: Martin Meermeyer
Maintainer: Martin Meermeyer

Diff between LinRegInteractive versions 0.3-0 dated 2014-11-12 and 0.3-1 dated 2015-04-23

 DESCRIPTION                      |   10 
 MD5                              |   24 
 build/vignette.rds               |binary
 inst/doc/LinRegInteractive.Rnw   | 1647 +++++++++++++++++++--------------------
 inst/doc/LinRegInteractive.pdf   |binary
 man/LinRegInteractive-package.Rd |    6 
 man/fxInteractive.Rd             |    2 
 man/fxInteractive.glm.Rd         |    2 
 man/fxInteractive.lm.Rd          |    2 
 man/fxInteractive.lme.Rd         |    2 
 man/munichrent03.Rd              |    2 
 vignettes/LinRegInteractive.Rnw  | 1647 +++++++++++++++++++--------------------
 vignettes/LinRegInteractive.tex  |   11 
 13 files changed, 1670 insertions(+), 1685 deletions(-)

More information about LinRegInteractive at CRAN
Permanent link

Package soilDB updated to version 1.5-4 with previous version 1.5-2 dated 2015-02-25

Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette

Diff between soilDB versions 1.5-2 dated 2015-02-25 and 1.5-4 dated 2015-04-23

 DESCRIPTION                         |   11 -
 MD5                                 |   34 +--
 NEWS                                |   20 +-
 R/AAAA.R                            |    2 
 R/fetchNASIS.R                      |   24 +-
 R/getHzErrorsNASIS.R                |    2 
 R/get_colors_from_NASIS_db.R        |    1 
 R/get_extended_data_from_NASIS_db.R |   16 -
 R/get_hz_data_from_NASIS_db.R       |   14 -
 R/get_site_data_from_NASIS_db.R     |   10 -
 R/nasis_component_data.R            |  343 ++++++++++++++++++------------------
 R/utils.R                           |   24 ++
 data/andic.subset.rda               |binary
 data/cisne.rda                      |binary
 data/gSSURGO.chunk.rda              |binary
 data/gopheridge.rda                 |binary
 data/loafercreek.rda                |binary
 man/fetchNASIS.Rd                   |   25 +-
 18 files changed, 280 insertions(+), 246 deletions(-)

More information about soilDB at CRAN
Permanent link

Package aqp updated to version 1.8-6 with previous version 1.8 dated 2015-02-20

Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette , Pierre Roudier
Maintainer: Dylan Beaudette

Diff between aqp versions 1.8 dated 2015-02-20 and 1.8-6 dated 2015-04-23

 DESCRIPTION                        |   12 +--
 MD5                                |   25 ++++---
 NAMESPACE                          |    4 +
 NEWS                               |   13 +++
 R/SoilProfileCollection-methods.R  |   19 ++---
 R/aggregateSoilDepth.R             |only
 R/evalGenHz.R                      |  121 ++++++++++++++++++++-----------------
 R/profile_plot.R                   |   85 +++++++++++++++++++++----
 R/setters.R                        |    5 -
 man/SPC-plotting.Rd                |   18 ++++-
 man/SPC-slab-methods.Rd            |    9 +-
 man/SPC-unique-methods.Rd          |only
 man/SoilProfileCollection-class.Rd |   28 --------
 man/aggregateSoilDepth.Rd          |only
 man/plotMultipleSPC.Rd             |only
 man/profileGroupLabels.Rd          |only
 16 files changed, 209 insertions(+), 130 deletions(-)

More information about aqp at CRAN
Permanent link

Wed, 22 Apr 2015

Package Rdistance updated to version 1.2.2 with previous version 1.2.1 dated 2015-04-01

Title: Distance Sampling Analyses
Description: Analysis of distance sampling data collected on line transect surveys. Estimates distance-based detection functions and abundances.
Author: Trent McDonald [cre, aut], Ryan Nielson [aut], Jason Carlisle [aut], Ben Augustine [ctb], James Griswald [ctb], Joel Reynolds [ctb], Pham Quang [ctb], Earl Becker [ctb], Aaron Christ [ctb], Brook Russelland [ctb], Patrick McKann [ctb]
Maintainer: Trent McDonald

Diff between Rdistance versions 1.2.1 dated 2015-04-01 and 1.2.2 dated 2015-04-22

 Rdistance-1.2.1/Rdistance/data/sparrow.covs.rda                           |only
 Rdistance-1.2.1/Rdistance/data/sparrow.dists.rda                          |only
 Rdistance-1.2.1/Rdistance/man/sparrow.covs.Rd                             |only
 Rdistance-1.2.1/Rdistance/man/sparrow.dists.Rd                            |only
 Rdistance-1.2.1/Rdistance/vignettes/vignette.sparrow.example.R            |only
 Rdistance-1.2.2/Rdistance/DESCRIPTION                                     |   12 -
 Rdistance-1.2.2/Rdistance/MD5                                             |   46 ++-
 Rdistance-1.2.2/Rdistance/R/F.abund.estim.r                               |  118 +---------
 Rdistance-1.2.2/Rdistance/R/F.automated.CDA.r                             |   15 -
 Rdistance-1.2.2/Rdistance/R/F.dfunc.estim.R                               |   11 
 Rdistance-1.2.2/Rdistance/R/perp.dists.R                                  |    4 
 Rdistance-1.2.2/Rdistance/R/zzz.R                                         |    2 
 Rdistance-1.2.2/Rdistance/build                                           |only
 Rdistance-1.2.2/Rdistance/data/sparrow.detections.rda                     |only
 Rdistance-1.2.2/Rdistance/data/sparrow.transects.rda                      |only
 Rdistance-1.2.2/Rdistance/inst                                            |only
 Rdistance-1.2.2/Rdistance/man/AIC.dfunc.Rd                                |   10 
 Rdistance-1.2.2/Rdistance/man/ESW.Rd                                      |   10 
 Rdistance-1.2.2/Rdistance/man/F.abund.estim.Rd                            |   32 +-
 Rdistance-1.2.2/Rdistance/man/F.automated.CDA.Rd                          |   18 -
 Rdistance-1.2.2/Rdistance/man/F.dfunc.estim.Rd                            |   63 +----
 Rdistance-1.2.2/Rdistance/man/Rdistance-package.Rd                        |   23 -
 Rdistance-1.2.2/Rdistance/man/coef.dfunc.Rd                               |   10 
 Rdistance-1.2.2/Rdistance/man/perp.dists.Rd                               |   12 -
 Rdistance-1.2.2/Rdistance/man/sparrow.detections.Rd                       |only
 Rdistance-1.2.2/Rdistance/man/sparrow.transects.Rd                        |only
 Rdistance-1.2.2/Rdistance/vignettes/Rdistance_BeginnerTutorial.Rmd        |only
 Rdistance-1.2.2/Rdistance/vignettes/Rdistance_CustomDetectionFunction.Rmd |only
 28 files changed, 148 insertions(+), 238 deletions(-)

More information about Rdistance at CRAN
Permanent link

Package NAM updated to version 1.3 with previous version 1.2 dated 2015-04-07

Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier

Diff between NAM versions 1.2 dated 2015-04-07 and 1.3 dated 2015-04-22

 DESCRIPTION        |    8 
 MD5                |   18 -
 NAMESPACE          |    3 
 R/gibbs.R          |   16 -
 R/gwas.R           |   90 +++++
 R/gwas2.R          |  813 +++++++++++++++++++++++++++++------------------------
 R/manhattan.R      |   47 +--
 man/NAM-package.Rd |    4 
 man/gibbs.Rd       |  151 ++++-----
 man/gwas.Rd        |    7 
 10 files changed, 668 insertions(+), 489 deletions(-)

More information about NAM at CRAN
Permanent link

Package GCD updated to version 3.0.5 with previous version 3.0.4 dated 2014-05-22

Title: Global Charcoal Database
Description: Contains the Global Charcoal database data. Data include charcoal series (age, depth, charcoal quantity, associated units and methods) and informations on sedimentary sites (localisation, depositional environment, biome, etc.).
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez

Diff between GCD versions 3.0.4 dated 2014-05-22 and 3.0.5 dated 2015-04-22

 GCD-3.0.4/GCD/R/potveg.R            |only
 GCD-3.0.4/GCD/man/plot.potveg.Rd    |only
 GCD-3.0.4/GCD/man/potveg.Rd         |only
 GCD-3.0.5/GCD/DESCRIPTION           |   15 +--
 GCD-3.0.5/GCD/MD5                   |   18 +--
 GCD-3.0.5/GCD/NAMESPACE             |    5 -
 GCD-3.0.5/GCD/NEWS                  |    9 +
 GCD-3.0.5/GCD/R/GCD-package.R       |only
 GCD-3.0.5/GCD/man/GCD-internal.Rd   |   10 +-
 GCD-3.0.5/GCD/man/GCD-package.Rd    |   49 +++++-----
 GCD-3.0.5/GCD/man/paleofiredata.Rd  |   30 +++---
 GCD-3.0.5/GCD/man/paleofiresites.Rd |  168 +++++++++++++++++++++---------------
 12 files changed, 169 insertions(+), 135 deletions(-)

More information about GCD at CRAN
Permanent link

Package zoib updated to version 1.3.0 with previous version 1.2.1 dated 2015-03-26

Title: Bayesian Inference for Beta Regression and Zero/One Inflated Beta Regression
Description: Fits beta regression and zero/one inflated beta regression and obtains Bayesian Inference of the model via the Markov Chain Monte Carlo approach implemented in JAGS.
Author: Fang Liu with contributions from Yunchuan Kong
Maintainer: Fang Liu

Diff between zoib versions 1.2.1 dated 2015-03-26 and 1.3.0 dated 2015-04-22

 DESCRIPTION              |    8 +++----
 MD5                      |   50 +++++++++++++++++++++++------------------------
 R/fixed01.R              |    2 -
 R/zoib.R                 |   40 +++++++++++++++++++++++++++----------
 inst/bugs/fixed.bug      |    5 +---
 inst/bugs/fixed0.bug     |    4 +--
 inst/bugs/fixed01.bug    |   19 ++++++++++-------
 inst/bugs/fixed1.bug     |    6 ++---
 inst/bugs/joint_1z.bug   |    6 ++---
 inst/bugs/joint_1z0.bug  |    6 ++---
 inst/bugs/joint_1z01.bug |    5 ++--
 inst/bugs/joint_1z1.bug  |    5 ++--
 inst/bugs/joint_2z.bug   |    5 ++--
 inst/bugs/joint_2z0.bug  |    5 ++--
 inst/bugs/joint_2z01.bug |    5 ++--
 inst/bugs/joint_2z1.bug  |    5 ++--
 inst/bugs/sep_1z.bug     |    4 +--
 inst/bugs/sep_1z0.bug    |    4 +--
 inst/bugs/sep_1z01.bug   |    4 +--
 inst/bugs/sep_1z1.bug    |    5 ++--
 inst/bugs/sep_2z.bug     |    5 ++--
 inst/bugs/sep_2z0.bug    |    5 ++--
 inst/bugs/sep_2z01.bug   |    5 ++--
 inst/bugs/sep_2z1.bug    |    5 ++--
 man/zoib-package.Rd      |    6 ++---
 man/zoib.Rd              |   10 +++++----
 26 files changed, 131 insertions(+), 98 deletions(-)

More information about zoib at CRAN
Permanent link

New package treeperm with initial version 1.6
Package: treeperm
Type: Package
Title: Exact and Asymptotic K Sample Permutation Test
Version: 1.6
Date: 2015-04-22
Author: Qiao Kang
Maintainer: Qiao Kang
Depends: R (>= 2.14.1)
Description: An implementation of permutation tests in R, supporting both exact and asymptotic K sample test of data locations. The p value of exact tests is found using tree algorithms. Tree algorithms treat permutations of input data as tree nodes and perform constraint depth-first searches for permutations that fall into the critical region of a test systematically. Pruning of tree search and optimisations at C level enable exact tests for certain large data sets.
License: GPL-2
Packaged: 2015-04-22 16:47:23 UTC; sony
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-22 22:49:55

More information about treeperm at CRAN
Permanent link

New package TickExec with initial version 1.0
Package: TickExec
Type: Package
Title: Execution Functions for Tick Data Back Test
Version: 1.0
Date: 2015-04-20
Author: HKUST
Maintainer: SONG Yang
Description: Functions to execute orders in backtesting using tick data. A testing platform was established by the four major execution functions, namely 'LimitBuy', 'LimitSell', 'MarketSell' and 'MarketSell', which enclosed all tedious aspects (such as queueing for order executions and calculate actual executed volumes) for order execution using tick data. Such that one can focus on the logic of strategies, rather than its execution.
License: GPL-3
Packaged: 2015-04-22 17:17:08 UTC; Ian
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 22:31:08

More information about TickExec at CRAN
Permanent link

Package rplexos updated to version 1.0 with previous version 0.13 dated 2015-03-18

Title: Read and Analyze PLEXOS Solutions
Description: Efficiently read and analyze PLEXOS solutions by converting them into SQLite databases that can be easily queried. It supports collation of solutions that may have been divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], Marcin Kalicinski [ctb] (for the included RapidXml source), National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.13 dated 2015-03-18 and 1.0 dated 2015-04-22

 DESCRIPTION                      |   20 -
 MD5                              |   69 +++---
 NAMESPACE                        |    4 
 R/debug.R                        |   25 ++
 R/process_folder.R               |    8 
 R/process_input.R                |    2 
 R/process_solution.R             |    6 
 R/query.R                        |   34 +--
 build/vignette.rds               |binary
 inst/doc/rplexos.R               |   77 ++++++
 inst/doc/rplexos.Rmd             |  172 +++++++++++++--
 inst/doc/rplexos.html            |  439 ++++++++++++++++++---------------------
 inst/extdata                     |only
 man/get_query.Rd                 |    2 
 man/is_sample_stats.Rd           |    2 
 man/list_folders.Rd              |    2 
 man/location_solution_rplexos.Rd |only
 man/plexos_open.Rd               |    2 
 man/process_folder.Rd            |    2 
 man/query_class_member.Rd        |    2 
 man/query_config.Rd              |    2 
 man/query_log.Rd                 |    2 
 man/query_master.Rd              |    7 
 man/query_master_each.Rd         |    4 
 man/query_phase.Rd               |    2 
 man/query_property.Rd            |    2 
 man/query_sql.Rd                 |    2 
 man/query_time.Rd                |    2 
 man/rplexos.Rd                   |    2 
 man/start_debug_rplexos.Rd       |    2 
 man/start_parallel_rplexos.Rd    |    2 
 man/valid_columns.Rd             |    2 
 src/RcppExports.cpp              |   28 --
 tests                            |only
 vignettes/rplexos.Rmd            |  170 +++++++++++++--
 35 files changed, 712 insertions(+), 385 deletions(-)

More information about rplexos at CRAN
Permanent link

New package shinydashboard with initial version 0.4.0
Package: shinydashboard
Title: Create Dashboards with 'Shiny'
Version: 0.4.0
Authors@R: c( person("Winston", "Chang", role = c("aut", "cre"), email = "winston@rstudio.com"), person(family = "RStudio", role = "cph"), person(family = "Almasaeed Studio", role = c("ctb", "cph")), person(family = "Adobe Systems Incorporated", role = c("ctb", "cph"), comment = "Source Sans Pro font") )
Description: Create dashboards with 'Shiny'. This package provides a theme on top of 'Shiny', making it easy to create attractive dashboards.
URL: http://rstudio.github.io/shinydashboard/
Depends: R (>= 3.0)
License: GPL-2 | file LICENSE
Imports: shiny (>= 0.11.1), htmltools (>= 0.2.6)
NeedsCompilation: no
Packaged: 2015-04-22 15:21:29 UTC; winston
Author: Winston Chang [aut, cre], RStudio [cph], Almasaeed Studio [ctb, cph], Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang
Repository: CRAN
Date/Publication: 2015-04-22 23:08:28

More information about shinydashboard at CRAN
Permanent link

Package probemod updated to version 0.2.1 with previous version 0.2 dated 2015-04-21

Title: Statistical Tools for Probing Moderation Effects
Description: Contains functions that are useful for probing moderation effects (or interactions) including techniques such as pick-a-point (also known as spotlight analysis) and Johnson-Neyman (also known as floodlight analysis). Plot function is also provided to facilitate visualization of results from each of these techniques.
Author: Jiat Chow Tan [aut, cre]
Maintainer: Jiat Chow Tan

Diff between probemod versions 0.2 dated 2015-04-21 and 0.2.1 dated 2015-04-22

 DESCRIPTION    |    8 ++++----
 MD5            |   12 ++++++------
 NEWS           |   11 +++++++----
 R/jn.R         |   20 +++++++++++---------
 R/pickapoint.R |   19 +++++++++++--------
 R/plot.jn.R    |    4 ++--
 man/plot.jn.Rd |    4 ++--
 7 files changed, 43 insertions(+), 35 deletions(-)

More information about probemod at CRAN
Permanent link

Package paleofire updated to version 1.1.6 with previous version 1.1.5 dated 2014-12-01

Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez

Diff between paleofire versions 1.1.5 dated 2014-12-01 and 1.1.6 dated 2015-04-22

 paleofire-1.1.5/paleofire/man/1paleofiRe-package.Rd     |only
 paleofire-1.1.6/paleofire/DESCRIPTION                   |   17 
 paleofire-1.1.6/paleofire/MD5                           |  126 +++----
 paleofire-1.1.6/paleofire/NAMESPACE                     |    5 
 paleofire-1.1.6/paleofire/NEWS                          |   20 +
 paleofire-1.1.6/paleofire/R/contiguous.R                |only
 paleofire-1.1.6/paleofire/R/kdffreq.R                   |only
 paleofire-1.1.6/paleofire/R/paleofire-package.R         |only
 paleofire-1.1.6/paleofire/R/pfAddData.R                 |   56 +++
 paleofire-1.1.6/paleofire/R/pfBoxCox.R                  |   35 +
 paleofire-1.1.6/paleofire/R/pfCircular.R                |   68 +++
 paleofire-1.1.6/paleofire/R/pfComposite.R               |   80 ++++
 paleofire-1.1.6/paleofire/R/pfCompositeLF.R             |  126 ++++++-
 paleofire-1.1.6/paleofire/R/pfDiagnostic.R              |   58 +++
 paleofire-1.1.6/paleofire/R/pfDotMap.r                  |  282 ++++++++++++----
 paleofire-1.1.6/paleofire/R/pfExtract.R                 |   28 +
 paleofire-1.1.6/paleofire/R/pfGridding.R                |  205 ++++++++++-
 paleofire-1.1.6/paleofire/R/pfInteractive.R             |   33 +
 paleofire-1.1.6/paleofire/R/pfKruskal.R                 |   83 ++++
 paleofire-1.1.6/paleofire/R/pfMinMax.R                  |   31 +
 paleofire-1.1.6/paleofire/R/pfPublication.R             |    3 
 paleofire-1.1.6/paleofire/R/pfResolution.R              |   23 +
 paleofire-1.1.6/paleofire/R/pfSimpleGrid.r              |only
 paleofire-1.1.6/paleofire/R/pfSiteSel.R                 |  133 +++++++
 paleofire-1.1.6/paleofire/R/pfToKml.R                   |   20 +
 paleofire-1.1.6/paleofire/R/pfTransform.R               |   69 +++
 paleofire-1.1.6/paleofire/R/potveg.R                    |only
 paleofire-1.1.6/paleofire/R/pretreatment.R              |   72 ++++
 paleofire-1.1.6/paleofire/R/zzz.R                       |   48 ++
 paleofire-1.1.6/paleofire/build/vignette.rds            |binary
 paleofire-1.1.6/paleofire/data/countries.rda            |only
 paleofire-1.1.6/paleofire/data/datalist                 |    1 
 paleofire-1.1.6/paleofire/inst/doc/paleofire-paper.Rnw  |    1 
 paleofire-1.1.6/paleofire/inst/doc/paleofire-paper.pdf  |binary
 paleofire-1.1.6/paleofire/man/checkGCDversion.Rd        |   28 -
 paleofire-1.1.6/paleofire/man/contiguous.Rd             |only
 paleofire-1.1.6/paleofire/man/kdffreq.Rd                |only
 paleofire-1.1.6/paleofire/man/paleofire-internal.Rd     |   14 
 paleofire-1.1.6/paleofire/man/paleofire-package.Rd      |only
 paleofire-1.1.6/paleofire/man/pfAddData.Rd              |   75 ++--
 paleofire-1.1.6/paleofire/man/pfBoxCox.Rd               |   55 +--
 paleofire-1.1.6/paleofire/man/pfCircular.Rd             |   65 +--
 paleofire-1.1.6/paleofire/man/pfComposite.Rd            |   77 ++--
 paleofire-1.1.6/paleofire/man/pfCompositeLF.Rd          |  106 +++---
 paleofire-1.1.6/paleofire/man/pfDiagnostic.Rd           |  131 +++----
 paleofire-1.1.6/paleofire/man/pfDotMap.Rd               |  209 +++++++----
 paleofire-1.1.6/paleofire/man/pfExtract.Rd              |   32 -
 paleofire-1.1.6/paleofire/man/pfGridding.Rd             |  127 ++++---
 paleofire-1.1.6/paleofire/man/pfInteractive.Rd          |   34 -
 paleofire-1.1.6/paleofire/man/pfKruskal.Rd              |   51 +-
 paleofire-1.1.6/paleofire/man/pfMinMax.Rd               |   30 -
 paleofire-1.1.6/paleofire/man/pfPublication.Rd          |    2 
 paleofire-1.1.6/paleofire/man/pfResolution.Rd           |   42 --
 paleofire-1.1.6/paleofire/man/pfSimpleGrid.Rd           |only
 paleofire-1.1.6/paleofire/man/pfSiteSel.Rd              |   56 +--
 paleofire-1.1.6/paleofire/man/pfToKml.Rd                |   33 -
 paleofire-1.1.6/paleofire/man/pfTransform.Rd            |  131 +++----
 paleofire-1.1.6/paleofire/man/plot.CHAR.Rd              |   34 -
 paleofire-1.1.6/paleofire/man/plot.contiguous.Rd        |only
 paleofire-1.1.6/paleofire/man/plot.kdffreq.Rd           |only
 paleofire-1.1.6/paleofire/man/plot.pfCircular.Rd        |   52 +-
 paleofire-1.1.6/paleofire/man/plot.pfComposite.Rd       |   54 +--
 paleofire-1.1.6/paleofire/man/plot.pfCompositeLF.Rd     |   68 ++-
 paleofire-1.1.6/paleofire/man/plot.pfGridding.Rd        |  102 +++--
 paleofire-1.1.6/paleofire/man/plot.pfKruskal.Rd         |   62 +--
 paleofire-1.1.6/paleofire/man/plot.pfSiteSel.Rd         |   59 +--
 paleofire-1.1.6/paleofire/man/plot.potveg.Rd            |only
 paleofire-1.1.6/paleofire/man/potveg.Rd                 |only
 paleofire-1.1.6/paleofire/man/pretreatment.Rd           |   67 +--
 paleofire-1.1.6/paleofire/man/summary.pfSiteSel.Rd      |   35 -
 paleofire-1.1.6/paleofire/man/triCube.Rd                |only
 paleofire-1.1.6/paleofire/vignettes/paleofire-paper.Rnw |    1 
 72 files changed, 2421 insertions(+), 1034 deletions(-)

More information about paleofire at CRAN
Permanent link

Package markdown updated to version 0.7.7 with previous version 0.7.4 dated 2014-08-24

Title: 'Markdown' Rendering for R
Description: Provides R bindings to the 'Sundown' 'Markdown' rendering library (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting syntax that can be converted to 'XHTML' or other formats. See http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie

Diff between markdown versions 0.7.4 dated 2014-08-24 and 0.7.7 dated 2015-04-22

 DESCRIPTION                     |   19 +++++++------
 MD5                             |   44 ++++++++++++++++----------------
 NEWS                            |   19 +++++++++++++
 R/renderMarkdown.R              |   55 +++++++++++++++++++++-------------------
 R/rpubsUpload.R                 |   55 ++++++++++++++++++++++++++++++++--------
 README.md                       |    2 +
 build/vignette.rds              |binary
 inst/doc/markdown-examples.R    |    4 +-
 inst/doc/markdown-examples.html |    8 ++---
 inst/doc/markdown-output.R      |    4 +-
 inst/doc/markdown-output.html   |    8 ++---
 inst/examples/HTMLOptions.R     |    4 +-
 man/markdown.Rd                 |    1 
 man/markdownExtensions.Rd       |    1 
 man/markdownHTMLOptions.Rd      |    1 
 man/markdownToHTML.Rd           |    1 
 man/registeredRenderers.Rd      |    1 
 man/renderMarkdown.Rd           |   29 ++++++++++++---------
 man/rendererExists.Rd           |    1 
 man/rendererOutputType.Rd       |    1 
 man/rpubsUpload.Rd              |    1 
 man/smartypants.Rd              |    1 
 tests/tests.Rout.save           |   12 ++++----
 23 files changed, 172 insertions(+), 100 deletions(-)

More information about markdown at CRAN
Permanent link

Package mapStats updated to version 2.4 with previous version 2.3 dated 2015-02-19

Title: Geographic Display of Survey Data Statistics
Description: Automated calculation and visualization of survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman

Diff between mapStats versions 2.3 dated 2015-02-19 and 2.4 dated 2015-04-22

 DESCRIPTION              |    8 +++---
 MD5                      |   21 +++++++++--------
 R/calcStats.R            |   32 ++++++++++++++++++++++++++-
 R/jiggleClass.R          |   44 +++++++++++++++++++++++++------------
 R/mapStats.R             |    4 +--
 R/nobsEach.R             |only
 R/plotStats.R            |   55 +++++++++++++++++++++++++++++++++++------------
 demo/map_examples.R      |   32 +++++++++++++++------------
 man/jiggleClass.Rd       |   43 ++++++++++++++++++++++++++++++------
 man/mapStats-internal.Rd |    9 ++++++-
 man/mapStats-package.Rd  |    2 -
 man/mapStats.Rd          |    4 ++-
 12 files changed, 186 insertions(+), 68 deletions(-)

More information about mapStats at CRAN
Permanent link

New package emg with initial version 1.0.6
Package: emg
Type: Package
Title: Exponentially Modified Gaussian (EMG) Distribution
Version: 1.0.6
Date: 2015-04-21
Author: Shawn Garbett, Mark Kozdoba
Maintainer: Shawn Garbett
Depends: R (>= 1.8.0), stats, stats4
Description: Provides basic distribution functions for a mixture model of a Gaussian and exponential distribution.
License: GPL-2
LazyLoad: yes
Packaged: 2015-04-22 05:09:58 UTC; sgarbett
NeedsCompilation: no
X-CRAN-Comment: Archived on 2014-08-19 as maintainer address bounced.
Repository: CRAN
Date/Publication: 2015-04-22 22:42:07

More information about emg at CRAN
Permanent link

New package discSurv with initial version 1.0.0
Package: discSurv
Version: 1.0.0
Title: Discrete Time Survival Analysis
Date: 2015-04-22
Author: Thomas Welchowski and Matthias Schmid
Maintainer: Thomas Welchowski
Description: Provides data transformations, estimation utilities, predictive evaluation measures and simulation functions for discrete time survival analysis.
Imports: functional, Matrix, matrixcalc, mvtnorm, numDeriv, caret, mgcv
Suggests: Ecdat, pec, survival, randomForest
License: GPL-3
LazyLoad: yes
Packaged: 2015-04-22 14:10:33 UTC; Welchowski
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 21:58:21

More information about discSurv at CRAN
Permanent link

New package cellranger with initial version 0.1.0
Package: cellranger
Title: Translate Spreadsheet Cell Ranges to Rows and Columns
Version: 0.1.0
Authors@R: c( person("Jennifer", "Bryan", , "jenny@stat.ubc.ca", c("cre", "aut")), person("Hadley", "Wickham", , "hadley@rstudio.com", "ctb") )
Description: Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
Depends: R (>= 3.0.0)
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/jennybc/cellranger
BugReports: https://github.com/jennybc/cellranger/issues
Suggests: testthat
Packaged: 2015-04-22 17:10:55 UTC; jenny
Author: Jennifer Bryan [cre, aut], Hadley Wickham [ctb]
Maintainer: Jennifer Bryan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-22 21:58:18

More information about cellranger at CRAN
Permanent link

Package broman updated to version 0.55-2 with previous version 0.48-2 dated 2014-05-07

Title: Karl Broman's R Code
Description: Miscellaneous R functions.
Author: Karl W Broman , with contributions from Aimee Teo Broman
Maintainer: Karl W Broman

Diff between broman versions 0.48-2 dated 2014-05-07 and 0.55-2 dated 2015-04-22

 broman-0.48-2/broman/R/get.R                  |only
 broman-0.48-2/broman/R/loadwork.R             |only
 broman-0.48-2/broman/inst/tests               |only
 broman-0.48-2/broman/man/attachwork.Rd        |only
 broman-0.48-2/broman/man/get0.Rd              |only
 broman-0.48-2/broman/man/loadwork.Rd          |only
 broman-0.48-2/broman/tests/run-all.R          |only
 broman-0.55-2/broman/DESCRIPTION              |   19 -
 broman-0.55-2/broman/MD5                      |  189 ++++++-----
 broman-0.55-2/broman/NAMESPACE                |   20 -
 broman-0.55-2/broman/R/arrowlocator.R         |   25 -
 broman-0.55-2/broman/R/attrnames.R            |only
 broman-0.55-2/broman/R/brocolors.R            |  433 +++++++++++++-------------
 broman-0.55-2/broman/R/cf.R                   |   14 
 broman-0.55-2/broman/R/colwalpha.R            |only
 broman-0.55-2/broman/R/convert2hex.R          |   55 ---
 broman-0.55-2/broman/R/errors2pushbullet.R    |only
 broman-0.55-2/broman/R/exit.R                 |only
 broman-0.55-2/broman/R/fisher.R               |   46 +-
 broman-0.55-2/broman/R/grayplot.R             |  231 +++++++------
 broman-0.55-2/broman/R/help.R                 |    7 
 broman-0.55-2/broman/R/histlines.R            |   30 -
 broman-0.55-2/broman/R/holmans_triangle.R     |  272 +++++++---------
 broman-0.55-2/broman/R/kbdate.R               |   16 
 broman-0.55-2/broman/R/lenuniq.R              |only
 broman-0.55-2/broman/R/loadfile.R             |only
 broman-0.55-2/broman/R/make.R                 |   28 +
 broman-0.55-2/broman/R/manyboxplot.R          |   85 ++---
 broman-0.55-2/broman/R/mypairs.R              |   37 +-
 broman-0.55-2/broman/R/myround.R              |   29 -
 broman-0.55-2/broman/R/normalize.R            |   41 +-
 broman-0.55-2/broman/R/note.R                 |only
 broman-0.55-2/broman/R/objectsizes.R          |   19 -
 broman-0.55-2/broman/R/pastedot.R             |   18 -
 broman-0.55-2/broman/R/permtest.R             |  124 +++----
 broman-0.55-2/broman/R/qr.R                   |   23 -
 broman-0.55-2/broman/R/quantileSE.R           |   25 -
 broman-0.55-2/broman/R/revrainbow.R           |    9 
 broman-0.55-2/broman/R/rmvn.R                 |   15 
 broman-0.55-2/broman/R/runningmean.R          |  160 ++++-----
 broman-0.55-2/broman/R/simp.R                 |   53 +--
 broman-0.55-2/broman/R/strwidth2lines.R       |    6 
 broman-0.55-2/broman/R/strwidth2xlim.R        |   22 -
 broman-0.55-2/broman/R/theme_karl.R           |only
 broman-0.55-2/broman/R/util.R                 |   11 
 broman-0.55-2/broman/R/venn_diagram.R         |  302 ++++++++----------
 broman-0.55-2/broman/R/winsorize.R            |   19 -
 broman-0.55-2/broman/R/xlimlabel.R            |   24 -
 broman-0.55-2/broman/README.md                |only
 broman-0.55-2/broman/inst/README.md           |only
 broman-0.55-2/broman/inst/STATUS.txt          |   86 ++++-
 broman-0.55-2/broman/man/arrowlocator.Rd      |    6 
 broman-0.55-2/broman/man/attachfile.Rd        |   16 
 broman-0.55-2/broman/man/attrnames.Rd         |only
 broman-0.55-2/broman/man/brocolors.Rd         |    6 
 broman-0.55-2/broman/man/bromanversion.Rd     |    6 
 broman-0.55-2/broman/man/cf.Rd                |    6 
 broman-0.55-2/broman/man/chisq.Rd             |    6 
 broman-0.55-2/broman/man/colwalpha.Rd         |only
 broman-0.55-2/broman/man/convert2hex.Rd       |    6 
 broman-0.55-2/broman/man/done.Rd              |only
 broman-0.55-2/broman/man/errors2pushbullet.Rd |only
 broman-0.55-2/broman/man/exit.Rd              |only
 broman-0.55-2/broman/man/fisher.Rd            |    6 
 broman-0.55-2/broman/man/grayplot.Rd          |   16 
 broman-0.55-2/broman/man/h.Rd                 |    6 
 broman-0.55-2/broman/man/hex2dec.Rd           |    3 
 broman-0.55-2/broman/man/histlines.Rd         |    6 
 broman-0.55-2/broman/man/kbdate.Rd            |    6 
 broman-0.55-2/broman/man/lenuniq.Rd           |only
 broman-0.55-2/broman/man/loadfile.Rd          |   16 
 broman-0.55-2/broman/man/make.Rd              |   16 
 broman-0.55-2/broman/man/manyboxplot.Rd       |    6 
 broman-0.55-2/broman/man/mypairs.Rd           |    6 
 broman-0.55-2/broman/man/myround.Rd           |    6 
 broman-0.55-2/broman/man/normalize.Rd         |    6 
 broman-0.55-2/broman/man/note.Rd              |only
 broman-0.55-2/broman/man/objectsizes.Rd       |    6 
 broman-0.55-2/broman/man/paired.perm.test.Rd  |    6 
 broman-0.55-2/broman/man/paste..Rd            |    6 
 broman-0.55-2/broman/man/paste00.Rd           |    6 
 broman-0.55-2/broman/man/perm.test.Rd         |    6 
 broman-0.55-2/broman/man/plot_crayons.Rd      |   21 -
 broman-0.55-2/broman/man/qqline2.Rd           |    3 
 broman-0.55-2/broman/man/qr2.Rd               |    6 
 broman-0.55-2/broman/man/quantileSE.Rd        |    6 
 broman-0.55-2/broman/man/revrainbow.Rd        |    6 
 broman-0.55-2/broman/man/rmvn.Rd              |    6 
 broman-0.55-2/broman/man/runningmean.Rd       |    3 
 broman-0.55-2/broman/man/runningratio.Rd      |    3 
 broman-0.55-2/broman/man/simp.Rd              |    6 
 broman-0.55-2/broman/man/strwidth2lines.Rd    |    3 
 broman-0.55-2/broman/man/strwidth2xlim.Rd     |    3 
 broman-0.55-2/broman/man/theme_karl.Rd        |only
 broman-0.55-2/broman/man/triarrow.Rd          |    6 
 broman-0.55-2/broman/man/trilines.Rd          |    6 
 broman-0.55-2/broman/man/triplot.Rd           |    6 
 broman-0.55-2/broman/man/tripoints.Rd         |    6 
 broman-0.55-2/broman/man/venn.Rd              |    6 
 broman-0.55-2/broman/man/winsorize.Rd         |    6 
 broman-0.55-2/broman/man/xlimlabel.Rd         |    3 
 broman-0.55-2/broman/src/normalize.c          |  134 ++++----
 broman-0.55-2/broman/src/runningmean.c        |  148 ++++----
 broman-0.55-2/broman/tests/testthat           |only
 broman-0.55-2/broman/tests/testthat.R         |only
 105 files changed, 1514 insertions(+), 1547 deletions(-)

More information about broman at CRAN
Permanent link

Package sjPlot updated to version 1.8 with previous version 1.7 dated 2015-03-11

Title: Data Visualization for Statistics in Social Science
Description: Collection of several plotting and table output functions for visualizing data.
Author: Daniel Lüdecke
Maintainer: Daniel Lüdecke

Diff between sjPlot versions 1.7 dated 2015-03-11 and 1.8 dated 2015-04-22

 sjPlot-1.7/sjPlot/R/efc.R                    |only
 sjPlot-1.7/sjPlot/R/sjImportSPSS.R           |only
 sjPlot-1.7/sjPlot/R/sjRecode.R               |only
 sjPlot-1.7/sjPlot/R/sjStatistics.R           |only
 sjPlot-1.7/sjPlot/data                       |only
 sjPlot-1.7/sjPlot/man/chisq_gof.Rd           |only
 sjPlot-1.7/sjPlot/man/cramer.Rd              |only
 sjPlot-1.7/sjPlot/man/cronb.Rd               |only
 sjPlot-1.7/sjPlot/man/dicho.Rd               |only
 sjPlot-1.7/sjPlot/man/efc.Rd                 |only
 sjPlot-1.7/sjPlot/man/efc2.Rd                |only
 sjPlot-1.7/sjPlot/man/efc3.Rd                |only
 sjPlot-1.7/sjPlot/man/eta_sq.Rd              |only
 sjPlot-1.7/sjPlot/man/get_val_labels.Rd      |only
 sjPlot-1.7/sjPlot/man/get_var_labels.Rd      |only
 sjPlot-1.7/sjPlot/man/group_labels.Rd        |only
 sjPlot-1.7/sjPlot/man/group_str.Rd           |only
 sjPlot-1.7/sjPlot/man/group_var.Rd           |only
 sjPlot-1.7/sjPlot/man/levene_test.Rd         |only
 sjPlot-1.7/sjPlot/man/mean_n.Rd              |only
 sjPlot-1.7/sjPlot/man/mic.Rd                 |only
 sjPlot-1.7/sjPlot/man/mwu.Rd                 |only
 sjPlot-1.7/sjPlot/man/phi.Rd                 |only
 sjPlot-1.7/sjPlot/man/read_sas.Rd            |only
 sjPlot-1.7/sjPlot/man/read_spss.Rd           |only
 sjPlot-1.7/sjPlot/man/read_stata.Rd          |only
 sjPlot-1.7/sjPlot/man/recode_to.Rd           |only
 sjPlot-1.7/sjPlot/man/reliab_test.Rd         |only
 sjPlot-1.7/sjPlot/man/set_na.Rd              |only
 sjPlot-1.7/sjPlot/man/set_val_labels.Rd      |only
 sjPlot-1.7/sjPlot/man/set_var_labels.Rd      |only
 sjPlot-1.7/sjPlot/man/std_beta.Rd            |only
 sjPlot-1.7/sjPlot/man/std_e.Rd               |only
 sjPlot-1.7/sjPlot/man/str_pos.Rd             |only
 sjPlot-1.7/sjPlot/man/table_values.Rd        |only
 sjPlot-1.7/sjPlot/man/to_fac.Rd              |only
 sjPlot-1.7/sjPlot/man/to_label.Rd            |only
 sjPlot-1.7/sjPlot/man/to_sjPlot.Rd           |only
 sjPlot-1.7/sjPlot/man/to_value.Rd            |only
 sjPlot-1.7/sjPlot/man/weight.Rd              |only
 sjPlot-1.7/sjPlot/man/weight2.Rd             |only
 sjPlot-1.7/sjPlot/man/word_wrap.Rd           |only
 sjPlot-1.7/sjPlot/man/write_spss.Rd          |only
 sjPlot-1.7/sjPlot/man/write_stata.Rd         |only
 sjPlot-1.8/sjPlot/DESCRIPTION                |   20 
 sjPlot-1.8/sjPlot/MD5                        |  214 -
 sjPlot-1.8/sjPlot/NAMESPACE                  |   43 
 sjPlot-1.8/sjPlot/NEWS                       |   48 
 sjPlot-1.8/sjPlot/R/helpfunctions.R          | 1373 +++++-----
 sjPlot-1.8/sjPlot/R/sjPlotAncovaLSMeans.R    | 1025 +++++---
 sjPlot-1.8/sjPlot/R/sjPlotAnova.R            | 1046 ++++----
 sjPlot-1.8/sjPlot/R/sjPlotClusterAnalysis.R  | 1786 ++++++--------
 sjPlot-1.8/sjPlot/R/sjPlotCorr.R             |   37 
 sjPlot-1.8/sjPlot/R/sjPlotDist.R             | 1088 ++++----
 sjPlot-1.8/sjPlot/R/sjPlotFrequencies.R      |  465 +--
 sjPlot-1.8/sjPlot/R/sjPlotGLME.R             | 3393 ++++++++++++++-------------
 sjPlot-1.8/sjPlot/R/sjPlotGroupFrequencies.R | 2449 +++++++++----------
 sjPlot-1.8/sjPlot/R/sjPlotInteractions.R     | 1261 +++++++---
 sjPlot-1.8/sjPlot/R/sjPlotLikert.R           |  169 -
 sjPlot-1.8/sjPlot/R/sjPlotLinreg.R           | 1836 +++++++-------
 sjPlot-1.8/sjPlot/R/sjPlotLinregMultiple.R   |  808 +++---
 sjPlot-1.8/sjPlot/R/sjPlotOdds.R             |  299 +-
 sjPlot-1.8/sjPlot/R/sjPlotOddsMultiple.R     |  190 -
 sjPlot-1.8/sjPlot/R/sjPlotPCA.R              |  206 +
 sjPlot-1.8/sjPlot/R/sjPlotPearsonsChi2Test.R |  295 +-
 sjPlot-1.8/sjPlot/R/sjPlotPropTable.R        |  434 +--
 sjPlot-1.8/sjPlot/R/sjPlotScatter.R          |  660 ++---
 sjPlot-1.8/sjPlot/R/sjPlotSetTheme.R         | 1615 ++++++------
 sjPlot-1.8/sjPlot/R/sjPlotStackFrequencies.R |  260 +-
 sjPlot-1.8/sjPlot/R/sjTabCorr.R              | 1069 ++++----
 sjPlot-1.8/sjPlot/R/sjTabDataFrame.R         |  179 -
 sjPlot-1.8/sjPlot/R/sjTabFrequencies.R       |  103 
 sjPlot-1.8/sjPlot/R/sjTabGrpmean.R           |   42 
 sjPlot-1.8/sjPlot/R/sjTabItemAnalysis.R      |  110 
 sjPlot-1.8/sjPlot/R/sjTabLinReg.R            |  312 +-
 sjPlot-1.8/sjPlot/R/sjTabMannWhitney.R       |only
 sjPlot-1.8/sjPlot/R/sjTabOdds.R              |  155 -
 sjPlot-1.8/sjPlot/R/sjTabPCA.R               |   99 
 sjPlot-1.8/sjPlot/R/sjTabPropTable.R         |  291 --
 sjPlot-1.8/sjPlot/R/sjTabSPSS.R              |   84 
 sjPlot-1.8/sjPlot/R/sjTabStackFrq.R          |  237 +
 sjPlot-1.8/sjPlot/R/zzz.R                    |only
 sjPlot-1.8/sjPlot/README.md                  |   75 
 sjPlot-1.8/sjPlot/man/adjust_plot_range.Rd   |    5 
 sjPlot-1.8/sjPlot/man/dist_chisq.Rd          |    2 
 sjPlot-1.8/sjPlot/man/dist_f.Rd              |    2 
 sjPlot-1.8/sjPlot/man/dist_norm.Rd           |    2 
 sjPlot-1.8/sjPlot/man/dist_t.Rd              |    2 
 sjPlot-1.8/sjPlot/man/sj.setGeomColors.Rd    |    2 
 sjPlot-1.8/sjPlot/man/sjPlot-package.Rd      |   26 
 sjPlot-1.8/sjPlot/man/sjc.cluster.Rd         |   12 
 sjPlot-1.8/sjPlot/man/sjc.dend.Rd            |    7 
 sjPlot-1.8/sjPlot/man/sjc.elbow.Rd           |    8 
 sjPlot-1.8/sjPlot/man/sjc.grpdisc.Rd         |    7 
 sjPlot-1.8/sjPlot/man/sjc.kgap.Rd            |    2 
 sjPlot-1.8/sjPlot/man/sjc.qclus.Rd           |   12 
 sjPlot-1.8/sjPlot/man/sjp.aov1.Rd            |   14 
 sjPlot-1.8/sjPlot/man/sjp.chi2.Rd            |    4 
 sjPlot-1.8/sjPlot/man/sjp.corr.Rd            |    5 
 sjPlot-1.8/sjPlot/man/sjp.emm.int.Rd         |  106 
 sjPlot-1.8/sjPlot/man/sjp.frq.Rd             |   19 
 sjPlot-1.8/sjPlot/man/sjp.glm.Rd             |   21 
 sjPlot-1.8/sjPlot/man/sjp.glmer.Rd           |  428 +--
 sjPlot-1.8/sjPlot/man/sjp.glmm.Rd            |   54 
 sjPlot-1.8/sjPlot/man/sjp.grpfrq.Rd          |   23 
 sjPlot-1.8/sjPlot/man/sjp.int.Rd             |  268 +-
 sjPlot-1.8/sjPlot/man/sjp.likert.Rd          |   69 
 sjPlot-1.8/sjPlot/man/sjp.lm.Rd              |   23 
 sjPlot-1.8/sjPlot/man/sjp.lmer.Rd            |  395 +--
 sjPlot-1.8/sjPlot/man/sjp.lmm.Rd             |   53 
 sjPlot-1.8/sjPlot/man/sjp.pca.Rd             |   82 
 sjPlot-1.8/sjPlot/man/sjp.scatter.Rd         |   13 
 sjPlot-1.8/sjPlot/man/sjp.setTheme.Rd        |   26 
 sjPlot-1.8/sjPlot/man/sjp.stackfrq.Rd        |   77 
 sjPlot-1.8/sjPlot/man/sjp.xtab.Rd            |   73 
 sjPlot-1.8/sjPlot/man/sjt.corr.Rd            |  377 +--
 sjPlot-1.8/sjPlot/man/sjt.df.Rd              |  309 +-
 sjPlot-1.8/sjPlot/man/sjt.frq.Rd             |  453 +--
 sjPlot-1.8/sjPlot/man/sjt.glm.Rd             |  673 ++---
 sjPlot-1.8/sjPlot/man/sjt.grpmean.Rd         |    7 
 sjPlot-1.8/sjPlot/man/sjt.itemanalysis.Rd    |  396 +--
 sjPlot-1.8/sjPlot/man/sjt.lm.Rd              |  827 +++---
 sjPlot-1.8/sjPlot/man/sjt.mwu.Rd             |only
 sjPlot-1.8/sjPlot/man/sjt.pca.Rd             |  396 +--
 sjPlot-1.8/sjPlot/man/sjt.stackfrq.Rd        |  430 +--
 sjPlot-1.8/sjPlot/man/sjt.xtab.Rd            |  461 +--
 sjPlot-1.8/sjPlot/man/view_spss.Rd           |  255 +-
 sjPlot-1.8/sjPlot/tests                      |only
 128 files changed, 15652 insertions(+), 14550 deletions(-)

More information about sjPlot at CRAN
Permanent link

Package RadOnc updated to version 1.1.0 with previous version 1.0.9 dated 2014-11-21

Title: Analytical Tools for Radiation Oncology
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from Varian's 'Eclipse' platform and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson
Maintainer: Reid F. Thompson

Diff between RadOnc versions 1.0.9 dated 2014-11-21 and 1.1.0 dated 2015-04-22

 RadOnc-1.0.9/RadOnc/R/getStructureList.R     |only
 RadOnc-1.0.9/RadOnc/build                    |only
 RadOnc-1.0.9/RadOnc/inst/doc/RadOnc.R        |only
 RadOnc-1.0.9/RadOnc/inst/doc/RadOnc.Rnw      |only
 RadOnc-1.0.9/RadOnc/man/getStructureList.Rd  |only
 RadOnc-1.1.0/RadOnc/DESCRIPTION              |   12 -
 RadOnc-1.1.0/RadOnc/MD5                      |   39 ++----
 RadOnc-1.1.0/RadOnc/NAMESPACE                |    2 
 RadOnc-1.1.0/RadOnc/R/CLASSES.R              |    2 
 RadOnc-1.1.0/RadOnc/R/DVH.R                  |   40 +++++-
 RadOnc-1.1.0/RadOnc/R/convert.DVH.R          |   72 +++++++----
 RadOnc-1.1.0/RadOnc/R/mean.DVH.R             |   28 ----
 RadOnc-1.1.0/RadOnc/R/plot.DVH.R             |   18 +-
 RadOnc-1.1.0/RadOnc/R/read.DICOM.RT.R        |    3 
 RadOnc-1.1.0/RadOnc/R/read.DVH.R             |  166 ++++++++++++++++++++-------
 RadOnc-1.1.0/RadOnc/R/subset.R               |only
 RadOnc-1.1.0/RadOnc/inst/NEWS.Rd             |   46 +++++++
 RadOnc-1.1.0/RadOnc/inst/doc/RadOnc.pdf      |binary
 RadOnc-1.1.0/RadOnc/man/DVH-class.Rd         |    2 
 RadOnc-1.1.0/RadOnc/man/DVH.list-class.Rd    |    4 
 RadOnc-1.1.0/RadOnc/man/plot-methods.Rd      |    5 
 RadOnc-1.1.0/RadOnc/man/structure3D-class.Rd |    7 -
 RadOnc-1.1.0/RadOnc/man/subset.Rd            |only
 RadOnc-1.1.0/RadOnc/vignettes/RadOnc.Rnw     |   35 +++--
 24 files changed, 328 insertions(+), 153 deletions(-)

More information about RadOnc at CRAN
Permanent link

Package MRIaggr updated to version 1.1 with previous version 1.0 dated 2015-03-10

Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne

Diff between MRIaggr versions 1.0 dated 2015-03-10 and 1.1 dated 2015-04-22

 MRIaggr-1.0/MRIaggr/man/calcCriteriaGR.Rd              |only
 MRIaggr-1.0/MRIaggr/man/calcRegionalIntensity.Rd       |only
 MRIaggr-1.0/MRIaggr/man/calcSigmaGR.Rd                 |only
 MRIaggr-1.0/MRIaggr/man/constSweave.Rd                 |only
 MRIaggr-1.1/MRIaggr/DESCRIPTION                        |   13 
 MRIaggr-1.1/MRIaggr/MD5                                |  141 +-
 MRIaggr-1.1/MRIaggr/NAMESPACE                          |   14 
 MRIaggr-1.1/MRIaggr/R/Associated_functions.R           | 1161 +++++++++--------
 MRIaggr-1.1/MRIaggr/R/Class_Carto3D.R                  |   63 
 MRIaggr-1.1/MRIaggr/R/Class_MRIaggr.R                  |  963 ++++++++------
 MRIaggr-1.1/MRIaggr/R/GR_functions.R                   |  440 +++---
 MRIaggr-1.1/MRIaggr/R/Generic_functions.R              |   23 
 MRIaggr-1.1/MRIaggr/R/RcppExports.R                    |    4 
 MRIaggr-1.1/MRIaggr/data/MRIaggr.Pat1_red.RData        |binary
 MRIaggr-1.1/MRIaggr/demo/Analysis.R                    |    6 
 MRIaggr-1.1/MRIaggr/demo/preProcessing.R               |   13 
 MRIaggr-1.1/MRIaggr/inst/List_of_arguments.R           |  804 ++++++-----
 MRIaggr-1.1/MRIaggr/inst/NEWS                          |only
 MRIaggr-1.1/MRIaggr/inst/TODO                          |only
 MRIaggr-1.1/MRIaggr/inst/Tests/Test2-1_IRMaggr.R       |   30 
 MRIaggr-1.1/MRIaggr/inst/Tests/Test2-3_fctsAssociees.R |   39 
 MRIaggr-1.1/MRIaggr/inst/Tests/Test2-4_fctsGR.R        |   14 
 MRIaggr-1.1/MRIaggr/inst/calcCriteriaGR.Rd             |only
 MRIaggr-1.1/MRIaggr/inst/calcSigmaGR.Rd                |only
 MRIaggr-1.1/MRIaggr/man/Carto3D-class.Rd               |   26 
 MRIaggr-1.1/MRIaggr/man/Carto3D2MRIaggr.Rd             |   11 
 MRIaggr-1.1/MRIaggr/man/EDK.Rd                         |    6 
 MRIaggr-1.1/MRIaggr/man/MRIaggr-class.Rd               |   61 
 MRIaggr-1.1/MRIaggr/man/affectContrast.Rd              |    8 
 MRIaggr-1.1/MRIaggr/man/affectDescStats.Rd             |    3 
 MRIaggr-1.1/MRIaggr/man/affectHemisphere.Rd            |    6 
 MRIaggr-1.1/MRIaggr/man/array2df.Rd                    |    4 
 MRIaggr-1.1/MRIaggr/man/calcAUPRC.Rd                   |    3 
 MRIaggr-1.1/MRIaggr/man/calcBrainMask.Rd               |    6 
 MRIaggr-1.1/MRIaggr/man/calcDistMask.Rd                |    5 
 MRIaggr-1.1/MRIaggr/man/calcFilter.Rd                  |   19 
 MRIaggr-1.1/MRIaggr/man/calcGR.Rd                      |    5 
 MRIaggr-1.1/MRIaggr/man/calcGroupsMask.Rd              |   13 
 MRIaggr-1.1/MRIaggr/man/calcGroupsW.Rd                 |    4 
 MRIaggr-1.1/MRIaggr/man/calcHemi_cpp.Rd                |   17 
 MRIaggr-1.1/MRIaggr/man/calcHemisphere.Rd              |    7 
 MRIaggr-1.1/MRIaggr/man/calcROCthreshold.Rd            |    3 
 MRIaggr-1.1/MRIaggr/man/calcRegionaContrast.Rd         |only
 MRIaggr-1.1/MRIaggr/man/calcSmoothMask.Rd              |    4 
 MRIaggr-1.1/MRIaggr/man/calcTableHypoReperf.Rd         |    2 
 MRIaggr-1.1/MRIaggr/man/calcThresholdMRIaggr.Rd        |   16 
 MRIaggr-1.1/MRIaggr/man/calcTissueType.Rd              |   13 
 MRIaggr-1.1/MRIaggr/man/calcW.Rd                       |   18 
 MRIaggr-1.1/MRIaggr/man/constCarto3D.Rd                |    7 
 MRIaggr-1.1/MRIaggr/man/constCompressMRIaggr.Rd        |    2 
 MRIaggr-1.1/MRIaggr/man/constLatex.Rd                  |only
 MRIaggr-1.1/MRIaggr/man/constMRIaggr.Rd                |   51 
 MRIaggr-1.1/MRIaggr/man/constReduceMRIaggr.Rd          |    4 
 MRIaggr-1.1/MRIaggr/man/df2array.Rd                    |   15 
 MRIaggr-1.1/MRIaggr/man/heatmapMRIaggr.Rd              |    3 
 MRIaggr-1.1/MRIaggr/man/initConstLatex.Rd              |only
 MRIaggr-1.1/MRIaggr/man/initFilter.Rd                  |    2 
 MRIaggr-1.1/MRIaggr/man/initMask.Rd                    |only
 MRIaggr-1.1/MRIaggr/man/initParameter.Rd               |    2 
 MRIaggr-1.1/MRIaggr/man/multiplot.Rd                   |   10 
 MRIaggr-1.1/MRIaggr/man/outline.Rd                     |    2 
 MRIaggr-1.1/MRIaggr/man/outlineMRIaggr.Rd              |    2 
 MRIaggr-1.1/MRIaggr/man/readMRI.Rd                     |   43 
 MRIaggr-1.1/MRIaggr/man/selectContrast.Rd              |   15 
 MRIaggr-1.1/MRIaggr/man/selectCoords.Rd                |   11 
 MRIaggr-1.1/MRIaggr/man/selectDefault_value.Rd         |    4 
 MRIaggr-1.1/MRIaggr/man/selectDescStats.Rd             |    5 
 MRIaggr-1.1/MRIaggr/man/selectHemispheres.Rd           |    4 
 MRIaggr-1.1/MRIaggr/man/selectHistory.Rd               |    2 
 MRIaggr-1.1/MRIaggr/man/selectIdentifier.Rd            |    4 
 MRIaggr-1.1/MRIaggr/man/selectN.Rd                     |    3 
 MRIaggr-1.1/MRIaggr/man/selectParameter.Rd             |    4 
 MRIaggr-1.1/MRIaggr/man/selectVoxelDim.Rd              |    4 
 MRIaggr-1.1/MRIaggr/man/summary.MRIaggr.Rd             |    8 
 MRIaggr-1.1/MRIaggr/man/writeMRI.Rd                    |only
 MRIaggr-1.1/MRIaggr/man/writeMRIaggr.Rd                |only
 MRIaggr-1.1/MRIaggr/src/Associated_functions.cpp       |  172 +-
 MRIaggr-1.1/MRIaggr/src/RcppExports.cpp                |   19 
 MRIaggr-1.1/MRIaggr/tests                              |only
 79 files changed, 2444 insertions(+), 1942 deletions(-)

More information about MRIaggr at CRAN
Permanent link

Package QuantifQuantile updated to version 2.0 with previous version 1.0 dated 2014-08-28

Title: Estimation of Conditional Quantiles using Optimal Quantization
Description: Estimation of conditional quantiles using optimal quantization. Construction of an optimal grid of N quantizers, estimation of conditional quantiles and data driven selection of the size N of the grid. Graphical illustrations for the selection of N and of resulting estimated curves or surfaces when the dimension of the covariate is one or two.
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier

Diff between QuantifQuantile versions 1.0 dated 2014-08-28 and 2.0 dated 2015-04-22

 QuantifQuantile-1.0/QuantifQuantile/R/plot.select.N.QuantifQuantile.R    |only
 QuantifQuantile-1.0/QuantifQuantile/man/plot.select.N.QuantifQuantile.Rd |only
 QuantifQuantile-2.0/QuantifQuantile/DESCRIPTION                          |   12 
 QuantifQuantile-2.0/QuantifQuantile/MD5                                  |   30 -
 QuantifQuantile-2.0/QuantifQuantile/NAMESPACE                            |    5 
 QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.R                  |   43 +-
 QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.d.R                |   39 +-
 QuantifQuantile-2.0/QuantifQuantile/R/QuantifQuantile.d2.R               |   36 +-
 QuantifQuantile-2.0/QuantifQuantile/R/plot.QuantifQuantile.R             |  165 +++++++---
 QuantifQuantile-2.0/QuantifQuantile/R/print.QuantifQuantile.R            |   50 +--
 QuantifQuantile-2.0/QuantifQuantile/R/summary.QuantifQuantile.R          |    8 
 QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.Rd               |   22 -
 QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.d.Rd             |   19 -
 QuantifQuantile-2.0/QuantifQuantile/man/QuantifQuantile.d2.Rd            |   19 -
 QuantifQuantile-2.0/QuantifQuantile/man/plot.QuantifQuantile.Rd          |   37 +-
 QuantifQuantile-2.0/QuantifQuantile/man/print.QuantifQuantile.Rd         |    4 
 QuantifQuantile-2.0/QuantifQuantile/man/summary.QuantifQuantile.Rd       |    6 
 17 files changed, 306 insertions(+), 189 deletions(-)

More information about QuantifQuantile at CRAN
Permanent link

Package mclust updated to version 5.0.1 with previous version 5.0.0 dated 2015-04-09

Title: Normal Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut], Adrian E. Raftery [aut], Luca Scrucca [aut, cre], Thomas Brendan Murphy [ctb], Michael Fop [ctb]
Maintainer: Luca Scrucca

Diff between mclust versions 5.0.0 dated 2015-04-09 and 5.0.1 dated 2015-04-22

 DESCRIPTION                             |   10 +-
 MD5                                     |   42 +++++-----
 NAMESPACE                               |    7 +
 R/clustCombi.R                          |    9 +-
 R/init.R                                |  126 ++++++++++++++++----------------
 R/mclust.R                              |    7 -
 R/mclustda.R                            |    4 +
 build/vignette.rds                      |binary
 data/Baudry_etal_2010_JCGS_examples.rda |binary
 data/GvHD.rda                           |binary
 data/acidity.rda                        |binary
 data/chevron.rda                        |binary
 data/cross.rda                          |binary
 data/diabetes.rda                       |binary
 data/thyroid.rda                        |binary
 data/wreath.rda                         |binary
 inst/NEWS                               |    8 +-
 man/entPlot.Rd                          |    4 -
 man/hc.Rd                               |    7 +
 man/mclustModelNames.Rd                 |    5 +
 man/randomPairs.Rd                      |    4 -
 src/mclust.f                            |    2 
 22 files changed, 124 insertions(+), 111 deletions(-)

More information about mclust at CRAN
Permanent link

Package logmult updated to version 0.6.2 with previous version 0.6.1 dated 2015-01-13

Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using gnm, with support for convenient printing, plots, and jackknife/bootstrap standard errors. For complex survey data, models can be fitted from design objects from the 'survey' package. Currently supported models include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative layer effect model (Xie), and several association models: Goodman's row-column association models of the RC(M) and RC(M)-L families with one or several dimensions; two skew-symmetric association models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat

Diff between logmult versions 0.6.1 dated 2015-01-13 and 0.6.2 dated 2015-04-22

 DESCRIPTION |    8 +++---
 MD5         |    6 ++--
 NEWS        |    3 ++
 R/yrcskew.R |   75 +++++++++++++++++++++++++++++++-----------------------------
 4 files changed, 49 insertions(+), 43 deletions(-)

More information about logmult at CRAN
Permanent link

Package gnm updated to version 1.0-8 with previous version 1.0-7 dated 2014-01-02

Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Author: Heather Turner [aut, cre], David Firth [aut], Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Martin Maechler [ctb]
Maintainer: Heather Turner

Diff between gnm versions 1.0-7 dated 2014-01-02 and 1.0-8 dated 2015-04-22

 gnm-1.0-7/gnm/data/House2001.csv.gz         |only
 gnm-1.0-7/gnm/data/backPain.txt.gz          |only
 gnm-1.0-7/gnm/data/barley.csv.gz            |only
 gnm-1.0-7/gnm/data/barley.txt.gz            |only
 gnm-1.0-7/gnm/data/mentalHealth.txt.gz      |only
 gnm-1.0-7/gnm/data/voting.txt.gz            |only
 gnm-1.0-7/gnm/data/wheat.txt.gz             |only
 gnm-1.0-8/gnm/DESCRIPTION                   |   38 +-
 gnm-1.0-8/gnm/MD5                           |  374 +++++++++++++---------------
 gnm-1.0-8/gnm/R/Const.R                     |   15 +
 gnm-1.0-8/gnm/R/Diag.R                      |   15 +
 gnm-1.0-8/gnm/R/Dref.R                      |   15 +
 gnm-1.0-8/gnm/R/DrefWeights.R               |   15 +
 gnm-1.0-8/gnm/R/Exp.R                       |   15 +
 gnm-1.0-8/gnm/R/Inv.R                       |   15 +
 gnm-1.0-8/gnm/R/Log.R                       |   15 +
 gnm-1.0-8/gnm/R/Logistic.R                  |   15 +
 gnm-1.0-8/gnm/R/Logit.R                     |   15 +
 gnm-1.0-8/gnm/R/MPinv.R                     |   15 +
 gnm-1.0-8/gnm/R/Mult.R                      |   15 +
 gnm-1.0-8/gnm/R/MultHomog.R                 |   15 +
 gnm-1.0-8/gnm/R/Raise.R                     |   15 +
 gnm-1.0-8/gnm/R/Symm.R                      |   15 +
 gnm-1.0-8/gnm/R/Topo.R                      |   15 +
 gnm-1.0-8/gnm/R/add1.gnm.R                  |   23 +
 gnm-1.0-8/gnm/R/addterm.gnm.R               |   15 +
 gnm-1.0-8/gnm/R/alias.gnm.R                 |   15 +
 gnm-1.0-8/gnm/R/anova.gnm.R                 |   21 +
 gnm-1.0-8/gnm/R/asGnm.R                     |   15 +
 gnm-1.0-8/gnm/R/asGnm.default.R             |   15 +
 gnm-1.0-8/gnm/R/asGnm.glm.R                 |   15 +
 gnm-1.0-8/gnm/R/asGnm.lm.R                  |   15 +
 gnm-1.0-8/gnm/R/boxcox.gnm.R                |   15 +
 gnm-1.0-8/gnm/R/checkCall.R                 |   15 +
 gnm-1.0-8/gnm/R/checkEstimable.R            |   21 +
 gnm-1.0-8/gnm/R/cholInv.R                   |   15 +
 gnm-1.0-8/gnm/R/coef.gnm.R                  |   15 +
 gnm-1.0-8/gnm/R/confint.gnm.R               |   24 +
 gnm-1.0-8/gnm/R/confint.profile.gnm.R       |   18 +
 gnm-1.0-8/gnm/R/cooks.distance.gnm.R        |   18 +
 gnm-1.0-8/gnm/R/dfbeta.gnm.R                |   15 +
 gnm-1.0-8/gnm/R/dfbetas.gnm.R               |   15 +
 gnm-1.0-8/gnm/R/drop1.gnm.R                 |   23 +
 gnm-1.0-8/gnm/R/dropterm.gnm.R              |   15 +
 gnm-1.0-8/gnm/R/dummy.coef.gnm.R            |   17 +
 gnm-1.0-8/gnm/R/effects.gnm.R               |   15 +
 gnm-1.0-8/gnm/R/exitInfo.R                  |   15 +
 gnm-1.0-8/gnm/R/expandCategorical.R         |   57 ++--
 gnm-1.0-8/gnm/R/fitted.gnm.R                |   15 +
 gnm-1.0-8/gnm/R/getContrasts.R              |   17 +
 gnm-1.0-8/gnm/R/getData.R                   |   19 +
 gnm-1.0-8/gnm/R/glm.fit.e.R                 |   64 ++--
 gnm-1.0-8/gnm/R/gnm-defunct.R               |   15 +
 gnm-1.0-8/gnm/R/gnm.R                       |   43 ++-
 gnm-1.0-8/gnm/R/gnmFit.R                    |   21 +
 gnm-1.0-8/gnm/R/gnmStart.R                  |   15 +
 gnm-1.0-8/gnm/R/gnmTerms.R                  |   17 +
 gnm-1.0-8/gnm/R/gnmTools.R                  |   27 +-
 gnm-1.0-8/gnm/R/grp.sum.R                   |   15 +
 gnm-1.0-8/gnm/R/hashSplit.R                 |   15 +
 gnm-1.0-8/gnm/R/hatvalues.gnm.R             |   20 +
 gnm-1.0-8/gnm/R/influence.gnm.R             |   17 +
 gnm-1.0-8/gnm/R/instances.R                 |   15 +
 gnm-1.0-8/gnm/R/kappa.gnm.R                 |   17 +
 gnm-1.0-8/gnm/R/labels.gnm.R                |   15 +
 gnm-1.0-8/gnm/R/logtrans.gnm.R              |   15 +
 gnm-1.0-8/gnm/R/meanResiduals.R             |   24 +
 gnm-1.0-8/gnm/R/model.frame.gnm.R           |   30 +-
 gnm-1.0-8/gnm/R/model.matrix.gnm.R          |   15 +
 gnm-1.0-8/gnm/R/naToZero.R                  |   15 +
 gnm-1.0-8/gnm/R/nonlinTerms.R               |   15 +
 gnm-1.0-8/gnm/R/ofInterest.R                |   15 +
 gnm-1.0-8/gnm/R/ofInterestReplacement.R     |   17 +
 gnm-1.0-8/gnm/R/parameters.R                |   15 +
 gnm-1.0-8/gnm/R/pickCoef.R                  |   17 +
 gnm-1.0-8/gnm/R/plot.gnm.R                  |   18 +
 gnm-1.0-8/gnm/R/plot.profile.gnm.R          |   26 +
 gnm-1.0-8/gnm/R/pprod.R                     |   15 +
 gnm-1.0-8/gnm/R/prattle.R                   |   15 +
 gnm-1.0-8/gnm/R/predict.gnm.R               |  129 ++++++---
 gnm-1.0-8/gnm/R/print.coef.gnm.R            |   15 +
 gnm-1.0-8/gnm/R/print.gnm.R                 |   15 +
 gnm-1.0-8/gnm/R/print.meanResiduals.R       |   16 +
 gnm-1.0-8/gnm/R/print.profile.gnm.R         |   15 +
 gnm-1.0-8/gnm/R/print.summary.gnm.R         |   27 +-
 gnm-1.0-8/gnm/R/print.vcov.gnm.R            |   15 +
 gnm-1.0-8/gnm/R/profile.gnm.R               |   24 +
 gnm-1.0-8/gnm/R/proj.gnm.R                  |   17 +
 gnm-1.0-8/gnm/R/psum.R                      |   15 +
 gnm-1.0-8/gnm/R/quick.glm.fit.R             |   17 +
 gnm-1.0-8/gnm/R/quickRank.R                 |   21 +
 gnm-1.0-8/gnm/R/residSVD.R                  |   15 +
 gnm-1.0-8/gnm/R/residuals.gnm.R             |   31 +-
 gnm-1.0-8/gnm/R/rstandard.gnm.R             |   15 +
 gnm-1.0-8/gnm/R/rstudent.gnm.R              |   17 +
 gnm-1.0-8/gnm/R/se.R                        |   15 +
 gnm-1.0-8/gnm/R/sumExpression.R             |   15 +
 gnm-1.0-8/gnm/R/summary.gnm.R               |   34 ++
 gnm-1.0-8/gnm/R/summary.meanResiduals.R     |   15 +
 gnm-1.0-8/gnm/R/termPredictors.R            |   15 +
 gnm-1.0-8/gnm/R/termPredictors.default.R    |   15 +
 gnm-1.0-8/gnm/R/termPredictors.gnm.R        |   15 +
 gnm-1.0-8/gnm/R/unlistOneLevel.R            |   15 +
 gnm-1.0-8/gnm/R/update.gnm.R                |   18 +
 gnm-1.0-8/gnm/R/updateLinear.R              |   15 +
 gnm-1.0-8/gnm/R/variable.names.gnm.R        |   15 +
 gnm-1.0-8/gnm/R/vcov.gnm.R                  |   18 +
 gnm-1.0-8/gnm/R/wedderburn.R                |   34 +-
 gnm-1.0-8/gnm/R/weighted.MM.R               |   15 +
 gnm-1.0-8/gnm/R/weights.gnm.R               |   15 +
 gnm-1.0-8/gnm/build                         |only
 gnm-1.0-8/gnm/data/House2001.rda            |binary
 gnm-1.0-8/gnm/data/backPain.rda             |binary
 gnm-1.0-8/gnm/data/barley.rda               |binary
 gnm-1.0-8/gnm/data/barleyHeights.rda        |binary
 gnm-1.0-8/gnm/data/cautres.rda              |binary
 gnm-1.0-8/gnm/data/erikson.rda              |binary
 gnm-1.0-8/gnm/data/friend.rda               |binary
 gnm-1.0-8/gnm/data/mentalHealth.rda         |binary
 gnm-1.0-8/gnm/data/voting.rda               |binary
 gnm-1.0-8/gnm/data/wheat.rda                |binary
 gnm-1.0-8/gnm/data/yaish.rda                |binary
 gnm-1.0-8/gnm/demo/gnm.R                    |   23 -
 gnm-1.0-8/gnm/inst/NEWS                     |   37 ++
 gnm-1.0-8/gnm/inst/doc/gnmOverview.R        |only
 gnm-1.0-8/gnm/inst/doc/gnmOverview.Rnw      |  127 +++++----
 gnm-1.0-8/gnm/inst/doc/gnmOverview.pdf      |binary
 gnm-1.0-8/gnm/man/Diag.Rd                   |    2 
 gnm-1.0-8/gnm/man/Dref.Rd                   |    2 
 gnm-1.0-8/gnm/man/Exp.Rd                    |    4 
 gnm-1.0-8/gnm/man/House2001.Rd              |    3 
 gnm-1.0-8/gnm/man/MPinv.Rd                  |    2 
 gnm-1.0-8/gnm/man/Mult.Rd                   |    5 
 gnm-1.0-8/gnm/man/MultHomog.Rd              |    1 
 gnm-1.0-8/gnm/man/Symm.Rd                   |    2 
 gnm-1.0-8/gnm/man/Topo.Rd                   |    1 
 gnm-1.0-8/gnm/man/anova.gnm.Rd              |    4 
 gnm-1.0-8/gnm/man/asGnm.Rd                  |    1 
 gnm-1.0-8/gnm/man/backPain.Rd               |    3 
 gnm-1.0-8/gnm/man/barley.Rd                 |    3 
 gnm-1.0-8/gnm/man/barleyHeights.Rd          |    3 
 gnm-1.0-8/gnm/man/cautres.Rd                |    3 
 gnm-1.0-8/gnm/man/checkEstimable.Rd         |    3 
 gnm-1.0-8/gnm/man/confint.gnm.Rd            |    5 
 gnm-1.0-8/gnm/man/erikson.Rd                |    3 
 gnm-1.0-8/gnm/man/exitInfo.Rd               |    1 
 gnm-1.0-8/gnm/man/expandCategorical.Rd      |    2 
 gnm-1.0-8/gnm/man/friend.Rd                 |    3 
 gnm-1.0-8/gnm/man/getContrasts.Rd           |    4 
 gnm-1.0-8/gnm/man/gnm.Rd                    |    3 
 gnm-1.0-8/gnm/man/instances.Rd              |    1 
 gnm-1.0-8/gnm/man/meanResiduals.Rd          |    2 
 gnm-1.0-8/gnm/man/mentalHealth.Rd           |    3 
 gnm-1.0-8/gnm/man/nonlin.function.Rd        |    1 
 gnm-1.0-8/gnm/man/ofInterest.Rd             |    1 
 gnm-1.0-8/gnm/man/parameters.Rd             |    1 
 gnm-1.0-8/gnm/man/pickCoef.Rd               |    3 
 gnm-1.0-8/gnm/man/plot.gnm.Rd               |    4 
 gnm-1.0-8/gnm/man/predict.gnm.Rd            |    1 
 gnm-1.0-8/gnm/man/profile.gnm.Rd            |    9 
 gnm-1.0-8/gnm/man/residSVD.Rd               |    2 
 gnm-1.0-8/gnm/man/se.Rd                     |    3 
 gnm-1.0-8/gnm/man/summary.gnm.Rd            |    4 
 gnm-1.0-8/gnm/man/vcov.gnm.Rd               |    1 
 gnm-1.0-8/gnm/man/voting.Rd                 |    4 
 gnm-1.0-8/gnm/man/wedderburn.Rd             |    5 
 gnm-1.0-8/gnm/man/wheat.Rd                  |    3 
 gnm-1.0-8/gnm/man/yaish.Rd                  |    4 
 gnm-1.0-8/gnm/src/gnm.c                     |   16 +
 gnm-1.0-8/gnm/tests/RC.R                    |    1 
 gnm-1.0-8/gnm/tests/RC.Rout.save            |    7 
 gnm-1.0-8/gnm/tests/RChomog.R               |    2 
 gnm-1.0-8/gnm/tests/RChomog.Rout.save       |    8 
 gnm-1.0-8/gnm/tests/biplot.R                |    1 
 gnm-1.0-8/gnm/tests/biplot.Rout.save        |    7 
 gnm-1.0-8/gnm/tests/bwt.R                   |    1 
 gnm-1.0-8/gnm/tests/bwt.Rout.save           |    7 
 gnm-1.0-8/gnm/tests/diagonalRef.R           |    1 
 gnm-1.0-8/gnm/tests/diagonalRef.Rout.save   |    7 
 gnm-1.0-8/gnm/tests/doubleUnidiff.R         |    1 
 gnm-1.0-8/gnm/tests/doubleUnidiff.Rout.save |    7 
 gnm-1.0-8/gnm/tests/gammi.R                 |    1 
 gnm-1.0-8/gnm/tests/gammi.Rout.save         |    7 
 gnm-1.0-8/gnm/tests/logexcess.Rout.save     |    6 
 gnm-1.0-8/gnm/tests/logistic.Rout.save      |    6 
 gnm-1.0-8/gnm/tests/nls.Rout.save           |    6 
 gnm-1.0-8/gnm/tests/stereotype.R            |    1 
 gnm-1.0-8/gnm/tests/stereotype.Rout.save    |    7 
 gnm-1.0-8/gnm/tests/unidiff.R               |    1 
 gnm-1.0-8/gnm/tests/unidiff.Rout.save       |    7 
 gnm-1.0-8/gnm/vignettes/gnmOverview.Rnw     |  127 +++++----
 gnm-1.0-8/gnm/vignettes/screenshot1.png     |only
 gnm-1.0-8/gnm/vignettes/screenshot2.png     |only
 gnm-1.0-8/gnm/vignettes/screenshot3.png     |only
 194 files changed, 2283 insertions(+), 630 deletions(-)

More information about gnm at CRAN
Permanent link

Package csn (with last version 1.1.1) was removed from CRAN

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

2014-12-23 1.1.1
2014-07-01 1.1
2014-06-21 1.0

Permanent link
Package visreg updated to version 2.2-0 with previous version 2.1-1 dated 2015-02-25

Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, randomForest, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

Diff between visreg versions 2.1-1 dated 2015-02-25 and 2.2-0 dated 2015-04-22

 DESCRIPTION               |   12 ++++++------
 MD5                       |   26 ++++++++++++++------------
 NEWS                      |    5 +++++
 R/Response.R              |   28 ++++++++++++++++++++++++----
 R/Terms.R                 |    1 +
 R/makeYName.R             |only
 R/setupV.R                |    6 ++++--
 R/setupX.R                |    2 +-
 R/visreg.R                |   12 +++++++++---
 R/visreg2d.R              |   13 +++++--------
 R/visregLatticePlot.R     |    7 ++-----
 R/visregOverlayPlot.R     |    5 +----
 R/visregPlot.R            |   13 ++++++++-----
 inst/tests/mixed-models.R |   13 ++++++-------
 tests/randomForest.R      |only
 15 files changed, 86 insertions(+), 57 deletions(-)

More information about visreg at CRAN
Permanent link

Package sspse updated to version 0.5-1 with previous version 0.5 dated 2015-03-24

Title: Estimating Hidden Population Size using Respondent Driven Sampling Data
Description: An integrated set of tools to estimate the size of a networked population based on respondent-driven sampling data. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre, cph], Krista J. Gile [aut, cph]
Maintainer: Mark S. Handcock

Diff between sspse versions 0.5 dated 2015-03-24 and 0.5-1 dated 2015-04-22

 DESCRIPTION                |   12 ++++++------
 MD5                        |   28 ++++++++++++++--------------
 NAMESPACE                  |    2 +-
 R/plot.sspse.R             |    2 +-
 R/print.summary.sspse.R    |    2 +-
 R/sspse.utilities.R        |   26 +++++++++++++++++++++-----
 R/summary.size.R           |    2 +-
 inst/CITATION              |    6 +++---
 man/beginparallel.Rd       |    2 +-
 man/dsizeprior.Rd          |    2 +-
 man/plot.sspse.Rd          |    2 +-
 man/posteriorsize.Rd       |    2 +-
 man/print.summary.sspse.Rd |    2 +-
 man/sspse-package.Rd       |    2 +-
 man/summary.sspse.Rd       |    2 +-
 15 files changed, 55 insertions(+), 39 deletions(-)

More information about sspse at CRAN
Permanent link

Package seedy updated to version 1.2 with previous version 1.0 dated 2014-10-16

Title: Simulation of Evolutionary and Epidemiological Dynamics
Description: Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.
Author: Colin Worby
Maintainer: Colin Worby

Diff between seedy versions 1.0 dated 2014-10-16 and 1.2 dated 2015-04-22

 DESCRIPTION               |    8 ++++----
 MD5                       |   26 ++++++++++++++++----------
 R/diversity.range.R       |    4 ++--
 R/flat.r                  |only
 R/hump.r                  |only
 R/plotoutbreak.R          |    6 +++++-
 R/simfixoutbreak.r        |only
 R/simulateoutbreak.R      |   14 ++++++++++----
 R/simulatepopulation.R    |   21 ++++++++++++---------
 R/transroutes.r           |    3 ++-
 man/diversity.range.Rd    |   10 +++++-----
 man/flat.Rd               |only
 man/hump.Rd               |only
 man/seedy-package.Rd      |    4 ++--
 man/simfixoutbreak.Rd     |only
 man/simulateoutbreak.Rd   |   13 +++++++++++--
 man/simulatepopulation.Rd |   25 ++++++++++++++++---------
 17 files changed, 85 insertions(+), 49 deletions(-)

More information about seedy at CRAN
Permanent link

New package shinyjs with initial version 0.0.3.3
Package: shinyjs
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R Code
Version: 0.0.3.3
Authors@R: person("Dean", "Attali", email = "daattali@gmail.com", role = c("aut", "cre"))
Description: Perform common JavaScript operations in Shiny applications without having to know any JavaScript. Many useful JavaScript functions are made available by shinyjs with a simple R interface so that you don't have to write any JavaScript code. Even if you do know JavaScript, shinyjs can be used as convenience functions to avoid dealing with message passing and writing JavaScript code.
URL: https://github.com/daattali/shinyjs
Depends: R (>= 3.1.2)
Imports: shiny (>= 0.11.1)
Suggests: knitr (>= 1.7), testthat (>= 0.9.1)
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-04-21 16:30:06 UTC; Dean
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali
Repository: CRAN
Date/Publication: 2015-04-22 08:07:52

More information about shinyjs at CRAN
Permanent link

New package rversions with initial version 1.0.0
Package: rversions
Title: Query R Versions, Including r-release and r-oldrel
Version: 1.0.0
Authors@R: person("Gabor", "Csardi", , "csardi.gabor@gmail.com", role = c("aut", "cre"))
Description: Query the main R SVN repository to find the versions r-release and r-oldrel refer to, and also all previous R versions and their release dates.
License: MIT + file LICENSE
URL: https://github.com/metacran/rversions
BugReports: https://github.com/metacran/rversions/issues
Imports: RCurl, XML
NeedsCompilation: no
Packaged: 2015-04-21 19:50:01 UTC; gaborcsardi
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi
Repository: CRAN
Date/Publication: 2015-04-22 08:06:34

More information about rversions at CRAN
Permanent link

Package GSIF updated to version 0.4-5 with previous version 0.4-4 dated 2015-01-30

Title: Global Soil Information Facilities
Description: Global Soil Information Facilities - tools (standards and functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [ctb], Gerard Heuvelink [ctb], Brendan Malone [ctb]
Maintainer: Tomislav Hengl

Diff between GSIF versions 0.4-4 dated 2015-01-30 and 0.4-5 dated 2015-04-22

 DESCRIPTION                      |   12 ++--
 MD5                              |   58 ++++++++++-----------
 NAMESPACE                        |    6 +-
 R/AAAA.R                         |    2 
 R/AWCPTF.R                       |    2 
 R/LRI.R                          |    2 
 R/OCSKGM.R                       |    2 
 R/SoilGrid.validator.R           |only
 R/extract.list.R                 |   29 ++++++----
 R/fit.gstatModel.R               |   35 ++++++++----
 R/fit.regModel.R                 |  107 ++++++++++++++++++++++++++-------------
 R/fit.vgmModel.R                 |   36 ++++++-------
 R/predict.gstatModel.R           |   77 +++++++++++-----------------
 R/spsample.prob.R                |    6 +-
 data/afsp.rda                    |binary
 man/AWCPTF.Rd                    |    4 -
 man/ERDICM.Rd                    |    2 
 man/FAO.SoilProfileCollection.Rd |   11 +---
 man/LRI.Rd                       |    6 ++
 man/OCSKGM.Rd                    |    2 
 man/SoilGrid.validator.Rd        |only
 man/afsp.Rd                      |   75 ++++++---------------------
 man/cookfarm.Rd                  |   13 +++-
 man/edgeroi.Rd                   |    4 -
 man/extract.Rd                   |    5 +
 man/fit.gstatModel.Rd            |   63 +++++++++++-----------
 man/fit.regModel.Rd              |   26 ++++++++-
 man/fit.vgmModel.Rd              |    2 
 man/gstatModel.Rd                |    2 
 man/mpspline.Rd                  |    5 -
 man/spsample.prob.Rd             |   14 ++---
 31 files changed, 325 insertions(+), 283 deletions(-)

More information about GSIF at CRAN
Permanent link

Package genderizeR updated to version 1.1.0 with previous version 1.0.0 dated 2015-02-08

Title: Gender Prediction Based on First Names
Description: Utilizes the genderize.io API to predict gender from first names extracted from a text vector. The accuracy of prediction could be controlled by two parameters: counts of a first name in the database and probability of prediction.
Author: Kamil Wais [aut, cre]
Maintainer: Kamil Wais

Diff between genderizeR versions 1.0.0 dated 2015-02-08 and 1.1.0 dated 2015-04-22

 DESCRIPTION                     |   13 ++-
 LICENSE                         |    2 
 MD5                             |   48 +++++++-------
 NAMESPACE                       |    2 
 NEWS                            |   52 +++++++++++----
 R/findGivenNames.R              |   87 +++++++++++++++++++++----
 R/genderizeAPI.R                |  136 +++++++++++++++++++++++++++++++---------
 R/genderizeR.R                  |    2 
 R/numberOfNames.R               |    8 +-
 README.md                       |   43 +++++-------
 man/authorships.Rd              |    2 
 man/classificatonErrors.Rd      |    2 
 man/findGivenNames.Rd           |    9 ++
 man/genderize.Rd                |    2 
 man/genderizeAPI.Rd             |    8 +-
 man/genderizeBootstrapError.Rd  |    2 
 man/genderizePredict.Rd         |    2 
 man/genderizeR.Rd               |    2 
 man/genderizeTrain.Rd           |    2 
 man/givenNamesDB_authorships.Rd |    2 
 man/givenNamesDB_titles.Rd      |    2 
 man/numberOfNames.Rd            |    2 
 man/textPrepare.Rd              |    2 
 man/titles.Rd                   |    2 
 tests                           |only
 25 files changed, 299 insertions(+), 135 deletions(-)

More information about genderizeR at CRAN
Permanent link

Package bootSVD updated to version 0.2 with previous version 0.1 dated 2014-07-21

Title: Fast, Exact Bootstrap Principal Component Analysis for High Dimensional Data
Description: Implements fast, exact bootstrap Principal Component Analysis and Singular Value Decompositions for high dimensional data, as described in (arxiv.org/abs/1405.0922). For data matrices that are too large to operate on in memory, users can input objects with class 'ff' (see the 'ff' package), where the actual data is stored on disk. In response, this package will implement a block matrix algebra procedure for calculating the principal components (PCs) and bootstrap PCs. Depending on options set by the user, the 'parallel' package can be used to parallelize the calculation of the bootstrap PCs.
Author: Aaron Fisher
Maintainer: Aaron Fisher

Diff between bootSVD versions 0.1 dated 2014-07-21 and 0.2 dated 2015-04-22

 bootSVD-0.1/bootSVD/man/reindexDsByK.Rd          |only
 bootSVD-0.1/bootSVD/man/reindexPCsByK.Rd         |only
 bootSVD-0.2/bootSVD/DESCRIPTION                  |   16 
 bootSVD-0.2/bootSVD/MD5                          |   41 -
 bootSVD-0.2/bootSVD/NAMESPACE                    |    8 
 bootSVD-0.2/bootSVD/R/bootstrap_functions.R      |  746 ++++++++++++++++-------
 bootSVD-0.2/bootSVD/README.md                    |    5 
 bootSVD-0.2/bootSVD/man/As2Vs.Rd                 |   50 -
 bootSVD-0.2/bootSVD/man/EEG_leadingV.Rd          |   27 
 bootSVD-0.2/bootSVD/man/EEG_mu.Rd                |   27 
 bootSVD-0.2/bootSVD/man/EEG_score_var.Rd         |   30 
 bootSVD-0.2/bootSVD/man/bootPCA.Rd               |   14 
 bootSVD-0.2/bootSVD/man/bootSVD.Rd               |  253 +++----
 bootSVD-0.2/bootSVD/man/bootSVD_LD.Rd            |   93 --
 bootSVD-0.2/bootSVD/man/fastSVD.Rd               |   44 -
 bootSVD-0.2/bootSVD/man/ffmatrixmult.Rd          |only
 bootSVD-0.2/bootSVD/man/genBootIndeces.Rd        |   22 
 bootSVD-0.2/bootSVD/man/genQ.Rd                  |   15 
 bootSVD-0.2/bootSVD/man/getMomentsAndMomentCI.Rd |   59 -
 bootSVD-0.2/bootSVD/man/os.Rd                    |    6 
 bootSVD-0.2/bootSVD/man/qrSVD.Rd                 |   37 -
 bootSVD-0.2/bootSVD/man/reindexMatricesByK.Rd    |only
 bootSVD-0.2/bootSVD/man/reindexVectorsByK.Rd     |only
 bootSVD-0.2/bootSVD/man/simEEG.Rd                |   63 -
 24 files changed, 848 insertions(+), 708 deletions(-)

More information about bootSVD at CRAN
Permanent link

Tue, 21 Apr 2015

Package ensurer updated to version 1.1 with previous version 1.0 dated 2014-11-18

Title: Ensure Values at Runtime
Description: Add simple runtime contracts to R values. These ensure that values fulfil certain conditions and will raise appropriate errors if they do not.
Author: Stefan Milton Bache
Maintainer: Stefan Milton Bache

Diff between ensurer versions 1.0 dated 2014-11-18 and 1.1 dated 2015-04-21

 DESCRIPTION                       |   14 ++--
 LICENSE                           |    4 -
 MD5                               |   38 ++++++------
 NAMESPACE                         |    4 +
 NEWS                              |only
 R/check_that.R                    |only
 R/ensure_that.R                   |   20 ++++--
 R/ensurer.R                       |   54 +++++++++---------
 R/ensurer_env.R                   |   18 +++++-
 R/ensures_that.R                  |  113 ++++++++++++++++++++++++++------------
 R/utility_functions.R             |   13 +++-
 README.md                         |   63 ++++++++++++---------
 build/vignette.rds                |binary
 inst/doc/ensurer.R                |   18 +++---
 inst/doc/ensurer.Rmd              |   49 +++++++++-------
 inst/doc/ensurer.html             |   47 +++++++++------
 man/ensurer.Rd                    |   57 +++++++++----------
 man/ensures_that.Rd               |   78 +++++++++++++++-----------
 man/print.ensurer.Rd              |    3 -
 tests/testthat/test-ensure_that.r |   10 +++
 vignettes/ensurer.Rmd             |   37 +++++++-----
 21 files changed, 387 insertions(+), 253 deletions(-)

More information about ensurer at CRAN
Permanent link

Package effsize updated to version 0.5.4 with previous version 0.5.2 dated 2014-08-28

Title: Efficient Effect Size Computation
Description: A collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano

Diff between effsize versions 0.5.2 dated 2014-08-28 and 0.5.4 dated 2015-04-21

 DESCRIPTION            |   23 +++++++++++++----------
 MD5                    |   18 +++++++++++-------
 NAMESPACE              |    7 +++++++
 R/CliffDelta.R         |    8 ++++----
 R/CohenD.R             |   14 +++++++++++++-
 R/VD_A.R               |    2 +-
 man/cohen.d.Rd         |    4 ++++
 man/effsize-package.Rd |   17 +++++------------
 tests                  |only
 9 files changed, 58 insertions(+), 35 deletions(-)

More information about effsize at CRAN
Permanent link

Package causaleffect updated to version 1.1 with previous version 1.0 dated 2014-09-25

Title: Deriving Expressions of Joint Interventional Distributions in Causal Models
Description: An implementation of a conditional causal effect identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs.
Author: Santtu Tikka
Maintainer: Santtu Tikka

Diff between causaleffect versions 1.0 dated 2014-09-25 and 1.1 dated 2015-04-21

 causaleffect-1.0/causaleffect/R/anRpackage-internal.R       |only
 causaleffect-1.1/causaleffect/DESCRIPTION                   |   12 +++---
 causaleffect-1.1/causaleffect/MD5                           |   16 ++++----
 causaleffect-1.1/causaleffect/NAMESPACE                     |    2 -
 causaleffect-1.1/causaleffect/R/causal.effect.R             |   22 +++++++++---
 causaleffect-1.1/causaleffect/R/getExpression.probability.R |    6 +--
 causaleffect-1.1/causaleffect/R/id.R                        |   16 ++++----
 causaleffect-1.1/causaleffect/R/idc.R                       |only
 causaleffect-1.1/causaleffect/man/causal.effect.Rd          |   20 +++++++---
 causaleffect-1.1/causaleffect/man/causaleffect-package.Rd   |   22 +++++++-----
 10 files changed, 70 insertions(+), 46 deletions(-)

More information about causaleffect at CRAN
Permanent link

Package RcppArmadillo updated to version 0.5.000.0 with previous version 0.4.650.1.1 dated 2015-02-26

Title: Rcpp Integration for the Armadillo Templated Linear Algebra Library
Description: R and Armadillo integration using Rcpp 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

Diff between RcppArmadillo versions 0.4.650.1.1 dated 2015-02-26 and 0.5.000.0 dated 2015-04-21

 ChangeLog                                           |   21 +
 DESCRIPTION                                         |    8 
 MD5                                                 |  132 +++----
 build/vignette.rds                                  |binary
 inst/NEWS.Rd                                        |   28 +
 inst/doc/RcppArmadillo-intro.pdf                    |binary
 inst/doc/RcppArmadillo-unitTests.pdf                |binary
 inst/include/armadillo                              |   32 +
 inst/include/armadillo_bits/Col_bones.hpp           |   10 
 inst/include/armadillo_bits/Col_meat.hpp            |   60 ++-
 inst/include/armadillo_bits/Cube_meat.hpp           |   20 -
 inst/include/armadillo_bits/Mat_bones.hpp           |    8 
 inst/include/armadillo_bits/Mat_meat.hpp            |  144 +++++++
 inst/include/armadillo_bits/Op_bones.hpp            |    3 
 inst/include/armadillo_bits/Proxy.hpp               |   48 ++
 inst/include/armadillo_bits/Row_bones.hpp           |   10 
 inst/include/armadillo_bits/Row_meat.hpp            |   60 ++-
 inst/include/armadillo_bits/SpCol_bones.hpp         |   41 --
 inst/include/armadillo_bits/SpCol_meat.hpp          |  157 --------
 inst/include/armadillo_bits/SpMat_bones.hpp         |   10 
 inst/include/armadillo_bits/SpMat_meat.hpp          |   78 +++-
 inst/include/armadillo_bits/SpProxy.hpp             |    2 
 inst/include/armadillo_bits/SpRow_bones.hpp         |   40 --
 inst/include/armadillo_bits/SpRow_meat.hpp          |  180 ---------
 inst/include/armadillo_bits/arma_cmath.hpp          |    6 
 inst/include/armadillo_bits/arma_config.hpp         |   11 
 inst/include/armadillo_bits/arma_ostream_meat.hpp   |   24 +
 inst/include/armadillo_bits/arma_version.hpp        |   12 
 inst/include/armadillo_bits/atlas_wrapper.hpp       |   56 +-
 inst/include/armadillo_bits/auxlib_meat.hpp         |   94 ++++-
 inst/include/armadillo_bits/compiler_setup.hpp      |   28 +
 inst/include/armadillo_bits/config.hpp              |   52 +-
 inst/include/armadillo_bits/debug.hpp               |  119 +++++-
 inst/include/armadillo_bits/diagview_meat.hpp       |   10 
 inst/include/armadillo_bits/diskio_meat.hpp         |  194 +++++++++-
 inst/include/armadillo_bits/field_meat.hpp          |   10 
 inst/include/armadillo_bits/fn_accu.hpp             |   78 +++-
 inst/include/armadillo_bits/fn_all.hpp              |   11 
 inst/include/armadillo_bits/fn_any.hpp              |   11 
 inst/include/armadillo_bits/fn_eigs_gen.hpp         |    2 
 inst/include/armadillo_bits/fn_elem.hpp             |   14 
 inst/include/armadillo_bits/fn_join.hpp             |   55 ++
 inst/include/armadillo_bits/fn_n_unique.hpp         |    2 
 inst/include/armadillo_bits/fn_nonzeros.hpp         |only
 inst/include/armadillo_bits/fn_norm_sparse.hpp      |    1 
 inst/include/armadillo_bits/fn_randg.hpp            |    9 
 inst/include/armadillo_bits/fn_repmat.hpp           |   18 
 inst/include/armadillo_bits/fn_sort_index.hpp       |  271 --------------
 inst/include/armadillo_bits/fn_spsolve.hpp          |only
 inst/include/armadillo_bits/fn_svds.hpp             |only
 inst/include/armadillo_bits/forward_bones.hpp       |   54 ++
 inst/include/armadillo_bits/gmm_diag_meat.hpp       |   17 
 inst/include/armadillo_bits/include_superlu.hpp     |only
 inst/include/armadillo_bits/mtOp_bones.hpp          |   13 
 inst/include/armadillo_bits/mul_gemm.hpp            |    2 
 inst/include/armadillo_bits/mul_gemv.hpp            |    2 
 inst/include/armadillo_bits/op_nonzeros_bones.hpp   |only
 inst/include/armadillo_bits/op_nonzeros_meat.hpp    |only
 inst/include/armadillo_bits/op_shuffle_meat.hpp     |    2 
 inst/include/armadillo_bits/op_sort_index_bones.hpp |only
 inst/include/armadillo_bits/op_sort_index_meat.hpp  |only
 inst/include/armadillo_bits/sp_auxlib_bones.hpp     |   24 +
 inst/include/armadillo_bits/sp_auxlib_meat.hpp      |  374 +++++++++++++++++++-
 inst/include/armadillo_bits/spdiagview_bones.hpp    |only
 inst/include/armadillo_bits/spdiagview_meat.hpp     |only
 inst/include/armadillo_bits/spglue_join_bones.hpp   |only
 inst/include/armadillo_bits/spglue_join_meat.hpp    |only
 inst/include/armadillo_bits/spop_misc_bones.hpp     |   25 +
 inst/include/armadillo_bits/spop_misc_meat.hpp      |   80 ++++
 inst/include/armadillo_bits/subview_meat.hpp        |    8 
 inst/include/armadillo_bits/superlu_bones.hpp       |only
 inst/include/armadillo_bits/superlu_wrapper.hpp     |only
 inst/include/armadillo_bits/typedef_elem.hpp        |   37 +
 inst/include/armadillo_bits/unwrap.hpp              |    4 
 74 files changed, 1874 insertions(+), 948 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

Package nLTT updated to version 1.1 with previous version 1.0 dated 2015-01-19

Title: Calculate the NLTT Statistic
Description: Provides functions to calculate the normalised Lineage-Through-Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
Author: Thijs Janzen
Maintainer: Thijs Janzen

Diff between nLTT versions 1.0 dated 2015-01-19 and 1.1 dated 2015-04-21

 nLTT-1.0/nLTT/man/normLTTdiffABS.Rd |only
 nLTT-1.0/nLTT/man/normLTTdiffSQ.Rd  |only
 nLTT-1.1/nLTT/DESCRIPTION           |   12 ++++++------
 nLTT-1.1/nLTT/MD5                   |   15 +++++++--------
 nLTT-1.1/nLTT/R/nLTTDiff.R          |   10 ++++++++++
 nLTT-1.1/nLTT/man/ABC_SMC_nLTT.Rd   |    2 +-
 nLTT-1.1/nLTT/man/MCMC_nLTT.Rd      |    2 +-
 nLTT-1.1/nLTT/man/nLTT-internal.Rd  |    4 +++-
 nLTT-1.1/nLTT/man/nLTT-package.Rd   |   25 ++++++++++++++++---------
 nLTT-1.1/nLTT/man/nLTTstat.Rd       |only
 10 files changed, 44 insertions(+), 26 deletions(-)

More information about nLTT at CRAN
Permanent link

Package GUILDS updated to version 1.2.1 with previous version 1.2 dated 2014-09-07

Title: Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure
Description: The GUILDS package combines a range of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
Author: Thijs Janzen
Maintainer: Thijs Janzen

Diff between GUILDS versions 1.2 dated 2014-09-07 and 1.2.1 dated 2015-04-21

 DESCRIPTION                             |   16 ++++++++--------
 MD5                                     |   14 +++++++-------
 man/GUILDS-package.Rd                   |   17 +++++++++--------
 man/logLikelihood.ESF.Rd                |    2 +-
 man/logLikelihood.Guilds.Conditional.Rd |    4 ++--
 man/logLikelihood.Guilds.Rd             |    6 +++---
 man/maxLikelihood.Guilds.Conditional.Rd |    2 +-
 man/maxLikelihood.Guilds.Rd             |    2 +-
 8 files changed, 32 insertions(+), 31 deletions(-)

More information about GUILDS at CRAN
Permanent link

Package aoos updated to version 0.2.0 with previous version 0.1.0 dated 2014-12-19

Title: Another Object Orientation System
Description: Another implementation of object-orientation in R. Has reference semantics and is built around S4.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz

Diff between aoos versions 0.1.0 dated 2014-12-19 and 0.2.0 dated 2015-04-21

 DESCRIPTION                           |   20 +--
 MD5                                   |   61 +++++++----
 NAMESPACE                             |   11 +-
 NEWS                                  |   31 +++++
 R/Accessor.R                          |only
 R/Binary.R                            |only
 R/Class.R                             |only
 R/Private.R                           |only
 R/Show.R                              |only
 R/aoos.R                              |   34 ++----
 R/defineClass.R                       |   83 ++++++++++-----
 R/public-interfaces.R                 |   30 +++++
 build/vignette.rds                    |binary
 inst/doc/Introduction.R               |  108 --------------------
 inst/doc/Introduction.Rmd             |  162 +------------------------------
 inst/doc/Introduction.html            |  177 +---------------------------------
 inst/doc/aoosClasses.R                |only
 inst/doc/aoosClasses.Rmd              |only
 inst/doc/aoosClasses.html             |only
 inst/doc/referenceClasses.R           |only
 inst/doc/referenceClasses.Rmd         |only
 inst/doc/referenceClasses.html        |only
 man/Accessor.Rd                       |only
 man/Binary.Rd                         |only
 man/Class.Rd                          |only
 man/Private.Rd                        |only
 man/Show.Rd                           |only
 man/aoos.Rd                           |    2 
 man/defineClass.Rd                    |   31 ++++-
 man/publicInterface.Rd                |    8 +
 tests/testthat.R                      |    2 
 tests/testthat/test-Accessor.R        |only
 tests/testthat/test-Binary.R          |only
 tests/testthat/test-Class.R           |only
 tests/testthat/test-basics.R          |   82 +++++++++++++--
 tests/testthat/test-inheritance.R     |   46 ++++++--
 tests/testthat/test-publicInterface.R |   68 ++++++++++++-
 tests/testthat/test-self.R            |    8 -
 tests/testthat/test-summary.R         |   10 -
 vignettes/Introduction.Rmd            |  162 +------------------------------
 vignettes/aoosClasses.Rmd             |only
 vignettes/referenceClasses.Rmd        |only
 42 files changed, 426 insertions(+), 710 deletions(-)

More information about aoos at CRAN
Permanent link

Package sitar updated to version 1.0.2 with previous version 1.0.1 dated 2014-06-27

Title: Super Imposition by Translation and Rotation Growth Curve Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole

Diff between sitar versions 1.0.1 dated 2014-06-27 and 1.0.2 dated 2015-04-21

 sitar-1.0.1/sitar/man/funcall.rd             |only
 sitar-1.0.1/sitar/man/makess.rd              |only
 sitar-1.0.1/sitar/man/mplot.rd               |only
 sitar-1.0.1/sitar/man/recalib.rd             |only
 sitar-1.0.1/sitar/man/xaxsd.rd               |only
 sitar-1.0.2/sitar/DESCRIPTION                |   16 +-
 sitar-1.0.2/sitar/MD5                        |   61 ++++----
 sitar-1.0.2/sitar/NAMESPACE                  |    8 -
 sitar-1.0.2/sitar/NEWS                       |   34 ++++
 sitar-1.0.2/sitar/R/LMSfit.R                 |only
 sitar-1.0.2/sitar/R/lms2z.R                  |   10 -
 sitar-1.0.2/sitar/R/mplot.R                  |   16 +-
 sitar-1.0.2/sitar/R/plot.sitar.R             |   60 +++++---
 sitar-1.0.2/sitar/R/predict.R                |only
 sitar-1.0.2/sitar/R/sitar.R                  |   85 ++++++-----
 sitar-1.0.2/sitar/R/sitarlib.R               |  196 +++++----------------------
 sitar-1.0.2/sitar/R/update.sitar.R           |only
 sitar-1.0.2/sitar/man/LMSfit.Rd              |only
 sitar-1.0.2/sitar/man/cLMS.Rd                |    4 
 sitar-1.0.2/sitar/man/funcall.Rd             |only
 sitar-1.0.2/sitar/man/getData.sitar.Rd       |only
 sitar-1.0.2/sitar/man/getVarCov.sitar.Rd     |only
 sitar-1.0.2/sitar/man/heights.Rd             |   25 +++
 sitar-1.0.2/sitar/man/lms2z.Rd               |   14 -
 sitar-1.0.2/sitar/man/makess.Rd              |only
 sitar-1.0.2/sitar/man/mplot.Rd               |only
 sitar-1.0.2/sitar/man/plot.sitar.Rd          |   10 -
 sitar-1.0.2/sitar/man/plotclean.Rd           |   10 -
 sitar-1.0.2/sitar/man/predict.sitar.Rd       |only
 sitar-1.0.2/sitar/man/print.summary.sitar.Rd |    2 
 sitar-1.0.2/sitar/man/recalib.Rd             |only
 sitar-1.0.2/sitar/man/sitar-package.Rd       |   40 +++--
 sitar-1.0.2/sitar/man/sitar.Rd               |   43 +++--
 sitar-1.0.2/sitar/man/summary.sitar.Rd       |    8 -
 sitar-1.0.2/sitar/man/uk90.Rd                |   12 +
 sitar-1.0.2/sitar/man/ukwhopt.Rd             |   17 +-
 sitar-1.0.2/sitar/man/velout.Rd              |    7 
 sitar-1.0.2/sitar/man/who06.Rd               |    4 
 sitar-1.0.2/sitar/man/xaxsd.Rd               |only
 sitar-1.0.2/sitar/man/y2plot.Rd              |    8 -
 40 files changed, 348 insertions(+), 342 deletions(-)

More information about sitar at CRAN
Permanent link

Package RDML updated to version 0.8-4 with previous version 0.8-3 dated 2015-04-08

Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object.
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh

Diff between RDML versions 0.8-3 dated 2015-04-08 and 0.8-4 dated 2015-04-21

 CHANGELOG                  |    6 
 DESCRIPTION                |   17 +-
 MD5                        |   30 +--
 NAMESPACE                  |   24 +-
 R/RDML.AsDendrogram.R      |    2 
 R/RDML.Merge.R             |    4 
 R/RDML.R                   |   10 -
 R/RDML.init.R              |  242 ++++++++++++++++------------
 man/RDML.class.Rd          |  378 ++++++++++++++++++++++-----------------------
 man/asdendrogram-method.Rd |   60 +++----
 man/astable-method.Rd      |  156 +++++++++---------
 man/getfdata-method.Rd     |  114 ++++++-------
 man/merge-method.Rd        |   50 ++---
 man/names.RDML.Rd          |   48 ++---
 man/new-method.Rd          |   78 ++++-----
 man/setfdata-method.Rd     |  102 ++++++------
 16 files changed, 678 insertions(+), 643 deletions(-)

More information about RDML at CRAN
Permanent link


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