Sat, 10 Jan 2015

Package tcR updated to version 1.1 with previous version 1.0 dated 2014-12-12

Title: Data Analysis of T-cell Receptor Repertoires
Description: Platform for the advanced analysis of T-cell receptor repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov, Mikhail Pogorelyy
Maintainer: Vadim Nazarov

Diff between tcR versions 1.0 dated 2014-12-12 and 1.1 dated 2015-01-10

 DESCRIPTION                   |   13 +--
 MD5                           |  161 +++++++++++++++++++++---------------------
 R/crosses.R                   |   26 +++---
 R/dataproc.R                  |    6 -
 R/diversity.R                 |  133 +++++++++++++++++++++++++++++++---
 R/measures.R                  |   34 +++++++-
 R/plots.R                     |   12 ++-
 R/shared.R                    |    6 +
 R/stats.R                     |   18 ++--
 README.md                     |only
 inst/doc/tcrvignette.R        |   22 +++--
 inst/doc/tcrvignette.Rnw      |    6 +
 inst/doc/tcrvignette.pdf      |binary
 man/AA_TABLE.Rd               |    3 
 man/apply.symm.Rd             |    3 
 man/assymetry.Rd              |    3 
 man/barcodes.to.reads.Rd      |    3 
 man/beta.prob.Rd              |    3 
 man/bootstrap.tcr.Rd          |    3 
 man/check.distribution.Rd     |    3 
 man/codon.variants.Rd         |    3 
 man/column.summary.Rd         |    3 
 man/contamination.stats.Rd    |    3 
 man/convergence.index.Rd      |    3 
 man/cosine.sharing.Rd         |    3 
 man/cosine.similarity.Rd      |   16 ++--
 man/entropy.Rd                |    3 
 man/entropy.seg.Rd            |    3 
 man/find.clonotypes.Rd        |    3 
 man/find.similar.sequences.Rd |    3 
 man/freq.segments.Rd          |    3 
 man/gc.content.Rd             |    3 
 man/generate.kmers.Rd         |    3 
 man/generate.tcr.Rd           |    3 
 man/get.all.substrings.Rd     |    3 
 man/get.deletions.alpha.Rd    |    3 
 man/get.inframes.Rd           |    3 
 man/get.kmers.Rd              |    3 
 man/get.n.barcodes.Rd         |    3 
 man/gibbs.sampler.Rd          |    3 
 man/has.class.Rd              |    3 
 man/intersect.Rd              |   29 +++----
 man/inverse.simpson.Rd        |   22 ++++-
 man/kmer.profile.Rd           |    3 
 man/kmer.table.Rd             |    3 
 man/loglikelihood.Rd          |    3 
 man/matrixdiagcopy.Rd         |    3 
 man/mitcr.stats.Rd            |    3 
 man/parse.file.Rd             |    3 
 man/parse.file.list.Rd        |    3 
 man/parse.folder.Rd           |    3 
 man/pca.segments.Rd           |    3 
 man/permutedf.Rd              |    3 
 man/rarefaction.Rd            |   11 +-
 man/revcomp.Rd                |    3 
 man/reverse.string.Rd         |    3 
 man/sample.clones.Rd          |    3 
 man/sample2D.Rd               |    3 
 man/segments.alphabets.Rd     |    3 
 man/segments.list.Rd          |    3 
 man/set.pb.Rd                 |    3 
 man/set.rank.Rd               |    3 
 man/shared.repertoire.Rd      |    6 +
 man/spectratyping.Rd          |    3 
 man/startmitcr.Rd             |    3 
 man/tailbound.proportion.Rd   |    3 
 man/top.cross.Rd              |    3 
 man/top.fun.Rd                |    3 
 man/twinsdata.Rd              |    3 
 man/vis.V.usage.Rd            |    3 
 man/vis.clonal.dynamics.Rd    |    3 
 man/vis.count.len.Rd          |    3 
 man/vis.group.boxplot.Rd      |    3 
 man/vis.heatmap.Rd            |    3 
 man/vis.kmer.histogram.Rd     |    3 
 man/vis.number.count.Rd       |    3 
 man/vis.pca.Rd                |    3 
 man/vis.radarlike.Rd          |    3 
 man/vis.rarefaction.Rd        |    5 +
 man/vis.top.proportions.Rd    |    3 
 src/Makevars                  |    2 
 vignettes/tcrvignette.Rnw     |    6 +
 82 files changed, 475 insertions(+), 242 deletions(-)

More information about tcR at CRAN
Permanent link

Package RcppClassic updated to version 0.9.6 with previous version 0.9.5 dated 2014-01-25

Title: Deprecated 'classic' Rcpp API
Description: The RcppClassic package provides a deprecated C++ library which facilitates the integration of R and C++. New projects should use the new Rcpp API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss, and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel

Diff between RcppClassic versions 0.9.5 dated 2014-01-25 and 0.9.6 dated 2015-01-10

 RcppClassic-0.9.5/RcppClassic/inst/examples/RcppClassicExample/R/foo.R                           |only
 RcppClassic-0.9.5/RcppClassic/inst/examples/RcppClassicExample/src/foo.cpp                       |only
 RcppClassic-0.9.5/RcppClassic/vignettes/Makefile                                                 |only
 RcppClassic-0.9.5/RcppClassic/vignettes/unitTests-results                                        |only
 RcppClassic-0.9.6/RcppClassic/ChangeLog                                                          |   21 ++++
 RcppClassic-0.9.6/RcppClassic/DESCRIPTION                                                        |   11 +-
 RcppClassic-0.9.6/RcppClassic/MD5                                                                |   37 +++----
 RcppClassic-0.9.6/RcppClassic/README.md                                                          |   13 +-
 RcppClassic-0.9.6/RcppClassic/build/vignette.rds                                                 |binary
 RcppClassic-0.9.6/RcppClassic/cleanup                                                            |    3 
 RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.R                                       |    9 +
 RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.Rnw                                     |   50 ++++++----
 RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.pdf                                     |binary
 RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-unitTests.pdf                                 |binary
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/DESCRIPTION                       |   15 +--
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/NAMESPACE                         |    6 -
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/R/twoTimes.R                      |only
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/man/RcppClassicExample-package.Rd |    7 -
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/src/Makevars                      |    2 
 RcppClassic-0.9.6/RcppClassic/inst/examples/RcppClassicExample/src/twoTimesImpl.cpp              |only
 RcppClassic-0.9.6/RcppClassic/src/Makevars                                                       |   10 +-
 RcppClassic-0.9.6/RcppClassic/vignettes/RcppClassic-intro.Rnw                                    |   50 ++++++----
 22 files changed, 140 insertions(+), 94 deletions(-)

More information about RcppClassic at CRAN
Permanent link

Package hsphase updated to version 2.0.1 with previous version 2.0.0 dated 2014-06-27

Title: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data
Author: Mohammad Ferdosi , Cedric Gondro
Maintainer: Mohammad Ferdosi

Diff between hsphase versions 2.0.0 dated 2014-06-27 and 2.0.1 dated 2015-01-10

 DESCRIPTION            |   11 ++++++-----
 MD5                    |    8 ++++----
 build/vignette.rds     |binary
 inst/CITATION          |   12 ++++++------
 man/hsphase-package.Rd |    4 ++--
 5 files changed, 18 insertions(+), 17 deletions(-)

More information about hsphase at CRAN
Permanent link

Package eRm updated to version 0.15-5 with previous version 0.15-4 dated 2014-02-05

Title: Extended Rasch Modeling
Description: eRm fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Löf-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices. An eRm platform is provided at R-forge (see URL).
Author: Patrick Mair [cre, aut], Reinhold Hatzinger [aut], Marco J. Maier [aut], Thomas Rusch [ctb]
Maintainer: Patrick Mair

Diff between eRm versions 0.15-4 dated 2014-02-05 and 0.15-5 dated 2015-01-10

 eRm-0.15-4/eRm/R/pifit.internal.r              |only
 eRm-0.15-4/eRm/inst/NEWSRd2txt.R               |only
 eRm-0.15-4/eRm/inst/doc/UCML.pdf               |only
 eRm-0.15-4/eRm/inst/doc/UCML.svg               |only
 eRm-0.15-4/eRm/inst/doc/eRm_object_tree.pdf    |only
 eRm-0.15-4/eRm/inst/doc/eRmvig.bib             |only
 eRm-0.15-4/eRm/inst/doc/modelhierarchy.pdf     |only
 eRm-0.15-4/eRm/vignettes/UCML.svg              |only
 eRm-0.15-5/eRm/.Rinstignore                    |    8 
 eRm-0.15-5/eRm/DESCRIPTION                     |   26 
 eRm-0.15-5/eRm/MD5                             |  200 +--
 eRm-0.15-5/eRm/NAMESPACE                       |   29 
 eRm-0.15-5/eRm/NEWS                            |  228 ++-
 eRm-0.15-5/eRm/R/NPtest.R                      |    8 
 eRm-0.15-5/eRm/R/SepRel.R                      |only
 eRm-0.15-5/eRm/R/anova.eRm.R                   |only
 eRm-0.15-5/eRm/R/llra.internals.R              |  201 +--
 eRm-0.15-5/eRm/R/personfit.ppar.R              |   45 
 eRm-0.15-5/eRm/R/pifit.internal.R              |only
 eRm-0.15-5/eRm/R/plotGOF.LR.R                  |   16 
 eRm-0.15-5/eRm/R/plotGR.R                      |  101 -
 eRm-0.15-5/eRm/R/plotINFO.R                    |   46 
 eRm-0.15-5/eRm/R/plotPWmap.R                   |   58 
 eRm-0.15-5/eRm/R/plotTR.R                      |   60 
 eRm-0.15-5/eRm/build/partial.rdb               |only
 eRm-0.15-5/eRm/build/vignette.rds              |binary
 eRm-0.15-5/eRm/data/llraDat1.rda               |binary
 eRm-0.15-5/eRm/data/llraDat2.rda               |binary
 eRm-0.15-5/eRm/data/llradat3.rda               |binary
 eRm-0.15-5/eRm/data/lltmdat1.rda               |binary
 eRm-0.15-5/eRm/data/lltmdat2.rda               |binary
 eRm-0.15-5/eRm/data/lpcmdat.rda                |binary
 eRm-0.15-5/eRm/data/lrsmdat.rda                |binary
 eRm-0.15-5/eRm/data/pcmdat.rda                 |binary
 eRm-0.15-5/eRm/data/pcmdat2.rda                |binary
 eRm-0.15-5/eRm/data/raschdat1.rda              |binary
 eRm-0.15-5/eRm/data/raschdat1_RM_fitted.RData  |binary
 eRm-0.15-5/eRm/data/raschdat1_RM_lrres2.RData  |binary
 eRm-0.15-5/eRm/data/raschdat1_RM_plotDIF.RData |binary
 eRm-0.15-5/eRm/data/raschdat2.rda              |binary
 eRm-0.15-5/eRm/data/raschdat3.rda              |binary
 eRm-0.15-5/eRm/data/raschdat4.rda              |binary
 eRm-0.15-5/eRm/data/rsmdat.rda                 |binary
 eRm-0.15-5/eRm/data/xmpl.RData                 |binary
 eRm-0.15-5/eRm/data/xmplbig.RData              |binary
 eRm-0.15-5/eRm/inst/CITATION                   |  182 +-
 eRm-0.15-5/eRm/inst/NEWS.Rd                    |   12 
 eRm-0.15-5/eRm/inst/NEWS.pdf                   |binary
 eRm-0.15-5/eRm/inst/doc/eRm.R                  |  216 +--
 eRm-0.15-5/eRm/inst/doc/eRm.Rnw                |  450 +++----
 eRm-0.15-5/eRm/inst/doc/eRm.pdf                |binary
 eRm-0.15-5/eRm/man/IC.Rd                       |    1 
 eRm-0.15-5/eRm/man/LLRA.Rd                     |    8 
 eRm-0.15-5/eRm/man/LLTM.Rd                     |    1 
 eRm-0.15-5/eRm/man/LPCM.Rd                     |    7 
 eRm-0.15-5/eRm/man/LRSM.Rd                     |    7 
 eRm-0.15-5/eRm/man/LRtest.Rd                   |    5 
 eRm-0.15-5/eRm/man/MLoef.Rd                    |   52 
 eRm-0.15-5/eRm/man/NPtest.Rd                   |  203 +--
 eRm-0.15-5/eRm/man/PCM.Rd                      |    5 
 eRm-0.15-5/eRm/man/RM.Rd                       |    5 
 eRm-0.15-5/eRm/man/RSM.Rd                      |    7 
 eRm-0.15-5/eRm/man/RSctr.Rd                    |    1 
 eRm-0.15-5/eRm/man/RSmpl.Rd                    |    1 
 eRm-0.15-5/eRm/man/RaschSampler.Rd             |    7 
 eRm-0.15-5/eRm/man/SepRel.Rd                   |only
 eRm-0.15-5/eRm/man/Waldtest.Rd                 |    1 
 eRm-0.15-5/eRm/man/anova.eRm.Rd                |only
 eRm-0.15-5/eRm/man/anova.llra.Rd               |    1 
 eRm-0.15-5/eRm/man/build_W.Rd                  |    5 
 eRm-0.15-5/eRm/man/collapse_W.Rd               |    5 
 eRm-0.15-5/eRm/man/eRm-package.Rd              |   32 
 eRm-0.15-5/eRm/man/eRm.data.Rd                 |    1 
 eRm-0.15-5/eRm/man/gofIRT.Rd                   |    1 
 eRm-0.15-5/eRm/man/item_info.Rd                |    5 
 eRm-0.15-5/eRm/man/itemfit.ppar.Rd             |    1 
 eRm-0.15-5/eRm/man/llra.datprep.Rd             |    5 
 eRm-0.15-5/eRm/man/llraDat1.Rd                 |   64 -
 eRm-0.15-5/eRm/man/llraDat2.Rd                 |   56 
 eRm-0.15-5/eRm/man/llradat3.Rd                 |   20 
 eRm-0.15-5/eRm/man/person.parameter.Rd         |    7 
 eRm-0.15-5/eRm/man/phi.range.Rd                |   21 
 eRm-0.15-5/eRm/man/plotDIF.Rd                  |    5 
 eRm-0.15-5/eRm/man/plotGR.Rd                   |    5 
 eRm-0.15-5/eRm/man/plotICC.Rd                  |    1 
 eRm-0.15-5/eRm/man/plotINFO.Rd                 |   46 
 eRm-0.15-5/eRm/man/plotPImap.Rd                |    3 
 eRm-0.15-5/eRm/man/plotPWmap.Rd                |   27 
 eRm-0.15-5/eRm/man/plotTR.Rd                   |    5 
 eRm-0.15-5/eRm/man/predict.ppar.Rd             |    1 
 eRm-0.15-5/eRm/man/print.eRm.Rd                |    3 
 eRm-0.15-5/eRm/man/rsampler.Rd                 |   36 
 eRm-0.15-5/eRm/man/rsctrl.Rd                   |   12 
 eRm-0.15-5/eRm/man/rsextrmat.Rd                |    1 
 eRm-0.15-5/eRm/man/rsextrobj.Rd                |    1 
 eRm-0.15-5/eRm/man/rstats.Rd                   |    1 
 eRm-0.15-5/eRm/man/sim.2pl.Rd                  |   61 
 eRm-0.15-5/eRm/man/sim.locdep.Rd               |    1 
 eRm-0.15-5/eRm/man/sim.rasch.Rd                |    1 
 eRm-0.15-5/eRm/man/sim.xdim.Rd                 |    1 
 eRm-0.15-5/eRm/man/stepwiseIt.Rd               |    1 
 eRm-0.15-5/eRm/man/summary.RSctr.Rd            |    1 
 eRm-0.15-5/eRm/man/summary.RSmpl.Rd            |    1 
 eRm-0.15-5/eRm/man/summary.llra.Rd             |    5 
 eRm-0.15-5/eRm/man/test_info.Rd                |   11 
 eRm-0.15-5/eRm/man/thresholds.Rd               |    1 
 eRm-0.15-5/eRm/man/xmpl.Rd                     |    1 
 eRm-0.15-5/eRm/vignettes/eRm.Rnw               |  450 +++----
 eRm-0.15-5/eRm/vignettes/eRmvig.bib            | 1534 +++++++++++++------------
 109 files changed, 2443 insertions(+), 2194 deletions(-)

More information about eRm at CRAN
Permanent link

New package BACA with initial version 0.99.0
Package: BACA
Type: Package
Title: Bubble Chart to compare Biological Annotations by using DAVID
Version: 0.99.0
Date: 2014-06-19
Author: Vittorio Fortino and Dario Greco
Maintainer: Vittorio Fortino
Description: R-based graphical tool to concisely visualise and compare biological annotations queried from the DAVID web service. It provides R functions to perform enrichment analysis (via DAVID - http://david.abcc.ncifcrf.gov) on several gene lists at once, and then visualizing all the results in one generated figure that allows R users to compare the enrichments found in the lists.
License: GPL (>= 2)
Depends: R (>= 3.0.0)
Imports: RDAVIDWebService, ggplot2, rJava
VignetteBuilder: knitr
Suggests: knitr
Packaged: 2015-01-10 12:13:54 UTC; vittoriofortino2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-10 17:04:39

More information about BACA at CRAN
Permanent link

Package nlme updated to version 3.1-119 with previous version 3.1-118 dated 2014-10-07

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), R-core [aut, cre]
Maintainer: R-core

Diff between nlme versions 3.1-118 dated 2014-10-07 and 3.1-119 dated 2015-01-10

 ChangeLog      |   12 +++++++++++-
 DESCRIPTION    |    8 ++++----
 MD5            |   19 ++++++++++---------
 R/gnls.R       |    2 +-
 R/lme.R        |    2 +-
 R/newMethods.R |    2 +-
 R/nlme.R       |    6 +++---
 R/pdMat.R      |    2 +-
 R/reStruct.R   |    2 +-
 man/bdf.Rd     |    3 ++-
 tests/nlme2.R  |only
 11 files changed, 35 insertions(+), 23 deletions(-)

More information about nlme at CRAN
Permanent link

Package MASS updated to version 7.3-37 with previous version 7.3-35 dated 2014-09-30

Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley

Diff between MASS versions 7.3-35 dated 2014-09-30 and 7.3-37 dated 2015-01-10

 DESCRIPTION                      |   10 +++++-----
 MD5                              |   24 ++++++++++++------------
 R/glmmPQL.R                      |    7 ++++---
 R/loglm.R                        |    2 +-
 R/neg.bin.R                      |    2 +-
 R/negbin.R                       |    3 +--
 R/polr.R                         |    1 -
 inst/NEWS                        |    2 +-
 inst/scripts/ch10.R              |   24 +++++++++++-------------
 man/bacteria.Rd                  |    6 ++++--
 man/corresp.Rd                   |    2 +-
 man/denumerate.Rd                |    2 +-
 tests/Examples/MASS-Ex.Rout.save |   26 +++++++++-----------------
 13 files changed, 51 insertions(+), 60 deletions(-)

More information about MASS at CRAN
Permanent link

Package boot updated to version 1.3-14 with previous version 1.3-13 dated 2014-09-30

Title: Bootstrap Functions (originally by Angelo Canty for S)
Description: functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Applications" by A. C. Davison and D. V. Hinkley (1997, CUP).
Author: Angelo Canty [aut], Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley

Diff between boot versions 1.3-13 dated 2014-09-30 and 1.3-14 dated 2015-01-10

 ChangeLog          |    5 +++++
 DESCRIPTION        |    8 ++++----
 MD5                |   10 +++++-----
 R/bootfuns.q       |    4 ----
 R/bootpracs.q      |    2 +-
 man/EEF.profile.Rd |    2 +-
 6 files changed, 16 insertions(+), 15 deletions(-)

More information about boot at CRAN
Permanent link

Package mbbefd updated to version 0.5 with previous version 0.1 dated 2013-10-30

Title: Maxwell Bolzano Bose Einstein Fermi Dirac distribution and exposure curve
Description: It contains the definition of Maxwell Bolzano Bose Einstein Fermi Dirac (MBBEFD) distribution (distribution function, density, quantile functions) as well as MBBEFD exposure curve, used in actuarial application to price reinsurance contracts. The vignette shows code snippets to fit the distribution to empirical data.
Author: Giorgio Spedicato
Maintainer: Giorgio Spedicato

Diff between mbbefd versions 0.1 dated 2013-10-30 and 0.5 dated 2015-01-10

 ChangeLog                      |    5 +
 DESCRIPTION                    |   14 +++--
 MD5                            |   29 ++++++----
 NEWS                           |    7 +-
 R/distributionDefinition.R     |   51 ++++++++++++-------
 build                          |only
 inst/CITATION                  |    8 +--
 inst/doc/mbbefd.R              |   86 ++++++++++++++++++++++++++++----
 inst/doc/mbbefd.Rnw            |  109 ++++++++++++++++++++++++++++++++++++++---
 inst/doc/mbbefd.pdf            |binary
 man/mbbefd-package.Rd          |    9 +--
 man/mbbefdDistribution.Rd      |   16 +++---
 tests                          |only
 vignettes/mbbefd-distrPlot.pdf |only
 vignettes/mbbefd-drateplot.pdf |only
 vignettes/mbbefd.Rnw           |  109 ++++++++++++++++++++++++++++++++++++++---
 vignettes/mbbefd.bib           |   43 ++++++++++------
 17 files changed, 395 insertions(+), 91 deletions(-)

More information about mbbefd at CRAN
Permanent link

Package ctv updated to version 0.8-1 with previous version 0.8-0 dated 2014-07-31

Title: CRAN Task Views
Description: Server-side and client-side tools for task views to CRAN-style repositories
Author: Achim Zeileis [aut, cre], Kurt Hornik [aut]
Maintainer: Achim Zeileis

Diff between ctv versions 0.8-0 dated 2014-07-31 and 0.8-1 dated 2015-01-10

 ctv-0.8-0/ctv/inst/ctv/Bayesian.html                  |only
 ctv-0.8-0/ctv/inst/ctv/ChemPhys.html                  |only
 ctv-0.8-0/ctv/inst/ctv/ClinicalTrials.html            |only
 ctv-0.8-0/ctv/inst/ctv/Cluster.html                   |only
 ctv-0.8-0/ctv/inst/ctv/DifferentialEquations.html     |only
 ctv-0.8-0/ctv/inst/ctv/Distributions.html             |only
 ctv-0.8-0/ctv/inst/ctv/Econometrics.html              |only
 ctv-0.8-0/ctv/inst/ctv/Environmetrics.html            |only
 ctv-0.8-0/ctv/inst/ctv/ExperimentalDesign.html        |only
 ctv-0.8-0/ctv/inst/ctv/Finance.html                   |only
 ctv-0.8-0/ctv/inst/ctv/Genetics.html                  |only
 ctv-0.8-0/ctv/inst/ctv/Graphics.html                  |only
 ctv-0.8-0/ctv/inst/ctv/HighPerformanceComputing.html  |only
 ctv-0.8-0/ctv/inst/ctv/MachineLearning.html           |only
 ctv-0.8-0/ctv/inst/ctv/MedicalImaging.html            |only
 ctv-0.8-0/ctv/inst/ctv/MetaAnalysis.html              |only
 ctv-0.8-0/ctv/inst/ctv/Multivariate.html              |only
 ctv-0.8-0/ctv/inst/ctv/NaturalLanguageProcessing.html |only
 ctv-0.8-0/ctv/inst/ctv/NumericalMathematics.html      |only
 ctv-0.8-0/ctv/inst/ctv/OfficialStatistics.html        |only
 ctv-0.8-0/ctv/inst/ctv/Optimization.html              |only
 ctv-0.8-0/ctv/inst/ctv/Pharmacokinetics.html          |only
 ctv-0.8-0/ctv/inst/ctv/Phylogenetics.html             |only
 ctv-0.8-0/ctv/inst/ctv/Psychometrics.html             |only
 ctv-0.8-0/ctv/inst/ctv/ReproducibleResearch.html      |only
 ctv-0.8-0/ctv/inst/ctv/Robust.html                    |only
 ctv-0.8-0/ctv/inst/ctv/SocialSciences.html            |only
 ctv-0.8-0/ctv/inst/ctv/Spatial.html                   |only
 ctv-0.8-0/ctv/inst/ctv/SpatioTemporal.html            |only
 ctv-0.8-0/ctv/inst/ctv/Survival.html                  |only
 ctv-0.8-0/ctv/inst/ctv/TimeSeries.html                |only
 ctv-0.8-0/ctv/inst/ctv/WebTechnologies.html           |only
 ctv-0.8-0/ctv/inst/ctv/gR.html                        |only
 ctv-0.8-1/ctv/DESCRIPTION                             |    8 
 ctv-0.8-1/ctv/MD5                                     |  113 -
 ctv-0.8-1/ctv/NEWS                                    |    6 
 ctv-0.8-1/ctv/R/ctv-server.R                          |   52 
 ctv-0.8-1/ctv/build/vignette.rds                      |binary
 ctv-0.8-1/ctv/inst/ctv/Bayesian.ctv                   |   10 
 ctv-0.8-1/ctv/inst/ctv/ChemPhys.ctv                   |   13 
 ctv-0.8-1/ctv/inst/ctv/ClinicalTrials.ctv             |    4 
 ctv-0.8-1/ctv/inst/ctv/Cluster.ctv                    |   55 
 ctv-0.8-1/ctv/inst/ctv/DifferentialEquations.ctv      |    9 
 ctv-0.8-1/ctv/inst/ctv/Distributions.ctv              |   22 
 ctv-0.8-1/ctv/inst/ctv/Econometrics.ctv               |   26 
 ctv-0.8-1/ctv/inst/ctv/Environmetrics.ctv             |    9 
 ctv-0.8-1/ctv/inst/ctv/ExperimentalDesign.ctv         |    7 
 ctv-0.8-1/ctv/inst/ctv/Finance.ctv                    |   72 -
 ctv-0.8-1/ctv/inst/ctv/Genetics.ctv                   |   19 
 ctv-0.8-1/ctv/inst/ctv/Graphics.ctv                   |   16 
 ctv-0.8-1/ctv/inst/ctv/HighPerformanceComputing.ctv   |   58 
 ctv-0.8-1/ctv/inst/ctv/MachineLearning.ctv            |   45 
 ctv-0.8-1/ctv/inst/ctv/MedicalImaging.ctv             |   27 
 ctv-0.8-1/ctv/inst/ctv/MetaAnalysis.ctv               |   61 
 ctv-0.8-1/ctv/inst/ctv/Multivariate.ctv               |   11 
 ctv-0.8-1/ctv/inst/ctv/NaturalLanguageProcessing.ctv  |    4 
 ctv-0.8-1/ctv/inst/ctv/NumericalMathematics.ctv       |   70 -
 ctv-0.8-1/ctv/inst/ctv/OfficialStatistics.ctv         |   46 
 ctv-0.8-1/ctv/inst/ctv/Optimization.ctv               |   79 -
 ctv-0.8-1/ctv/inst/ctv/Pharmacokinetics.ctv           |   21 
 ctv-0.8-1/ctv/inst/ctv/Phylogenetics.ctv              |   17 
 ctv-0.8-1/ctv/inst/ctv/Psychometrics.ctv              |   56 
 ctv-0.8-1/ctv/inst/ctv/ReproducibleResearch.ctv       |  143 --
 ctv-0.8-1/ctv/inst/ctv/Robust.ctv                     |   71 -
 ctv-0.8-1/ctv/inst/ctv/SocialSciences.ctv             |    2 
 ctv-0.8-1/ctv/inst/ctv/Spatial.ctv                    |   35 
 ctv-0.8-1/ctv/inst/ctv/SpatioTemporal.ctv             | 1103 +++++++++---------
 ctv-0.8-1/ctv/inst/ctv/Survival.ctv                   |  284 +++-
 ctv-0.8-1/ctv/inst/ctv/TimeSeries.ctv                 |   27 
 ctv-0.8-1/ctv/inst/ctv/WebTechnologies.ctv            |  980 ++++++++++-----
 ctv-0.8-1/ctv/inst/doc/ctv-howto.R                    |    2 
 ctv-0.8-1/ctv/inst/doc/ctv-howto.Rnw                  |   11 
 ctv-0.8-1/ctv/inst/doc/ctv-howto.pdf                  |binary
 ctv-0.8-1/ctv/vignettes/ctv-howto.Rnw                 |   11 
 74 files changed, 2044 insertions(+), 1561 deletions(-)

More information about ctv at CRAN
Permanent link

Package aoristic updated to version 0.6 with previous version 0.5 dated 2014-07-31

Title: aoristic analysis with spatial output (kml)
Description: 'Aoristic' is one of the past tenses in Greek and represents an uncertain occurrence time. Aoristic analysis suggested by Ratcliffe (2002) is a method to analyze events that do not have exact times of occurrence but have starting times and ending times. For example, a property crime database (e.g., burglary) typically has a starting time and ending time of the crime that could have occurred. Aoristic analysis allocates the probability of a crime incident occurring at every hour over a 24-hour period. The probability is aggregated over a study area to create an aoristic graph. Using crime incident data with lat/lon, DateTimeFrom, and DateTimeTo, functions in this package create a total of three (3) kml files and corresponding aoristic graphs: 1) density and contour; 2) grid count; and 3) shapefile boundary. (see also: https://sites.google.com/site/georgekick/software)
Author: George Kikuchi
Maintainer: George Kikuchi

Diff between aoristic versions 0.5 dated 2014-07-31 and 0.6 dated 2015-01-10

 DESCRIPTION               |   11 ++++++-----
 MD5                       |   38 +++++++++++++++++++-------------------
 NAMESPACE                 |   16 +++++++++++++++-
 R/aoristic-package.R      |    6 +++---
 R/aoristic.all.graph.R    |   12 ++++++++++--
 R/aoristic.density.R      |    5 ++++-
 R/aoristic.grid.R         |    3 ++-
 R/aoristic.shp.R          |    7 ++++++-
 R/aoristic.spdf.R         |    3 ++-
 demo/aoristic.R           |    6 ++++++
 man/CouncilDistrict.Rd    |    5 +++--
 man/aoristic-package.Rd   |    3 ++-
 man/aoristic.Rd           |    5 +++--
 man/aoristic.all.graph.Rd |   13 +++++++++++--
 man/aoristic.density.Rd   |    3 ++-
 man/aoristic.df.Rd        |    3 ++-
 man/aoristic.grid.Rd      |    3 ++-
 man/aoristic.shp.Rd       |    3 ++-
 man/aoristic.spdf.Rd      |    5 +++--
 man/arlington.Rd          |    5 +++--
 20 files changed, 106 insertions(+), 49 deletions(-)

More information about aoristic at CRAN
Permanent link

Package Rsymphony updated to version 0.1-18 with previous version 0.1-17 dated 2013-11-13

Title: SYMPHONY in R
Description: An R interface to the SYMPHONY solver for mixed-integer linear programs.
Author: Reinhard Harter [aut], Kurt Hornik [aut, cre], Stefan Theussl [aut], Cyrille Szymanski [ctb]
Maintainer: Kurt Hornik

Diff between Rsymphony versions 0.1-17 dated 2013-11-13 and 0.1-18 dated 2015-01-10

 Rsymphony-0.1-17/Rsymphony/src/SYMPHONY           |only
 Rsymphony-0.1-18/Rsymphony/DESCRIPTION            |   14 
 Rsymphony-0.1-18/Rsymphony/MD5                    | 1351 ----------------------
 Rsymphony-0.1-18/Rsymphony/cleanup                |    7 
 Rsymphony-0.1-18/Rsymphony/configure              |   44 
 Rsymphony-0.1-18/Rsymphony/man/Rsymphony_solve.Rd |    2 
 Rsymphony-0.1-18/Rsymphony/src/Makevars.in        |   16 
 7 files changed, 30 insertions(+), 1404 deletions(-)

More information about Rsymphony at CRAN
Permanent link

New package neuRosim with initial version 0.2-12
Package: neuRosim
Type: Package
Title: Functions to Generate fMRI Data Including Activated Data, Noise Data and Resting State Data
Version: 0.2-12
Date: 2015-01-09
Author: Marijke Welvaert with contributions from Joke Durnez, Beatrijs Moerkerke, Yves Rosseel and Geert Verdoolaege
Maintainer: Marijke Welvaert
Depends: R (>= 3.1.1), deSolve
Description: The package allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments.
License: GPL (>= 2)
LazyLoad: yes
Repository: CRAN
Date/Publication: 2015-01-10 10:01:21
Packaged: 2015-01-09 00:52:20 UTC; wel18s
NeedsCompilation: yes

More information about neuRosim at CRAN
Permanent link

Package kernlab updated to version 0.9-20 with previous version 0.9-19 dated 2013-11-03

Title: Kernel-based Machine Learning Lab
Description: Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods kernlab includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre], Alex Smola [aut], Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou

Diff between kernlab versions 0.9-19 dated 2013-11-03 and 0.9-20 dated 2015-01-10

 DESCRIPTION           |    6 +++---
 MD5                   |   28 ++++++++++++++--------------
 build/vignette.rds    |binary
 data/income.rda       |binary
 data/musk.rda         |binary
 data/promotergene.rda |binary
 data/reuters.rda      |binary
 data/spam.rda         |binary
 data/spirals.rda      |binary
 data/ticdata.rda      |binary
 inst/COPYRIGHTS       |    4 ++++
 inst/doc/kernlab.pdf  |binary
 src/msufsort.cpp      |    1 +
 src/msufsort.h        |   29 +++++++++++++++++++----------
 src/svm.cpp           |    7 ++++++-
 15 files changed, 47 insertions(+), 28 deletions(-)

More information about kernlab at CRAN
Permanent link

New package IFP with initial version 0.1.1
Package: IFP
Version: 0.1.1
Date: 2014-12-28
Title: Identifying Functional Polymorphisms
Author: Leeyoung Park
Maintainer: Leeyoung Park
Description: A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
License: GPL (>= 2)
Depends: R (>= 2.11.1)
Imports: haplo.stats,coda
Suggests:
URL: http://www.r-project.org
NeedsCompilation: yes
Repository: CRAN
Packaged: 2015-01-07 14:58:19 UTC; x998ply
Date/Publication: 2015-01-10 10:01:19

More information about IFP at CRAN
Permanent link

Package celestial updated to version 1.2 with previous version 1.1 dated 2013-08-10

Title: Collection of common astronomical conversion routines
Description: This package includes a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former.
Author: Aaron Robotham
Maintainer: Aaron Robotham

Diff between celestial versions 1.1 dated 2013-08-10 and 1.2 dated 2015-01-10

 DESCRIPTION              |   10 +++++-----
 MD5                      |   12 +++++++++---
 NEWS                     |    4 ++++
 R/cosdist.R              |only
 R/cosvol.R               |only
 R/skyarea.R              |only
 man/celestial-package.Rd |    4 ++--
 man/cosdist.Rd           |only
 man/cosvol.Rd            |only
 man/skyarea.Rd           |only
 10 files changed, 20 insertions(+), 10 deletions(-)

More information about celestial at CRAN
Permanent link


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