Thu, 11 Sep 2014

Package GENLIB (with last version 1.0) was removed from CRAN

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

2014-09-11 1.0

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Package VennDiagram updated to version 1.6.8 with previous version 1.6.7 dated 2014-07-03

Title: Generate high-resolution Venn and Euler plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros

Diff between VennDiagram versions 1.6.7 dated 2014-07-03 and 1.6.8 dated 2014-09-11

 DESCRIPTION            |    6 ++--
 MD5                    |    8 +++---
 NAMESPACE              |    1 
 R/draw.pairwise.venn.R |   59 +++++++++++++++++++++++++------------------------
 TODO                   |    1 
 5 files changed, 40 insertions(+), 35 deletions(-)

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New package lefse with initial version 0.1
Package: lefse
Type: Package
Title: Phylogenetic and Functional Analyses for Ecology
Version: 0.1
Date: 2014-09-04
Author: Nathan G. Swenson
Maintainer: Nathan G. Swenson
Description: Utilizing phylogenetic and functional information for the analyses of ecological datasets. The analyses include methods for quantifying the phylogenetic and functional diversity of assemblages.
License: GPL-2 | GPL-3
Depends: R (>= 2.10)
Imports: ape, picante, geiger, fBasics, SDMTools, vegan
Packaged: 2014-09-05 10:37:55 UTC; nathanswenson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 21:03:26

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New package GENLIB with initial version 1.0
Package: GENLIB
Type: Package
Title: Genealogical Data Analysis
Version: 1.0
Date: 2012-04-04
Author: Louis Houde, Jean-Francois Lefebvre, Valery Roy-Lagace, Sebastien Lemieux
Maintainer: Marie-Helene Roy-Gagnon
Description: Takes genealogical data frames and calculates different demographic variables such as genetic contribution, kinship, etc...
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 3.0), Rcpp (>= 0.9.10)
Imports: kinship2, methods, bootstrap, Matrix, lattice, quadprog, foreach, parallel, doParallel
LinkingTo: Rcpp
Packaged: 2014-09-11 16:31:06 UTC; sainte-justine\lefjea01
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 21:02:19

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Package intsvy updated to version 1.4 with previous version 1.3 dated 2014-03-13

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA and PIAAC)
Author: Daniel Caro , Przemyslaw Biecek
Maintainer: Daniel Caro

Diff between intsvy versions 1.3 dated 2014-03-13 and 1.4 dated 2014-09-11

 intsvy-1.3/intsvy/data                        |only
 intsvy-1.3/intsvy/man/file.names.Rd           |only
 intsvy-1.3/intsvy/man/iea.country.Rd          |only
 intsvy-1.3/intsvy/man/pisa.country.Rd         |only
 intsvy-1.4/intsvy/DESCRIPTION                 |   17 
 intsvy-1.4/intsvy/MD5                         |  164 ++++----
 intsvy-1.4/intsvy/NAMESPACE                   |   83 ++--
 intsvy-1.4/intsvy/R/adj.input.R               |   22 -
 intsvy-1.4/intsvy/R/adj.measlev.R             |   12 
 intsvy-1.4/intsvy/R/is.vlabeled.R             |   24 -
 intsvy-1.4/intsvy/R/piaac.mean.R              |only
 intsvy-1.4/intsvy/R/piaac.mean.pv.R           |only
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 intsvy-1.4/intsvy/R/piaac.table.R             |only
 intsvy-1.4/intsvy/R/pirls.ben.pv.R            |   90 ++--
 intsvy-1.4/intsvy/R/pirls.mean.R              |   52 +-
 intsvy-1.4/intsvy/R/pirls.mean.pv.R           |   98 ++---
 intsvy-1.4/intsvy/R/pirls.reg.R               |   92 ++--
 intsvy-1.4/intsvy/R/pirls.reg.pv.R            |  112 ++---
 intsvy-1.4/intsvy/R/pirls.rho.R               |   62 +--
 intsvy-1.4/intsvy/R/pirls.rho.pv.R            |  146 +++----
 intsvy-1.4/intsvy/R/pirls.select.merge.R      |  486 ++++++++++++-------------
 intsvy-1.4/intsvy/R/pirls.table.R             |   86 ++--
 intsvy-1.4/intsvy/R/pirls.var.label.R         |   82 ++--
 intsvy-1.4/intsvy/R/pisa.ben.pv.R             |  132 +++---
 intsvy-1.4/intsvy/R/pisa.mean.R               |   64 +--
 intsvy-1.4/intsvy/R/pisa.mean.pv.R            |  119 ++++--
 intsvy-1.4/intsvy/R/pisa.reg.R                |   90 ++--
 intsvy-1.4/intsvy/R/pisa.reg.pv.R             |  123 +++---
 intsvy-1.4/intsvy/R/pisa.select.merge.R       |  350 +++++++++---------
 intsvy-1.4/intsvy/R/pisa.table.R              |   98 ++---
 intsvy-1.4/intsvy/R/pisa.var.label.R          |   94 ++--
 intsvy-1.4/intsvy/R/plot.intsvy.mean.R        |only
 intsvy-1.4/intsvy/R/plot.intsvy.reg.R         |only
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 intsvy-1.4/intsvy/R/timss.ben.pv.R            |   90 ++--
 intsvy-1.4/intsvy/R/timss.mean.R              |   52 +-
 intsvy-1.4/intsvy/R/timss.mean.pv.R           |   99 ++---
 intsvy-1.4/intsvy/R/timss.reg.R               |   92 ++--
 intsvy-1.4/intsvy/R/timss.reg.pv.R            |  112 ++---
 intsvy-1.4/intsvy/R/timss.rho.R               |   62 +--
 intsvy-1.4/intsvy/R/timss.rho.pv.R            |  146 +++----
 intsvy-1.4/intsvy/R/timss.table.R             |   86 ++--
 intsvy-1.4/intsvy/R/timssg4.select.merge.R    |  500 +++++++++++++-------------
 intsvy-1.4/intsvy/R/timssg4.var.label.R       |   82 ++--
 intsvy-1.4/intsvy/R/timssg8.select.merge.R    |  398 ++++++++++----------
 intsvy-1.4/intsvy/R/timssg8.var.label.R       |   80 ++--
 intsvy-1.4/intsvy/README.md                   |only
 intsvy-1.4/intsvy/man/adj.input.Rd            |   70 +--
 intsvy-1.4/intsvy/man/adj.measlev.Rd          |   74 +--
 intsvy-1.4/intsvy/man/intsvy-package.Rd       |   40 +-
 intsvy-1.4/intsvy/man/is.vlabeled.Rd          |   70 +--
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 intsvy-1.4/intsvy/man/pirls.ben.pv.Rd         |  108 ++---
 intsvy-1.4/intsvy/man/pirls.mean.Rd           |  100 ++---
 intsvy-1.4/intsvy/man/pirls.mean.pv.Rd        |  104 ++---
 intsvy-1.4/intsvy/man/pirls.reg.Rd            |  122 +++---
 intsvy-1.4/intsvy/man/pirls.reg.pv.Rd         |  112 ++---
 intsvy-1.4/intsvy/man/pirls.rho.Rd            |   98 ++---
 intsvy-1.4/intsvy/man/pirls.rho.pv.Rd         |  102 ++---
 intsvy-1.4/intsvy/man/pirls.select.merge.Rd   |   96 ++--
 intsvy-1.4/intsvy/man/pirls.table.Rd          |   98 ++---
 intsvy-1.4/intsvy/man/pirls.var.label.Rd      |   74 +--
 intsvy-1.4/intsvy/man/pisa.ben.pv.Rd          |   98 ++---
 intsvy-1.4/intsvy/man/pisa.mean.Rd            |  107 ++---
 intsvy-1.4/intsvy/man/pisa.mean.pv.Rd         |  112 +++--
 intsvy-1.4/intsvy/man/pisa.reg.Rd             |   95 ++--
 intsvy-1.4/intsvy/man/pisa.reg.pv.Rd          |  102 ++---
 intsvy-1.4/intsvy/man/pisa.select.merge.Rd    |  118 +++---
 intsvy-1.4/intsvy/man/pisa.table.Rd           |   96 ++--
 intsvy-1.4/intsvy/man/pisa.var.label.Rd       |   96 ++--
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 intsvy-1.4/intsvy/man/timss.ben.pv.Rd         |  112 ++---
 intsvy-1.4/intsvy/man/timss.mean.Rd           |  106 ++---
 intsvy-1.4/intsvy/man/timss.mean.pv.Rd        |  106 ++---
 intsvy-1.4/intsvy/man/timss.reg.Rd            |  100 ++---
 intsvy-1.4/intsvy/man/timss.reg.pv.Rd         |  106 ++---
 intsvy-1.4/intsvy/man/timss.rho.Rd            |   98 ++---
 intsvy-1.4/intsvy/man/timss.rho.pv.Rd         |  102 ++---
 intsvy-1.4/intsvy/man/timss.table.Rd          |  118 +++---
 intsvy-1.4/intsvy/man/timssg4.select.merge.Rd |  100 ++---
 intsvy-1.4/intsvy/man/timssg4.var.label.Rd    |   70 +--
 intsvy-1.4/intsvy/man/timssg8.select.merge.Rd |   96 ++--
 intsvy-1.4/intsvy/man/timssg8.var.label.Rd    |   72 +--
 intsvy-1.4/intsvy/vignettes                   |only
 93 files changed, 3946 insertions(+), 3829 deletions(-)

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Package snpEnrichment updated to version 1.4-1 with previous version 1.4-0 dated 2014-02-04

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

Diff between snpEnrichment versions 1.4-0 dated 2014-02-04 and 1.4-1 dated 2014-09-11

 ChangeLog                    |   21 ++++++++-----
 DESCRIPTION                  |    8 ++---
 MD5                          |   38 ++++++++++++------------
 NAMESPACE                    |    4 +-
 R/Global.R                   |   52 ++++++++++++++-------------------
 R/enrichment.R               |   66 +++++++++++++++++++++++++++++++------------
 data/toyEnrichment.RData     |binary
 man/Chromosome-class.Rd      |   28 +++++++++---------
 man/EnrichSNP-class.Rd       |    4 +-
 man/Enrichment-class.Rd      |   12 +++----
 man/compareEnrichment.Rd     |   30 +++++++++----------
 man/excludeSNP-methods.Rd    |    2 -
 man/initFiles.Rd             |   14 ++++-----
 man/mclapply2.Rd             |    4 +-
 man/plot-methods.Rd          |    2 -
 man/reSample-methods.Rd      |   22 +++++++-------
 man/readEnrichment.Rd        |   36 +++++++++++------------
 man/snpEnrichment-package.Rd |   44 ++++++++++++++--------------
 man/transcript-dataset.Rd    |    2 -
 man/writeLD.Rd               |   16 +++++-----
 20 files changed, 216 insertions(+), 189 deletions(-)

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Package knnIndep updated to version 2.0 with previous version 1.0 dated 2014-03-18

Title: Independence tests and benchmarks
Description: This package provides the implementation of an exact formula of the ith nearest neighbour distance distribution and implementations of tests of independence based on that formula. Furthermore the package provides a general framework to benchmark tests of independence.
Author: Sebastian Dümcke
Maintainer: Sebastian Dümcke

Diff between knnIndep versions 1.0 dated 2014-03-18 and 2.0 dated 2014-09-11

 DESCRIPTION               |   10 +++++-----
 MD5                       |   29 ++++++++++++++++++++---------
 NAMESPACE                 |    3 +++
 R/P_ceq.R                 |   17 ++++++-----------
 R/P_cge_aeq.R             |only
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 R/parameters.R            |   15 ++++++++++++++-
 R/power.plot.R            |    6 +++++-
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 21 files changed, 63 insertions(+), 35 deletions(-)

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Package glmmLasso updated to version 1.3.3 with previous version 1.3.2 dated 2014-09-10

Title: Variable selection for generalized linear mixed models by L1-penalized estimation
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll

Diff between glmmLasso versions 1.3.2 dated 2014-09-10 and 1.3.3 dated 2014-09-11

 DESCRIPTION                        |    8 ++++----
 MD5                                |   14 +++++++-------
 R/glmmLasso.r                      |   15 ++++++++++-----
 R/glmm_final.r                     |    6 ++++--
 R/glmm_final.smooth.r              |    6 ++++--
 R/glmm_final_multi_random.r        |    6 ++++--
 R/glmm_final_multi_random_smooth.r |    6 ++++--
 man/glmmLasso.rd                   |   13 +++++++------
 8 files changed, 44 insertions(+), 30 deletions(-)

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Package pkgKitten updated to version 0.1.2 with previous version 0.1.1 dated 2014-09-10

Title: Create Simple Packages Which Do Not Upset R CMD check
Description: Provides a function kitten() which creates cute little packages which pass R CMD check. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between pkgKitten versions 0.1.1 dated 2014-09-10 and 0.1.2 dated 2014-09-11

 ChangeLog     |    6 ++++++
 DESCRIPTION   |    8 ++++----
 MD5           |    8 ++++----
 R/pkgKitten.R |    2 +-
 inst/NEWS.Rd  |    7 +++++++
 5 files changed, 22 insertions(+), 9 deletions(-)

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Package pbkrtest updated to version 0.4-1 with previous version 0.4-0 dated 2014-08-11

Title: Parametric bootstrap and Kenward Roger based methods for mixed model comparison
Description: Test in linear mixed effects models. Attention is on linear mixed effects models as implemented in the lme4 package. The package implements a parametric bootstrap test The package implements a Kenward-Roger modification of F-tests
Author: Ulrich Halekoh Sren Hjsgaard
Maintainer: Sren Hjsgaard

Diff between pbkrtest versions 0.4-0 dated 2014-08-11 and 0.4-1 dated 2014-09-11

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 pbkrtest-0.4-1/pbkrtest/ChangeLog                           |   64 +-
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 pbkrtest-0.4-1/pbkrtest/NAMESPACE                           |   14 
 pbkrtest-0.4-1/pbkrtest/R/KR-vcovAdj.R                      |  187 ++++---
 pbkrtest-0.4-1/pbkrtest/R/get_ddf_Lb.R                      |  155 +++--
 pbkrtest-0.4-1/pbkrtest/build/vignette.rds                  |binary
 pbkrtest-0.4-1/pbkrtest/data/beets.txt.gz                   |binary
 pbkrtest-0.4-1/pbkrtest/data/budworm.txt.gz                 |binary
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.R    |  311 +++++-------
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.Rnw  |  179 ++----
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.pdf  |binary
 pbkrtest-0.4-1/pbkrtest/man/KRmodcomp.Rd                    |    2 
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 pbkrtest-0.4-1/pbkrtest/man/getKR.Rd                        |    2 
 pbkrtest-0.4-1/pbkrtest/man/get_ddf_Lb.Rd                   |   58 +-
 pbkrtest-0.4-1/pbkrtest/man/model2restrictionMatrix.Rd      |    2 
 pbkrtest-0.4-1/pbkrtest/man/pbkrtest-internal.Rd            |    8 
 pbkrtest-0.4-1/pbkrtest/man/vcovAdj.Rd                      |    2 
 pbkrtest-0.4-1/pbkrtest/vignettes/pbkrtest-introduction.Rnw |  179 ++----
 22 files changed, 635 insertions(+), 583 deletions(-)

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New package gapmap with initial version 0.0.1
Package: gapmap
Type: Package
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Version: 0.0.1
URL: https://bitbucket.org/biovizleuven/gapmap/
Date: 2014-09-10
Author: Ryo Sakai
Maintainer: Ryo Sakai
Description: The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters.
License: GPL-2 | GPL-3
Depends: ggplot2, grid, reshape2
Suggests: knitr, dendsort
VignetteBuilder: knitr
Packaged: 2014-09-11 10:21:51 UTC; Ryo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 13:06:15

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New package FRESA.CAD with initial version 1.0
Package: FRESA.CAD
Type: Package
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Version: 1.0
Date: 2014-09-10
Author: Jose Gerardo Tamez-Pena
Maintainer: Jose Gerardo Tamez-Pena
Description: FRESA.CAD provides a set of functions and feature selection algorithms for building Computer Aided Diagnosis Models
License: LGPL (>= 2)
Depends: R (>= 3.0.0),Hmisc,pROC,stringr,miscTools,survival
Suggests: class, cvTools, glmnet, speedglm, gplots, RColorBrewer, nlme, rpart
Packaged: 2014-09-11 12:24:47 UTC; Jose Tamez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 15:08:50

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Package rsubgroup updated to version 0.6 with previous version 0.5 dated 2014-08-06

Title: Subgroup Discovery and Analytics
Description: A collection of efficient and effective tools and algorithms for subgroup discovery and analytics. The package integrates an R interface to the org.vikamine.kernel library of the VIKAMINE system (http://www.vikamine.org) implementing subgroup discovery, pattern mining and analytics in Java.
Author: Martin Atzmueller
Maintainer: Martin Atzmueller

Diff between rsubgroup versions 0.5 dated 2014-08-06 and 0.6 dated 2014-09-11

 DESCRIPTION                    |   12 ++++++------
 MD5                            |   25 +++++++++++++------------
 NEWS                           |only
 R/classes.R                    |   11 +++++++++--
 R/subgroup.R                   |    9 +++++++--
 inst/java/subgroup.jar         |binary
 man/CreateSDTask.Rd            |    2 +-
 man/DiscoverSubgroups.Rd       |   11 +++++++----
 man/DiscoverSubgroupsByTask.Rd |   11 +++++++----
 man/Pattern-class.Rd           |    2 +-
 man/SDTaskConfig-class.Rd      |    3 ++-
 man/ToDataframe.Rd             |    2 +-
 man/as.target.Rd               |    2 +-
 man/subgroup-package.Rd        |    7 +++----
 14 files changed, 58 insertions(+), 39 deletions(-)

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New package lcmm with initial version 1.6.6
Package: lcmm
Type: Package
Title: Estimation of Extended Mixed Models Using Latent Classes and Latent Processes
Version: 1.6.6
Date: 2014-09-10
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
Description: Functions for the estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
License: GPL (>= 2.0)
Depends: R (>= 2.9.0), survival
LazyLoad: yes
Packaged: 2014-09-10 09:08:05 UTC; vp3
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 11:39:40

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New package gdsfmt with initial version 1.1.0
Package: gdsfmt
Type: Package
Title: R Interface to CoreArray Genomic Data Structure (GDS) files
Version: 1.1.0
Date: 2014-09-10
Depends: R (>= 2.14.0)
Imports: methods
Suggests: parallel, RUnit
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
BugReports: http://github.com/zhengxwen/gdsfmt/issues
Description: This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers with less than 8 bits, since a single genetic/genomic variant, such like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.
License: LGPL-3
URL: http://corearray.sourceforge.net/, http://github.com/zhengxwen/gdsfmt
Packaged: 2014-09-11 06:43:57 UTC; sts
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 12:33:04

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Package RankResponse updated to version 3.1.1 with previous version 3.0.3 dated 2014-04-03

Title: Ranking Responses in a Single Response Question or a Multiple Response Question
Description: Methods for ranking responses of a single response question or a multiple response question
Author: Hsiuying Wang, Yu-Chun Lin
Maintainer: Hsiuying Wang

Diff between RankResponse versions 3.0.3 dated 2014-04-03 and 3.1.1 dated 2014-09-11

 RankResponse-3.0.3/RankResponse/R/rank.LR.R      |only
 RankResponse-3.0.3/RankResponse/man/rank.LR.Rd   |only
 RankResponse-3.1.1/RankResponse/DESCRIPTION      |   10 +-
 RankResponse-3.1.1/RankResponse/MD5              |   32 ++++----
 RankResponse-3.1.1/RankResponse/R/rank.L2R.R     |   35 +--------
 RankResponse-3.1.1/RankResponse/R/rank.LN.R      |   54 ++------------
 RankResponse-3.1.1/RankResponse/R/rank.btmm.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.btnr.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.btqn.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.gs.R      |   72 ++++++++-----------
 RankResponse-3.1.1/RankResponse/R/rank.wald.R    |   85 ++++++++++-------------
 RankResponse-3.1.1/RankResponse/man/rank.L2R.Rd  |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.LN.Rd   |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btmm.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btnr.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btqn.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.gs.Rd   |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.wald.Rd |    4 -
 18 files changed, 125 insertions(+), 203 deletions(-)

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New package recosystem with initial version 0.2.3
Package: recosystem
Type: Package
Title: Recommender System using Matrix Factorization
Version: 0.2.3
Date: 2014-09-08
Authors@R: c(person(given = "Yixuan", family = "Qiu", role = c("aut", "cre"), email = "yixuan.qiu@cos.name"), person(given = "Chih-Jen", family = "Lin", role = c("aut","cph"), comment = "original C++ code"), person(given = "Yu-Chin", family = "Juan", role = c("aut","cph"), comment = "original C++ code"), person(given = "Yong", family = "Zhuang", role = c("aut","cph"), comment = "original C++ code"), person(given = "Wei-Sheng", family = "Chin", role = c("aut","cph"), comment = "original C++ code"))
Maintainer: Yixuan Qiu
Description: This package is an R wrapper of the libmf library (http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc.
License: BSD_3_clause + file LICENSE
Copyright: see file COPYRIGHTS
URL: https://github.com/yixuan/recosystem
BugReports: https://github.com/yixuan/recosystem/issues
SystemRequirements: C++11
Depends: methods
Imports: Rcpp (>= 0.11.0)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
Packaged: 2014-09-08 15:06:23 UTC; qyx
Author: Yixuan Qiu [aut, cre], Chih-Jen Lin [aut, cph] (original C++ code), Yu-Chin Juan [aut, cph] (original C++ code), Yong Zhuang [aut, cph] (original C++ code), Wei-Sheng Chin [aut, cph] (original C++ code)
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 10:00:26

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Package rplexos updated to version 0.9.1 with previous version 0.9 dated 2014-08-26

Title: Read and analyze PLEXOS solutions from R
Description: Read and analyze PLEXOS solutions from R
Author: Eduardo Ibanez
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.9 dated 2014-08-26 and 0.9.1 dated 2014-09-11

 DESCRIPTION           |    8 +--
 MD5                   |   35 +++++++-------
 NAMESPACE             |    3 -
 R/auxiliary.R         |   16 ++++++
 R/globalVariables.R   |    2 
 R/plexos_open.R       |   44 +++++++-----------
 R/process_folder.R    |    2 
 R/process_solution.R  |  111 ++++++++++++++++++++++++++---------------------
 R/query.R             |   67 +++++++++++++++++++++++-----
 man/list_folders.Rd   |    2 
 man/plexos_close.Rd   |    2 
 man/plexos_open.Rd    |    2 
 man/process_folder.Rd |    6 +-
 man/query_config.Rd   |only
 man/query_master.Rd   |    2 
 man/query_property.Rd |    2 
 man/rplexos.Rd        |    2 
 man/valid_columns.Rd  |    2 
 src/process_xml.cpp   |  117 ++++++++++++++++++++++++++++++++------------------
 19 files changed, 261 insertions(+), 164 deletions(-)

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New package rChoiceDialogs with initial version 1.0.6
Package: rChoiceDialogs
Type: Package
Title: rChoiceDialogs collection
Version: 1.0.6
Date: 2014-09-05
Authors@R: c(person("Alex","Lisovich",role=c("aut","cre"),email="alex.lisovich@gmail.com"), person("Roger","Day",role="aut",email="day01@pitt.edu"), person("Sun Microsystems, Inc",role="cph", comment="swing-layout-1.0.4.jar, download from http://www.java2s.com/Code/Jar/s/Downloadswinglayout104jar.htm"))
Description: Collection of portable choice dialog widgets
License: LGPL (>= 2.1)
Depends: rJava, utils
Imports: tcltk
Collate: 'zzz.R' 'rChoiceDialogs-package.R' 'rFileChooser.R' 'rListChooser.R' 'rMiscFunctions.R'
Packaged: 2014-09-10 20:49:54 UTC; alex
Author: Alex Lisovich [aut, cre], Roger Day [aut], Sun Microsystems, Inc [cph] (swing-layout-1.0.4.jar, download from http://www.java2s.com/Code/Jar/s/Downloadswinglayout104jar.htm)
Maintainer: Alex Lisovich
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 07:26:55

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Package lmms updated to version 1.1 with previous version 1.0 dated 2014-06-06

Title: Linear mixed effect model splines for modelling and analysis of time course data
Description: The package implements linear mixed effect model splines for modelling and differential expression for highly dimensional data sets: investNoise for quality control and filterNoise for removing non-informative trajectories; lmmSpline to model time course expression profiles and lmmsDE performs differential expression analysis to identify differential expression between groups, time and/or time x group interaction.
Author: Jasmin Straube, Kim-Anh Le Cao and Emma Huang with contributions of Dominique Gorse
Maintainer: Jasmin Straube

Diff between lmms versions 1.0 dated 2014-06-06 and 1.1 dated 2014-09-11

 DESCRIPTION                   |   16 +++++++++-------
 MD5                           |   39 ++++++++++++++++++++++++---------------
 NAMESPACE                     |    9 +++++++++
 R/AllClasses.R                |   17 +++++++++++++++++
 R/filterNoise-method.R        |only
 R/investNoise-method.R        |only
 R/lmmSpline-method.R          |    4 ++--
 R/lmmsDE-method.R             |    4 ++--
 R/plot.lmmsde-method.R        |   26 +++++++++++++-------------
 R/plot.lmmspline-method.R     |   27 ++++++++++++++-------------
 R/plot.noise-method.R         |only
 R/predict.lmmspline-method.R  |    2 +-
 R/summary.lmmsde-methods.R    |    1 +
 R/summary.lmmspline-methods.R |    1 +
 R/summary.noise-methods.R     |only
 man/filterNoise-methods.Rd    |only
 man/investNoise-methods.Rd    |only
 man/lmmSpline-methods.Rd      |    5 ++---
 man/lmms-package.Rd           |    3 ++-
 man/lmmsDE-methods.Rd         |    5 ++---
 man/noise-class.Rd            |only
 man/plot.lmmsde.Rd            |    4 ++--
 man/plot.noise.Rd             |only
 man/predict.lmmspline.Rd      |    2 +-
 man/summary.noise.Rd          |only
 25 files changed, 102 insertions(+), 63 deletions(-)

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New package OjaNP with initial version 0.9-8
Package: OjaNP
Type: Package
Title: Multivariate Methods Based on the Oja Median and Related Concepts
Version: 0.9-8
Date: 2014-09-10
Author: Daniel Fischer, Jyrki Mttnen, Klaus Nordhausen, Daniel Vogel
Maintainer: Klaus Nordhausen
Depends: R (>= 2.9.0), ICS, ICSNP
Description: The package provides functions for the Oja median, Oja signs and ranks and methods based upon them.
License: GPL (>= 2)
Encoding: latin1
LazyLoad: yes
Packaged: 2014-09-10 09:19:18 UTC; klaus
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 08:48:28

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Package DatABEL updated to version 0.9-5 with previous version 0.9-4.1 dated 2014-07-27

Title: file-based access to large matrices stored on HDD in binary format
Description: a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim Struchalin
Maintainer: Yurii Aulchenko

Diff between DatABEL versions 0.9-4.1 dated 2014-07-27 and 0.9-5 dated 2014-09-11

 DatABEL-0.9-4.1/DatABEL/CHANGES.LOG                    |only
 DatABEL-0.9-4.1/DatABEL/src/Rstaff.h                   |only
 DatABEL-0.9-5/DatABEL/ChangeLog                        |only
 DatABEL-0.9-5/DatABEL/DESCRIPTION                      |   22 
 DatABEL-0.9-5/DatABEL/MD5                              |  119 -
 DatABEL-0.9-5/DatABEL/NAMESPACE                        |   81 -
 DatABEL-0.9-5/DatABEL/R/DatABEL-package.R              |   32 
 DatABEL-0.9-5/DatABEL/R/apply2dfo.R                    |  406 +++--
 DatABEL-0.9-5/DatABEL/R/apply2dfo_util.R               |  129 +
 DatABEL-0.9-5/DatABEL/R/checkPackageVersionOnCRAN.R    |  130 +
 DatABEL-0.9-5/DatABEL/R/databel.R                      |   16 
 DatABEL-0.9-5/DatABEL/R/databel2matrix.R               |    1 
 DatABEL-0.9-5/DatABEL/R/databel2text.R                 |   13 
 DatABEL-0.9-5/DatABEL/R/databel_class.R                | 1033 ++++++++-------
 DatABEL-0.9-5/DatABEL/R/databel_class_internal.R       |  127 -
 DatABEL-0.9-5/DatABEL/R/extract_text_file_columns.R    |   39 
 DatABEL-0.9-5/DatABEL/R/get_temporary_file_name.R      |   40 
 DatABEL-0.9-5/DatABEL/R/make_empty_fvf.R               |   55 
 DatABEL-0.9-5/DatABEL/R/matrix2databel.R               |   49 
 DatABEL-0.9-5/DatABEL/R/text2databel.R                 |  273 ++--
 DatABEL-0.9-5/DatABEL/R/zzz.R                          |   12 
 DatABEL-0.9-5/DatABEL/build                            |only
 DatABEL-0.9-5/DatABEL/inst/doc/intro_DatABEL.R         |only
 DatABEL-0.9-5/DatABEL/inst/doc/intro_DatABEL.pdf       |binary
 DatABEL-0.9-5/DatABEL/man/DatABEL-package.Rd           |   29 
 DatABEL-0.9-5/DatABEL/man/apply2dfo.Rd                 |  100 -
 DatABEL-0.9-5/DatABEL/man/checkPackageVersionOnCRAN.Rd |only
 DatABEL-0.9-5/DatABEL/man/databel-class.Rd             |  212 +--
 DatABEL-0.9-5/DatABEL/man/databel.Rd                   |   16 
 DatABEL-0.9-5/DatABEL/man/databel2matrix.Rd            |   20 
 DatABEL-0.9-5/DatABEL/man/databel2text.Rd              |   21 
 DatABEL-0.9-5/DatABEL/man/extract_text_file_columns.Rd |   15 
 DatABEL-0.9-5/DatABEL/man/get_temporary_file_name.Rd   |   13 
 DatABEL-0.9-5/DatABEL/man/make_empty_fvf.Rd            |   28 
 DatABEL-0.9-5/DatABEL/man/matrix2databel.Rd            |   31 
 DatABEL-0.9-5/DatABEL/man/process_lm_output.Rd         |   25 
 DatABEL-0.9-5/DatABEL/man/text2databel.Rd              |  185 +-
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix.cpp           |   12 
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix.h             |  113 -
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix_R.cpp         |   13 
 DatABEL-0.9-5/DatABEL/src/CastUtils.cpp                |  294 ++--
 DatABEL-0.9-5/DatABEL/src/CastUtils.h                  |  144 +-
 DatABEL-0.9-5/DatABEL/src/FileVector.cpp               | 1159 +++++++++--------
 DatABEL-0.9-5/DatABEL/src/FileVector.h                 |  219 +--
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix.cpp           |  117 +
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix.h             |  173 +-
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix_R.cpp         |   10 
 DatABEL-0.9-5/DatABEL/src/Logger.cpp                   |    7 
 DatABEL-0.9-5/DatABEL/src/Logger.h                     |   30 
 DatABEL-0.9-5/DatABEL/src/RealHandlerWrapper.cpp       |   21 
 DatABEL-0.9-5/DatABEL/src/RealHandlerWrapper.h         |   10 
 DatABEL-0.9-5/DatABEL/src/ReusableFileHandle.cpp       |   31 
 DatABEL-0.9-5/DatABEL/src/ReusableFileHandle.h         |   28 
 DatABEL-0.9-5/DatABEL/src/Rstuff.h                     |only
 DatABEL-0.9-5/DatABEL/src/Transposer.cpp               |  239 ++-
 DatABEL-0.9-5/DatABEL/src/Transposer.h                 |   50 
 DatABEL-0.9-5/DatABEL/src/convert_util.cpp             |  567 ++++----
 DatABEL-0.9-5/DatABEL/src/convert_util.h               |   10 
 DatABEL-0.9-5/DatABEL/src/dautil.cpp                   |    2 
 DatABEL-0.9-5/DatABEL/src/dautil.h                     |    2 
 DatABEL-0.9-5/DatABEL/src/frutil.cpp                   |  243 +--
 DatABEL-0.9-5/DatABEL/src/frutil.h                     |   88 -
 DatABEL-0.9-5/DatABEL/src/iterator.cpp                 |    4 
 DatABEL-0.9-5/DatABEL/src/iterator_functions.cpp       |    2 
 64 files changed, 3742 insertions(+), 3118 deletions(-)

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New package funFEM with initial version 1.0
Package: funFEM
Type: Package
Title: Clustering in the Discriminative Functional Subspace
Version: 1.0
Date: 2014-09-06
Author: Charles Bouveyron
Depends: R (>= 2.10), MASS, fda, elasticnet
Maintainer: Charles Bouveyron
Description: The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace.
License: GPL-2
LazyLoad: yes
Packaged: 2014-09-10 07:52:48 UTC; charles
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 07:36:22

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