Thu, 28 Apr 2016

Package MDplot updated to version 0.3.1 with previous version 0.3 dated 2016-02-18

Title: Visualising Molecular Dynamics Analyses
Description: Provides automatization for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis.
Author: Christian Margreitter [aut, cre]
Maintainer: Christian Margreitter <christian.margreitter@gmail.com>

Diff between MDplot versions 0.3 dated 2016-02-18 and 0.3.1 dated 2016-04-28

 DESCRIPTION                |   10 ++++-----
 MD5                        |   38 +++++++++++++++++------------------
 NAMESPACE                  |    3 +-
 NEWS                       |   15 ++++++++++++--
 R/TIcurve.R                |   37 ++++++++++++++++++++++++++++++----
 R/clusters.R               |   48 +++++++++++++++++++++++++++++++++++++++------
 R/dssp.R                   |    2 +
 R/hbond.R                  |   30 ++++++++++++++++------------
 R/helperfunctions.R        |   12 +++++++++++
 R/ramachandran.R           |   20 +++++++++++-------
 R/rmsd.R                   |    7 ++++++
 R/rmsf.R                   |    2 +
 R/timeseries.R             |    9 +++++++-
 R/xrmsd.R                  |   32 ++++++++++++++++++++----------
 inst/bash/MDplot_bash.R    |   14 ++++++++++++-
 inst/bash/MDplot_install.R |    4 +--
 man/MDplot-internal.Rd     |    1 
 man/TIcurve.Rd             |    4 +++
 man/ramachandran.Rd        |    2 -
 man/xrmsd.Rd               |    2 +
 20 files changed, 220 insertions(+), 72 deletions(-)

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Package glmmLasso updated to version 1.4.3 with previous version 1.4.1 dated 2016-03-01

Title: Variable Selection for Generalized Linear Mixed Models by L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>

Diff between glmmLasso versions 1.4.1 dated 2016-03-01 and 1.4.3 dated 2016-04-28

 DESCRIPTION        |    8 ++++----
 MD5                |   12 ++++++------
 R/glmmLasso.r      |    4 ++--
 R/glmmLasso_RE.R   |   47 ++++++++++++++++++++++++++++++-----------------
 R/glmmLasso_noRE.R |   35 +++++++++++++++++++++++++----------
 man/glmmLasso.rd   |    4 ++--
 man/knee.Rd        |    2 +-
 7 files changed, 70 insertions(+), 42 deletions(-)

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Package fda.usc updated to version 1.2.3 with previous version 1.2.2 dated 2015-12-10

Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut], Manuel Oviedo de la Fuente [aut, cre], Pedro Galeano [ctb], Alicia Nieto [ctb], Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>

Diff between fda.usc versions 1.2.2 dated 2015-12-10 and 1.2.3 dated 2016-04-28

 DESCRIPTION                     |    8 
 MD5                             |   51 
 NAMESPACE                       |    7 
 NEWS                            |   10 
 R/GCV.S.R                       |    2 
 R/Ginv.R                        |    3 
 R/classif.DD.aux.r              |  199 +++
 R/classif.DD.r                  | 2061 +++++++++++++++++++---------------------
 R/depth.KFSD.R                  |only
 R/depth.RPD.r                   |    2 
 R/depth.mode.r                  |   10 
 R/dfv.test.R                    |  116 +-
 R/fda.usc.internal.R            |  218 ++--
 R/flm.Ftest.R                   |  100 -
 R/flm.test.R                    | 1006 +++++++++----------
 R/fregre.PPC.PPLS.R             |    6 
 R/fregre.basis.cv.R             |  442 ++++----
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 man/DepthFunctionalIntegrate.Rd |    4 
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 30 files changed, 2468 insertions(+), 2138 deletions(-)

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New package CalibrateSSB with initial version 1.0
Package: CalibrateSSB
Type: Package
Title: Weighting and Estimation for Panel Data with Non-Response
Version: 1.0
Date: 2016-04-28
Author: Oyvind Langsrud
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Depends: R (>= 3.0.0), survey
Description: Function to calculate weights and estimates for panel data with non-response.
License: GPL-2
NeedsCompilation: no
Packaged: 2016-04-28 10:45:59 UTC; oyl
Repository: CRAN
Date/Publication: 2016-04-28 15:55:19

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New package tidytext with initial version 0.1.0
Package: tidytext
Type: Package
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Version: 0.1.0
Date: 2016-04-27
Authors@R: c(person("Gabriela", "De Queiroz", email = "gabidequeiroz@gmail.com", role = c("ctb")), person("David", "Robinson", email = "admiral.david@gmail.com", role = c("aut")), person("Julia", "Silge", email = "julia.silge@gmail.com", role = c("aut", "cre")))
Description: Text mining for word processing and sentiment analysis using 'dplyr', 'ggplot2', and other tidy tools.
License: MIT + file LICENSE
LazyData: TRUE
URL: http://github.com/juliasilge/tidytext
BugReports: http://github.com/juliasilge/tidytext/issues
RoxygenNote: 5.0.1
Depends: R (>= 2.10)
Imports: dplyr, stringr, tidyr, plyr, broom, Matrix, tokenizers, janeaustenr, purrr, methods
Suggests: readr, XML, tm, wordcloud, knitr, rmarkdown, ggplot2, reshape2, topicmodels, quanteda, NLP, scales, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-04-28 00:32:40 UTC; juliasilge
Author: Gabriela De Queiroz [ctb], David Robinson [aut], Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Repository: CRAN
Date/Publication: 2016-04-28 11:50:08

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Package parsec updated to version 1.1.1 with previous version 1.1 dated 2015-06-22

Title: Partial Orders in Socio-Economics
Description: Implements basic partial order tools for multidimensional poverty evaluation with ordinal variables. Its main goal is to provide socio-economic scholars with an integrated set of elementary functions for multidimensional poverty evaluation, based on ordinal information. The package is organized in four main parts. The first two comprise functions for data management and basic partial order analysis; the third and the fourth are devoted to evaluation and implement both the poset-based approach and a more classical counting procedure.
Author: Alberto Arcagni [aut, cre], Marco Fattore [ctb]
Maintainer: Alberto Arcagni <alberto.arcagni@unimib.it>

Diff between parsec versions 1.1 dated 2015-06-22 and 1.1.1 dated 2016-04-28

 parsec-1.1.1/parsec/DESCRIPTION            |    8 +++----
 parsec-1.1.1/parsec/MD5                    |   30 ++++++++++++++---------------
 parsec-1.1.1/parsec/NAMESPACE              |    9 +++++---
 parsec-1.1.1/parsec/R/LE.R                 |only
 parsec-1.1.1/parsec/R/LE2incidence.R       |only
 parsec-1.1.1/parsec/R/gen.downset.R        |    1 
 parsec-1.1.1/parsec/R/gen.upset.R          |    1 
 parsec-1.1.1/parsec/R/getlambda.R          |    3 ++
 parsec-1.1.1/parsec/R/mrg.R                |    6 +----
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 parsec-1.1.1/parsec/man/cover2incidence.Rd |    2 -
 parsec-1.1.1/parsec/man/getlambda.Rd       |    6 ++---
 parsec-1.1.1/parsec/man/mrg.Rd             |    8 +++----
 parsec-1.1.1/parsec/man/parsec-package.Rd  |    4 +--
 parsec-1.1.1/parsec/man/var2prof.Rd        |    6 ++---
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 parsec-1.1/parsec/R/lexLE2incidence.R      |only
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 20 files changed, 45 insertions(+), 39 deletions(-)

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Package imager updated to version 0.20 with previous version 0.15 dated 2016-01-07

Title: Image Processing Library Based on CImg
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R.
Author: Simon Barthelme [aut, cre], Antoine Cecchi [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>

Diff between imager versions 0.15 dated 2016-01-07 and 0.20 dated 2016-04-28

 imager-0.15/imager/man/sub-.cimg.Rd                 |only
 imager-0.20/imager/DESCRIPTION                      |   14 
 imager-0.20/imager/MD5                              |   70 
 imager-0.20/imager/NAMESPACE                        |   10 
 imager-0.20/imager/NEWS                             |   52 
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 imager-0.20/imager/R/cimg_class.R                   |  291 
 imager-0.20/imager/R/conversions.R                  |   44 
 imager-0.20/imager/R/interpolation.R                |    6 
 imager-0.20/imager/R/splitcombine.R                 |   80 
 imager-0.20/imager/R/stencils.R                     |    3 
 imager-0.20/imager/R/utils.R                        |  145 
 imager-0.20/imager/README.md                        |   11 
 imager-0.20/imager/build                            |only
 imager-0.20/imager/inst/doc                         |only
 imager-0.20/imager/inst/extdata/HubbleDeepField.jpg |only
 imager-0.20/imager/inst/include/CImg.h              |15166 +++++++++++++-------
 imager-0.20/imager/inst/include/imager.h            |   12 
 imager-0.20/imager/man/as.cimg.Rd                   |    6 
 imager-0.20/imager/man/as.data.frame.cimg.Rd        |   11 
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 imager-0.20/imager/man/idply.Rd                     |    3 
 imager-0.20/imager/man/iiply.Rd                     |    5 
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 imager-0.20/imager/man/load.image.Rd                |    8 
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 imager-0.20/imager/man/save.image.Rd                |    8 
 imager-0.20/imager/man/threshold.Rd                 |    2 
 imager-0.20/imager/src/Makevars.in                  |    2 
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 40 files changed, 11131 insertions(+), 4866 deletions(-)

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Package IBDsim updated to version 0.9-6 with previous version 0.9-5 dated 2015-07-03

Title: Simulation of Chromosomal Regions Shared by Family Members
Description: R package for simulation of IBD sharing among family members. Using sex specific recombination rates from the Decode map (2010) of the human genome, phased chromosomes are simulated for all pedigree members, either by unconditional 'gene dropping' or conditional on a specified IBD pattern. Regions compatible with the query IBD pattern (possibly different from the conditional pattern) are subsequently detected and summarized.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>

Diff between IBDsim versions 0.9-5 dated 2015-07-03 and 0.9-6 dated 2016-04-28

 DESCRIPTION        |    8 +--
 MD5                |   17 ++++--
 NAMESPACE          |    2 
 NEWS               |only
 R/IBDsim.R         |  129 ++++++++++++++++++++++++++++-------------------------
 R/genedrop.R       |   52 +++++++++++++++------
 R/map_utils.R      |  129 ++++++++++++++++++++++++++++-------------------------
 R/meiosis.R        |   77 ++++++++++++++++---------------
 R/twoLocusIBD.R    |only
 man/IBDsim.Rd      |   22 +++++----
 man/twoLocusIBD.Rd |only
 11 files changed, 244 insertions(+), 192 deletions(-)

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Package HiCfeat updated to version 1.1 with previous version 1.0 dated 2015-10-05

Title: Multiple Logistic Regression for 3D Chromatin Domain Border Analysis
Description: We propose a multiple logistic regression model to assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

Diff between HiCfeat versions 1.0 dated 2015-10-05 and 1.1 dated 2016-04-28

 DESCRIPTION            |    8 ++++----
 MD5                    |    8 ++++----
 R/BorderAnalysisFun.R  |    7 ++++---
 build/partial.rdb      |binary
 man/HiCfeat-package.Rd |    2 +-
 5 files changed, 13 insertions(+), 12 deletions(-)

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Package GFD updated to version 0.2.2 with previous version 0.1.4 dated 2016-01-14

Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic, a permuted version thereof as well as the ANOVA-type statistic for general factorial designs, even with non-normal error terms and/or heteroscedastic variances, for crossed designs with an arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>

Diff between GFD versions 0.1.4 dated 2016-01-14 and 0.2.2 dated 2016-04-28

 DESCRIPTION              |   15 +
 MD5                      |   26 ++-
 NAMESPACE                |    2 
 R/Data.R                 |    1 
 R/GFD-function.R         |  364 ++---------------------------------------------
 R/GUI.R                  |  171 +++++++++++++++++++++-
 R/calculate_statistics.R |    6 
 R/plot_function.R        |only
 R/utility_functions.R    |   40 ++++-
 build                    |only
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 man/GFD.Rd               |   21 +-
 man/calculateGUI.Rd      |    1 
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 15 files changed, 259 insertions(+), 389 deletions(-)

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New package EpiWeek with initial version 1.1
Package: EpiWeek
Type: Package
Title: Conversion Between Epidemiological Weeks and Calendar Dates
Version: 1.1
Date: 2016-04-28
Author: Xiahong Zhao
Maintainer: Xiahong Zhao <zxiahong@gmail.com>
Description: Users can easily derive the calendar dates from epidemiological weeks, and vice versa.
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-04-28 01:38:50 UTC; ephzhao
Repository: CRAN
Date/Publication: 2016-04-28 11:50:00

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New package ClusterRankTest with initial version 1.0
Package: ClusterRankTest
Type: Package
Title: Rank Tests for Clustered Data
Version: 1.0
Date: 2016-04-21
Author: Sandipan Dutta, Somnath Datta
Maintainer: Sandipan Dutta <sandipan.dutta07@gmail.com>
Description: Nonparametric rank based tests (rank-sum tests and signed-rank tests) for clustered data, especially useful for clusters having informative cluster size and intra-cluster group size.
License: GPL-2 | GPL-3
Depends: graphics, stats, utils
Packaged: 2016-04-27 05:43:24 UTC; sandy
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-04-28 11:49:57

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