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(-)
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(-)
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 ++++---- R/predict.classif.DD.R |only R/rp.flm.test2.R |only R/rproc2fdata.R | 163 +-- man/DepthFunctional.Rd | 93 + man/DepthFunctionalIntegrate.Rd | 4 man/classif.DD.Rd | 64 - man/fda.usc-package.Rd | 6 man/fda.usc.internal.Rd | 10 man/gridfdata.Rd |only man/rp.flm.statistic.Rd |only man/rp.flm.test.Rd |only man/rproc2fdata.Rd | 25 src/rp_stat.f90 |only 30 files changed, 2468 insertions(+), 2138 deletions(-)
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 +---- parsec-1.1.1/parsec/man/LE.Rd |only parsec-1.1.1/parsec/man/LE2incidence.Rd |only 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 ++--- parsec-1.1/parsec/R/lexLE.R |only parsec-1.1/parsec/R/lexLE2incidence.R |only parsec-1.1/parsec/man/lexLE.Rd |only parsec-1.1/parsec/man/lexLE2incidence.Rd |only 20 files changed, 45 insertions(+), 39 deletions(-)
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 imager-0.20/imager/NEWS.md |only 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 imager-0.20/imager/man/crop.borders.Rd |only imager-0.20/imager/man/idply.Rd | 3 imager-0.20/imager/man/iiply.Rd | 5 imager-0.20/imager/man/ilply.Rd | 2 imager-0.20/imager/man/imager.combine.Rd | 25 imager-0.20/imager/man/imager.subset.Rd |only imager-0.20/imager/man/imdraw.Rd | 3 imager-0.20/imager/man/iminfo.Rd |only imager-0.20/imager/man/imsub.Rd | 2 imager-0.20/imager/man/imwarp.Rd | 2 imager-0.20/imager/man/interp.Rd | 6 imager-0.20/imager/man/load.example.Rd |only imager-0.20/imager/man/load.image.Rd | 8 imager-0.20/imager/man/periodic.part.Rd | 3 imager-0.20/imager/man/resize_uniform.Rd | 3 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 imager-0.20/imager/src/Makevars.win | 2 imager-0.20/imager/vignettes |only 40 files changed, 11131 insertions(+), 4866 deletions(-)
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(-)
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(-)
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 inst |only man/GFD.Rd | 21 +- man/calculateGUI.Rd | 1 man/startup.Rd | 1 vignettes |only 15 files changed, 259 insertions(+), 389 deletions(-)
More information about ClusterRankTest at CRAN
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