Title: Miscellaneous helper functions for B. Bischl.
Diff between BBmisc versions 1.1-164 dated 2012-11-14 and 1.1-166 dated 2012-11-16
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl
Maintainer: Bernd Bischl
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NEWS | 2 +-
R/checkArg.R | 2 ++
inst/tests/test_checkArg.R | 7 +++++++
5 files changed, 17 insertions(+), 8 deletions(-)
Title: HTML 5 Websocket Interface for R
Diff between websockets versions 1.1.5 dated 2012-09-13 and 1.1.6 dated 2012-11-16
Description: A simple HTML5 websocket interface for R.
Author: B. W. Lewis
Maintainer: Joe Cheng
DESCRIPTION | 14 ++++++++------
MD5 | 14 +++++++-------
NAMESPACE | 3 +++
NEWS | 4 ++++
R/websockets-internal.R | 2 --
R/websockets.R | 35 ++++++++++++++++++++---------------
inst/doc/websockets.pdf |binary
man/http_response.Rd | 3 ++-
8 files changed, 44 insertions(+), 31 deletions(-)
Title: Sampling Surface Simulation for Areal Sampling Methods
Diff between sampSurf versions 0.6-4 dated 2012-05-16 and 0.6-5 dated 2012-11-16
Description: This package provides the base classes and routines for
sampling surface simulation useful in the comparison of
different areal sampling methods in forestry, ecology and
natural resources.
Author: Jeffrey H. Gove
Maintainer: Jeffrey H. Gove
DESCRIPTION | 12 ++--
MD5 | 73 +++++++++++++------------
NAMESPACE | 9 +--
R/ArealSamplingClass.R | 76 +++++++++++++++++++++++++-
R/ArealSamplingConstructors.R | 104 ++++++++++++++++++++++++++++++++++--
R/TractConstructors.R | 2
R/bbox.R | 12 ++++
R/defStemEnv.R | 11 +++
R/heapIZ.R | 4 -
R/horizontalLineSampling.R |only
R/plotArealSampling.R | 43 ++++++++++++++
R/summaryArealSampling.R | 69 ++++++++++++++++++++++-
R/summarySampSurf.R | 4 -
inst/doc/ArealSamplingClass.pdf |binary
inst/doc/GettingStarted.pdf |binary
inst/doc/InclusionZoneClass.pdf |binary
inst/doc/InclusionZoneGridClass.pdf |binary
inst/doc/Overview.pdf |binary
inst/doc/StemClass.pdf |binary
inst/doc/TractClass.pdf |binary
inst/doc/monte.pdf |binary
inst/doc/sampSurfClass.pdf |binary
inst/doc/sampSurfExtensions.pdf |binary
man/ArealSampling-class.Rd | 2
man/InclusionZone-class.Rd | 1
man/angleGauge-class.Rd | 22 ++++++-
man/circularPlot-class.Rd | 23 +++----
man/circularPlot.Rd | 11 ++-
man/horizontalLineIZ-class.Rd |only
man/horizontalLineIZ-methods.Rd |only
man/horizontalLineIZ.Rd |only
man/horizontalPointIZ-class.Rd | 22 ++++---
man/horizontalPointIZ-methods.Rd | 3 -
man/izGrid-methods.Rd | 8 ++
man/lineSegment-class.Rd |only
man/lineSegment-methods.Rd |only
man/lineSegment.Rd |only
man/perimeter-methods.Rd | 7 ++
man/plot-methods.Rd | 91 +++++++++++++++++++++++++++++++
man/sampSurf-package.Rd | 27 ++++++---
man/standingTreeIZ-class.Rd | 2
41 files changed, 543 insertions(+), 95 deletions(-)
Title: Regression Methods for IBD Linkage With Covariates
Diff between ibdreg versions 0.1.3 dated 2010-02-09 and 0.2.1 dated 2012-11-16
Description: A method to test genetic linkage with covariates by
regression methods with response IBD sharing for relative
pairs. Account for correlations of IBD statistics and
covariates for relative pairs within the same pedigree.
Author: Jason P. Sinnwell and Daniel J. Schaid
Maintainer: Jason P. Sinnwell
ibdreg-0.1.3/ibdreg/INDEX |only
ibdreg-0.1.3/ibdreg/R/sr.class.q |only
ibdreg-0.1.3/ibdreg/R/sr.strsplit.q |only
ibdreg-0.1.3/ibdreg/README.ibdreg |only
ibdreg-0.1.3/ibdreg/TODO |only
ibdreg-0.1.3/ibdreg/man/sr.class.Rd |only
ibdreg-0.1.3/ibdreg/man/sr.strsplit.Rd |only
ibdreg-0.2.1/ibdreg/DESCRIPTION | 12 ++--
ibdreg-0.2.1/ibdreg/MD5 |only
ibdreg-0.2.1/ibdreg/NAMESPACE |only
ibdreg-0.2.1/ibdreg/R/create.ibd.dat.q | 2
ibdreg-0.2.1/ibdreg/R/create.pairs.frame.q | 2
ibdreg-0.2.1/ibdreg/R/exact.ibd.var.q | 2
ibdreg-0.2.1/ibdreg/R/ibd.df.merlin.q | 2
ibdreg-0.2.1/ibdreg/R/ibdreg.q | 6 +-
ibdreg-0.2.1/ibdreg/R/linkage.all.q | 2
ibdreg-0.2.1/ibdreg/R/linkage.tests.q | 2
ibdreg-0.2.1/ibdreg/R/print.ibd.var.q | 4 -
ibdreg-0.2.1/ibdreg/R/print.linkage.all.q | 2
ibdreg-0.2.1/ibdreg/R/print.linkage.tests.q | 2
ibdreg-0.2.1/ibdreg/R/resources.q | 38 ++++++--------
ibdreg-0.2.1/ibdreg/R/setFounderAlleles.q | 4 -
ibdreg-0.2.1/ibdreg/R/sim.ibd.var.q | 2
ibdreg-0.2.1/ibdreg/R/zzz.ibdreg.q | 40 ++++++++-------
ibdreg-0.2.1/ibdreg/inst/NEWS.Rd |only
ibdreg-0.2.1/ibdreg/inst/doc/manualIBDReg.pdf |binary
ibdreg-0.2.1/ibdreg/man/resources.Rd | 13 +++-
ibdreg-0.2.1/ibdreg/src/sim.mark.prop.c | 69 +++-----------------------
28 files changed, 76 insertions(+), 128 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.4.3 dated 2012-10-04 and 0.3.4.4 dated 2012-11-16
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.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 3.4.4). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the GNU LGPL version 3 or later, 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
ChangeLog | 6
DESCRIPTION | 10 -
MD5 | 24 +--
inst/NEWS.Rd | 10 +
inst/include/armadillo_bits/SpMat_meat.hpp | 16 +-
inst/include/armadillo_bits/SpSubview_meat.hpp | 21 ++-
inst/include/armadillo_bits/SpValProxy_bones.hpp | 7 -
inst/include/armadillo_bits/SpValProxy_meat.hpp | 152 ++---------------------
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/diskio_meat.hpp | 8 -
inst/include/armadillo_bits/fn_n_unique.hpp | 6
inst/include/armadillo_bits/operator_div.hpp | 2
man/RcppArmadillo-package.Rd | 2
13 files changed, 85 insertions(+), 181 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 1.7 dated 2012-10-26 and 1.8 dated 2012-11-16
Description: DDD implements maximum likelihood methods based on the
diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent. See Etienne
et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
10.1098/rspb.2011.1439. DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence. See Etienne & Haegeman
2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/dd_KI_ML.R | 10 +++++-----
R/dd_KI_simplex.R | 23 +++++++++++++++++++----
R/dd_ML.R | 8 ++++----
R/dd_SR_ML.R | 8 ++++----
R/dd_SR_loglik.R | 4 ++--
R/dd_SR_simplex.R | 21 ++++++++++++++++++---
R/dd_loglik.R | 4 ++--
R/dd_loglik_choosepar.R | 2 +-
R/dd_simplex.R | 23 ++++++++++++++++++-----
man/DDD-package.Rd | 24 +++++++++++++++---------
man/dd_KI_ML.Rd | 13 +++++++------
man/dd_ML.Rd | 2 +-
14 files changed, 113 insertions(+), 63 deletions(-)
More information about BioPhysConnectoR at CRAN
Permanent link
Title: Simulate QQ-Norm-Plot
Diff between StMoSim versions 2.1 dated 2012-02-24 and 2.2 dated 2012-11-16
Description: With this package you can simulate several lines into the
QQ-Norm-Plot under the assumption of Gaussian distribution
Author: Matthias Salvisberg
Maintainer: Matthias Salvisberg
DESCRIPTION | 8 ++---
MD5 | 4 +-
R/qqnormSim.R | 90 +++++++++++++++++++++-------------------------------------
3 files changed, 39 insertions(+), 63 deletions(-)
Title: Methods that apply to rows and columns of a matrix
Diff between matrixStats versions 0.5.3 dated 2012-09-13 and 0.6.2 dated 2012-11-16
Description: This packages provides methods operating on rows and
columns of matrices. The objective is to have all methods
being optimized for speed and memory consumption.
Author: Henrik Bengtsson, Hector Corrada Bravo, Robert Gentleman,
Harris Jaffee
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++++++-----
R/binCounts.R |only
R/binMeans.R |only
incl/binMeans.Rex |only
incl/weightedMedian.Rex | 13 ++++---------
inst/NEWS | 18 ++++++++++++++++++
man/binCounts.Rd |only
man/binMeans.Rd |only
man/matrixStats-package.Rd | 2 +-
man/weightedMedian.Rd | 13 ++++---------
src/binCounts.c |only
src/binMeans.c |only
tests/binMeans,binCounts.R |only
14 files changed, 44 insertions(+), 28 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-3 dated 2012-10-27 and 0.999-4 dated 2012-11-16
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme value and some more copula families. Methods for
density, distribution, random number generation, bivariate
dependence measures, perspective and contour plots. Fitting
copula models including variance estimates. Independence and
serial (univariate and multivariate) independence tests, and
other copula related tests. Goodness-of-fit tests for copulas
based on multipliers, the parametric bootstrap with several
transformation options. Merged former package 'nacopula' for
nested Archimedean copulas: Efficient sampling algorithms,
various estimators, goodness-of-fit tests and related tools and
special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
ChangeLog | 14 ++++++++
DESCRIPTION | 10 ++---
MD5 | 26 +++++++--------
NAMESPACE | 2 -
R/gof.R | 10 ++---
R/gumbelCopula.R | 9 ++---
R/nacopula.R | 2 +
R/stable.R | 21 +++++-------
inst/CITATION | 77 ++++++++++++++++++++++++++++++++--------------
inst/doc/Frank-Rmpfr.pdf |binary
inst/doc/nacopula-pkg.pdf |binary
man/assocMeasures.Rd | 10 ++++-
man/gnacopula.Rd | 13 +++++--
tests/rstable-ex.R | 62 ++++++++++++++++++++++++++++++++++---
14 files changed, 183 insertions(+), 73 deletions(-)
Title: Segmentation methods for array CGH analysis
Diff between cghseg versions 0.0.1 dated 2011-08-03 and 1.0.0 dated 2012-11-16
Description: cghseg is an R package dedicated to the analysis of CGH
profiles using segmentation models.
Author: Franck Picard, Mark Hoebeke, Emilie Lebarbier, Vincent Miele,
Guillem Rigaill, Stephane Robin
Maintainer: Franck Picard
cghseg-0.0.1/cghseg/src/polynome2.cc |only
cghseg-1.0.0/cghseg/DESCRIPTION | 19 +-
cghseg-1.0.0/cghseg/MD5 |only
cghseg-1.0.0/cghseg/NAMESPACE | 5
cghseg-1.0.0/cghseg/R/CGHdata.R | 5
cghseg-1.0.0/cghseg/R/CGHoptions.R | 54 +++++-
cghseg-1.0.0/cghseg/R/CGHresults.R | 7
cghseg-1.0.0/cghseg/R/DP2EM.R | 35 +---
cghseg-1.0.0/cghseg/R/ILS.R | 89 +++-------
cghseg-1.0.0/cghseg/R/ILSclust.R | 126 ++++-----------
cghseg-1.0.0/cghseg/R/cghseg.R | 132 ++++++++++++++++
cghseg-1.0.0/cghseg/R/getmBIC.R | 15 -
cghseg-1.0.0/cghseg/R/getmultiKmax.R | 6
cghseg-1.0.0/cghseg/R/getuniKmax.R | 69 ++++----
cghseg-1.0.0/cghseg/R/golden.search.R | 10 +
cghseg-1.0.0/cghseg/R/multiseg.R | 40 ++++
cghseg-1.0.0/cghseg/R/multisegclust.R | 125 ++++-----------
cghseg-1.0.0/cghseg/R/multisegmean.R | 94 ++++++++---
cghseg-1.0.0/cghseg/R/multisegmixt.R | 57 +++++-
cghseg-1.0.0/cghseg/R/multisegout.R | 13 -
cghseg-1.0.0/cghseg/R/unisegclust.R | 121 ++++++++++----
cghseg-1.0.0/cghseg/R/unisegmean.R | 28 ++-
cghseg-1.0.0/cghseg/R/unisegmixt.R | 48 +++--
cghseg-1.0.0/cghseg/R/zzz.R |only
cghseg-1.0.0/cghseg/man/CGHoptions-class.Rd | 9 -
cghseg-1.0.0/cghseg/man/alpha.Rd | 7
cghseg-1.0.0/cghseg/man/getuniKmax.Rd | 26 +--
cghseg-1.0.0/cghseg/man/nbprocs.Rd |only
cghseg-1.0.0/cghseg/man/uniseg.Rd | 3
cghseg-1.0.0/cghseg/src/ApproxSeg.c |only
cghseg-1.0.0/cghseg/src/ApproxSeg.h |only
cghseg-1.0.0/cghseg/src/ApproxSeg_2.c |only
cghseg-1.0.0/cghseg/src/Makevars |only
cghseg-1.0.0/cghseg/src/Rwrappers.cc | 221 ++++++++++++++++++++++++++-
cghseg-1.0.0/cghseg/src/Rwrappers.h | 3
cghseg-1.0.0/cghseg/src/accessToR.cc | 46 ++++-
cghseg-1.0.0/cghseg/src/colibriAnalysis.cc | 1
cghseg-1.0.0/cghseg/src/compactEM_algo.cc |only
cghseg-1.0.0/cghseg/src/compactEM_algo.h |only
cghseg-1.0.0/cghseg/src/compactEM_init.cc |only
cghseg-1.0.0/cghseg/src/compactEM_init.h |only
cghseg-1.0.0/cghseg/src/liste.cc | 197 +-----------------------
cghseg-1.0.0/cghseg/src/liste.h | 229 ++++++++++++++++++++++------
cghseg-1.0.0/cghseg/src/lvinc.cc |only
cghseg-1.0.0/cghseg/src/lvinc.h |only
cghseg-1.0.0/cghseg/src/polynome2.h | 213 ++++++++++++++++++++++++--
46 files changed, 1326 insertions(+), 727 deletions(-)
Title: Analysis of animal movements
Diff between adehabitatLT versions 0.3.6 dated 2012-05-31 and 0.3.7 dated 2012-11-16
Description: A collection of tools for the analysis of animal movements
Author: Clement Calenge, contributions from Stephane Dray and Manuela
Royer
Maintainer: Clement Calenge
DESCRIPTION | 8
MD5 | 18
R/plotltr.r | 7
data/albatross.rda |binary
data/capreochiz.rda |binary
data/hseal.rda |binary
data/ibexraw.rda |binary
data/teal.rda |binary
inst/doc/adehabitatLT.pdf | 1707 +++++++++++++++++++++++-----------------------
man/plotltr.Rd | 6
10 files changed, 882 insertions(+), 864 deletions(-)