Title: R interface to the CSDP semidefinite programming library
Description: R interface to the CSDP semidefinite programming library.
Installs version 6.1.1 of CSDP from the COIN-OR website if
required. An existing installation of CSDP may be used by
passing the proper configure arguments to the installation
command. See the INSTALL file for further details.
Author: Hector Corrada Bravo (CSDP by Brian Borchers)
Maintainer: Hector Corrada Bravo
Diff between Rcsdp versions 0.1.51 dated 2013-04-03 and 0.1.52 dated 2013-04-20
CHANGES | 6 ++++++ DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/Makevars.in | 5 +++-- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
Diff between phytools versions 0.2-40 dated 2013-04-08 and 0.2-50 dated 2013-04-20
phytools-0.2-40/phytools/R/reroot.R |only phytools-0.2-50/phytools/DESCRIPTION | 8 phytools-0.2-50/phytools/MD5 | 50 ++-- phytools-0.2-50/phytools/NAMESPACE | 8 phytools-0.2-50/phytools/R/anc.ML.R | 9 phytools-0.2-50/phytools/R/estDiversity.R | 79 ++++--- phytools-0.2-50/phytools/R/ltt95.R |only phytools-0.2-50/phytools/R/make.simmap.R | 21 + phytools-0.2-50/phytools/R/pbtree.R | 233 ++++++++++++++++++--- phytools-0.2-50/phytools/R/plotSimmap.R | 11 phytools-0.2-50/phytools/R/rerootingMethod.R | 37 ++- phytools-0.2-50/phytools/R/strahlerNumber.R |only phytools-0.2-50/phytools/R/utilities.R | 20 + phytools-0.2-50/phytools/man/anc.ML.Rd | 2 phytools-0.2-50/phytools/man/ancThresh.Rd | 2 phytools-0.2-50/phytools/man/estDiversity.Rd | 21 + phytools-0.2-50/phytools/man/ltt95.Rd |only phytools-0.2-50/phytools/man/make.simmap.Rd | 4 phytools-0.2-50/phytools/man/pbtree.Rd | 24 +- phytools-0.2-50/phytools/man/phenogram.Rd | 3 phytools-0.2-50/phytools/man/phyl.resid.Rd | 2 phytools-0.2-50/phytools/man/phylomorphospace.Rd | 2 phytools-0.2-50/phytools/man/phylomorphospace3d.Rd | 2 phytools-0.2-50/phytools/man/read.simmap.Rd | 33 +- phytools-0.2-50/phytools/man/reroot.Rd | 18 - phytools-0.2-50/phytools/man/rerootingMethod.Rd | 13 - phytools-0.2-50/phytools/man/strahlerNumber.Rd |only phytools-0.2-50/phytools/man/to.matrix.Rd |only phytools-0.2-50/phytools/man/untangle.Rd | 2 29 files changed, 438 insertions(+), 166 deletions(-)
Title: Package for statistical age models analysis in optically
stimulated luminescence dating
Description: Package for estimating parameters of statistical age
models in optically stimulated luminescence dating dynamically.
Author: Peng Jun
Maintainer: Peng Jun
Diff between RadialPlotter versions 1.0 dated 2013-03-21 and 1.5 dated 2013-04-20
DESCRIPTION | 9 + MD5 | 44 ++++++--- NEWS |only R/RadialPlotter.R | 204 +++++++++++++++++++++++++++++-------------- THANKS |only data/EDdata.RData |binary inst |only licences |only man/EDdata.Rd | 12 +- man/RadialPlotter-package.Rd | 18 ++- man/RadialPlotter.Rd | 119 +++++++++++++++++-------- src/AppCovar.f90 | 20 ++-- src/CAM.f90 | 12 +- src/FMMED.f90 | 10 +- src/FineComp.f90 | 2 src/FineED.f90 | 30 +++++- src/FineED1.f90 | 35 ++++++- src/GJordan.f90 | 2 src/MAM.f90 |only src/MamED.f90 |only src/NonReplaceSample.f90 |only src/alnorm.f90 |only src/fdhessian.f90 |only src/gradient.f90 |only src/inverse.f90 | 4 src/kmeans.f90 |only src/kmeans_02.f90 |only src/lbfgsb.f |only src/pnorm.f90 |only 29 files changed, 361 insertions(+), 160 deletions(-)
Title: Estimation in Dirichlet-Multinomial distribution.
Description: Estimate parameters in Dirichlet-Multinomial and compute
profile log-likelihoods.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink
Diff between dirmult versions 0.1.2 dated 2009-09-24 and 0.1.3-3 dated 2013-04-20
dirmult-0.1.2/dirmult/inst/doc |only dirmult-0.1.3-3/dirmult/DESCRIPTION | 10 +++-- dirmult-0.1.3-3/dirmult/MD5 |only dirmult-0.1.3-3/dirmult/NAMESPACE | 1 dirmult-0.1.3-3/dirmult/R/dirmult.R | 42 ++++++++++++++----------- dirmult-0.1.3-3/dirmult/dirmult.pdf |only dirmult-0.1.3-3/dirmult/inst/CITATION |only dirmult-0.1.3-3/dirmult/man/adapGridProf.Rd | 4 -- dirmult-0.1.3-3/dirmult/man/dirmult.Rd | 11 ++---- dirmult-0.1.3-3/dirmult/man/dirmult.summary.Rd | 11 ++++-- dirmult-0.1.3-3/dirmult/man/equalTheta.Rd | 5 +- dirmult-0.1.3-3/dirmult/man/estProfLogLik.Rd | 1 dirmult-0.1.3-3/dirmult/man/gridProf.Rd | 5 +- dirmult-0.1.3-3/dirmult/man/nullTest.Rd | 3 - dirmult-0.1.3-3/dirmult/man/rdirichlet.Rd |only dirmult-0.1.3-3/dirmult/man/simPop.Rd | 1 dirmult-0.1.3-3/dirmult/man/weirMoM.Rd | 1 17 files changed, 50 insertions(+), 45 deletions(-)
Title: Testing Linear Regression Models
Description: A collection of tests, data sets, and examples for
diagnostic checking in linear regression models. Furthermore,
some generic tools for inference in parametric models are
provided.
Author: Torsten Hothorn [aut], Achim Zeileis [aut, cre], Richard W.
Farebrother [aut] (pan.f), Clint Cummins [aut] (pan.f),
Giovanni Millo [ctb], David Mitchell [ctb]
Maintainer: Achim Zeileis
Diff between lmtest versions 0.9-30 dated 2012-05-31 and 0.9-31 dated 2013-04-20
DESCRIPTION | 25 +- MD5 | 56 +++--- NEWS | 11 + R/bgtest.R | 11 + R/lrtest.R | 2 R/waldci.R |only R/waldtest.R | 2 data/ChickEgg.rda |binary data/Mandible.rda |binary data/USDistLag.rda |binary data/bondyield.rda |binary data/currencysubstitution.rda |binary data/ftemp.rda |binary data/fyff.rda |binary data/gmdc.rda |binary data/growthofmoney.rda |binary data/ip.rda |binary data/jocci.rda |binary data/lhur.rda |binary data/moneydemand.rda |binary data/pw561.rda |binary data/unemployment.rda |binary data/valueofstocks.rda |binary data/wages.rda |binary inst/doc/lmtest-intro.R |only inst/doc/lmtest-intro.pdf |binary man/bgtest.Rd | 9 - man/bptest.Rd | 2 man/waldtest.Rd | 2 tests/Examples/lmtest-Ex.Rout.save | 321 ++++++++++++++++++------------------- 30 files changed, 234 insertions(+), 207 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
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 3.810.0). 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 MPL 2.0, 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
Diff between RcppArmadillo versions 0.3.800.1 dated 2013-03-12 and 0.3.810.0 dated 2013-04-20
ChangeLog | 21 + DESCRIPTION | 12 MD5 | 62 ++-- debian |only inst/NEWS.Rd | 15 inst/doc/RcppArmadillo-intro.R |only inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.R |only inst/doc/RcppArmadillo-unitTests.pdf |binary inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 26 - inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 37 +- inst/doc/unitTests/RcppArmadillo-unitTests.R | 16 - inst/include/RcppArmadilloExtensions/sample.h | 10 inst/include/armadillo | 8 inst/include/armadillo_bits/Mat_bones.hpp | 4 inst/include/armadillo_bits/Mat_meat.hpp | 26 + inst/include/armadillo_bits/SpMat_bones.hpp | 15 inst/include/armadillo_bits/SpMat_meat.hpp | 244 ++++++++++++++++ inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/config.hpp | 2 inst/include/armadillo_bits/fft_engine.hpp |only inst/include/armadillo_bits/fn_fft.hpp |only inst/include/armadillo_bits/fn_misc.hpp | 15 inst/include/armadillo_bits/op_fft_bones.hpp |only inst/include/armadillo_bits/op_fft_meat.hpp |only inst/include/armadillo_bits/spglue_times_meat.hpp | 2 inst/include/armadillo_bits/subview_bones.hpp | 7 inst/include/armadillo_bits/subview_cube_bones.hpp | 9 inst/include/armadillo_bits/subview_cube_meat.hpp | 62 +++- inst/include/armadillo_bits/subview_meat.hpp | 90 +++++ inst/include/armadillo_bits/traits.hpp | 32 +- inst/unitTests/runit.sample.R | 43 +- 32 files changed, 658 insertions(+), 106 deletions(-)
Title: Local Regression, Likelihood and Density Estimation.
Description: Local regression, likelihood and density estimation.
Author: Catherine Loader
Maintainer: Andy Liaw
Diff between locfit versions 1.5-9 dated 2013-03-22 and 1.5-9.1 dated 2013-04-20
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ src/S_enter.c | 26 +++++++++++++------------- src/lf_vari.c | 2 +- src/m_max.c | 4 ++-- src/minmax.c | 4 ++-- src/scb_cons.c | 18 +++++++++--------- 7 files changed, 36 insertions(+), 36 deletions(-)
Title: Regression Methods for IBD Linkage With Covariates
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
Diff between ibdreg versions 0.2.2 dated 2013-01-05 and 0.2.5 dated 2013-04-20
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/create.pairs.frame.q | 5 +++-- R/resources.q | 15 +++++++++------ src/mcmemory.h | 4 ++-- src/sim.mark.prop.c | 10 +++++----- 6 files changed, 29 insertions(+), 24 deletions(-)
Title: Global optimization by Differential Evolution
Description: This package provides the DEoptim function which performs
global optimization by differential evolution.
Author: David Ardia, Katharine Mullen, Brian Peterson, and Joshua
Ulrich, with contributions from Kris Boudt
Maintainer: Katharine Mullen
Diff between DEoptim versions 2.2-1 dated 2012-07-01 and 2.2-2 dated 2013-04-20
DESCRIPTION | 15 ++++++++++----- MD5 | 8 ++++---- NEWS | 5 ++++- R/zzz.R | 4 ++++ src/de4_0.c | 16 +++++++--------- 5 files changed, 29 insertions(+), 19 deletions(-)
Title: Density Estimation for Binned/Weighted Data
Description: This package collects algorithms/functions developed for
density estimation based on weighted or pre-binned data.
Author: Bin Wang
Maintainer: Bin Wang
Diff between bda versions 2.1.2-10 dated 2013-02-11 and 2.1.4-19 dated 2013-04-20
bda-2.1.2-10/bda/LICENCE |only bda-2.1.4-19/bda/DESCRIPTION | 9 +++++---- bda-2.1.4-19/bda/MD5 | 9 ++++----- bda-2.1.4-19/bda/R/bootKDE.R | 8 +++++--- bda-2.1.4-19/bda/src/bootkdef.f | 6 +++--- bda-2.1.4-19/bda/src/init.c | 4 ++-- 6 files changed, 19 insertions(+), 17 deletions(-)