Title: Analysis of habitat selection by animals
Diff between adehabitatHS versions 0.3.8 dated 2013-09-23 and 0.3.9 dated 2014-03-08
Description: A collection of tools for the analysis of habitat selection
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/widesIII.r | 2 +-
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Home range Estimation
Diff between adehabitatHR versions 0.4.10 dated 2013-09-23 and 0.4.11 dated 2014-03-08
Description: A collection of tools for the estimation of animals home range
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
R/CharHull.r | 39 +++++++++++++++++++++++++++++++--------
R/getverticeshr.r | 10 ++++++++++
R/kernel.area.r | 8 ++++++++
R/kernelUD.r | 4 ++--
R/kernelovelaphr.r | 44 ++++++++++++++++++++++----------------------
R/kerneloverlap.r | 44 ++++++++++++++++++++++----------------------
inst/doc/adehabitatHR.pdf |binary
man/CharHull.Rd | 4 ++--
man/kernelUD.Rd | 14 ++++++++------
11 files changed, 120 insertions(+), 77 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-113 dated 2013-11-17 and 3.1-114 dated 2014-03-08
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
ChangeLog | 11 ++++++++++-
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
R/lme.R | 11 ++++-------
R/newMethods.R | 1 +
inst/CITATION | 30 +++++++++++-------------------
man/lmeControl.Rd | 16 +++++++---------
man/lmeScale.Rd | 3 ++-
man/nlmeControl.Rd | 2 +-
tests/fitted.R |only
10 files changed, 49 insertions(+), 50 deletions(-)
Title: Basic statistical functions for package ff
Diff between ffbase versions 0.11.1 dated 2014-01-18 and 0.11.3 dated 2014-03-08
Description: Basic (statistical) functionality for package ff
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge
DESCRIPTION | 6
MD5 | 21 +-
NAMESPACE | 4
NEWS | 8
R/bigglm.R | 134 +++++++--------
R/ffdfdply.R | 2
R/hist2d.R |only
R/rbind_ffdf.R | 37 ++++
R/save_ffdf.R | 433 +++++++++++++++++++++++++-------------------------
R/table_ff.R | 228 +++++++++++++-------------
man/compact.Rd | 50 ++---
man/ffdfrbind.fill.Rd |only
man/hist2d.ff.Rd |only
13 files changed, 489 insertions(+), 434 deletions(-)
Title: Recursive Partitioning and Regression Trees
Diff between rpart versions 4.1-5 dated 2014-01-25 and 4.1-6 dated 2014-03-08
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of R port)
Maintainer: Brian Ripley
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/model.frame.rpart.R | 3 ++-
inst/doc/longintro.pdf |binary
inst/doc/usercode.pdf |binary
6 files changed, 14 insertions(+), 10 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-29 dated 2013-08-31 and 7.3-30 dated 2014-03-08
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
man/geyser.Rd | 13 +++++++++++--
3 files changed, 18 insertions(+), 9 deletions(-)
Title: Bootstrap Functions (originally by Angelo Canty for S)
Diff between boot versions 1.3-9 dated 2013-04-03 and 1.3-10 dated 2014-03-08
Description: functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Applications" by A. C. Davison and
D. V. Hinkley (1997, CUP).
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley
boot-1.3-10/boot/ChangeLog | 16 +++++++++++-----
boot-1.3-10/boot/DESCRIPTION | 28 ++++++++++++++--------------
boot-1.3-10/boot/MD5 | 14 ++++++--------
boot-1.3-10/boot/R/bootfuns.q | 5 ++++-
boot-1.3-10/boot/inst/bd.q |only
boot-1.3-10/boot/man/boot.Rd | 7 ++++++-
boot-1.3-10/boot/man/censboot.Rd | 2 +-
boot-1.3-9/boot/bd.q |only
boot-1.3-9/boot/extra-tests |only
9 files changed, 42 insertions(+), 30 deletions(-)
Title: vcd extensions and additions
Diff between vcdExtra versions 0.5-11 dated 2013-09-16 and 0.6-0 dated 2014-03-08
Description: Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data
and the gnm package for Generalized Nonlinear Models.
In particular, vcdExtra extends mosaic, assoc and sieve plots from vcd to handle glm() and gnm() models and
adds a 3D version in mosaic3d. Additionally, methods are provided for comparing and visualizing lists of
glm and loglm objects.
Author: Michael Friendly [aut, cre],
Heather Turner [ctb],
Achim Zeileis [ctb],
Duncan Murdoch [ctb],
David Firth [ctb]
Maintainer: Michael Friendly
DESCRIPTION | 20 ++++++----
MD5 | 86 ++++++++++++++++++++++++++--------------------
NAMESPACE | 8 +++-
NEWS | 18 +++++++++
R/logseries.R |only
R/mosaic3d.R | 17 ++++-----
R/seq_loglm.R | 14 ++++---
R/seq_mosaic.R |only
build/vignette.rds |binary
data/Abortion.rda |binary
data/Accident.RData |binary
data/Alligator.RData |binary
data/Bartlett.rda |binary
data/Caesar.rda |binary
data/Cancer.rda |binary
data/CyclingDeaths.RData |only
data/DaytonSurvey.RData |binary
data/Depends.RData |only
data/Detergent.rda |binary
data/Donner.RData |binary
data/Draft1970.RData |binary
data/Draft1970table.RData |binary
data/Dyke.rda |binary
data/Fungicide.rda |binary
data/GSS.rda |binary
data/Geissler.RData |only
data/Gilby.rda |binary
data/Hauser79.RData |binary
data/Heart.rda |binary
data/Heckman.rda |binary
data/Hoyt.rda |binary
data/ICU.rda |binary
data/JobSat.rda |binary
data/Mammograms.RData |binary
data/Mental.rda |binary
data/Mobility.rda |binary
data/ShakeWords.RData |only
data/TV.rda |binary
data/Titanicp.rda |binary
data/Vietnam.rda |binary
data/Yamaguchi87.RData |binary
man/Bartlett.Rd | 5 +-
man/CyclingDeaths.Rd |only
man/Depends.Rd |only
man/Geissler.Rd |only
man/ShakeWords.Rd |only
man/logseries.Rd |only
man/mosaic3d.Rd | 7 +++
man/seq_mosaic.Rd |only
man/vcdExtra-package.Rd | 4 +-
50 files changed, 111 insertions(+), 68 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.4.100.0 dated 2014-03-01 and 0.4.100.2.1 dated 2014-03-08
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. 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
ChangeLog | 21 +++++++++++++++-
DESCRIPTION | 8 +++---
MD5 | 28 +++++++++++-----------
R/RcppArmadillo.package.skeleton.R | 10 -------
inst/NEWS.Rd | 15 +++++++++++
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/RcppArmadilloConfig.h | 9 +++++--
inst/include/armadillo_bits/arma_version.hpp | 2 -
inst/include/armadillo_bits/memory.hpp | 2 -
inst/include/armadillo_bits/op_normalise_meat.hpp | 26 +++++++++++++++++---
inst/include/armadillo_bits/operator_minus.hpp | 21 ++++++++++++++++
inst/skeleton/rcpparma_hello_world.cpp | 11 ++++----
src/Makevars | 9 +++++++
src/Makevars.win | 10 +++++++
15 files changed, 130 insertions(+), 42 deletions(-)
Title: R Package for Covariate Balancing Propensity Score
Diff between CBPS versions 0.7 dated 2013-07-24 and 0.8 dated 2014-03-08
Description: CBPS is an R package that implements the covariate balancing propensity score proposed by Imai and Ratkovic (2014; JRSSB). The propensity score is estimated such that it maximizes the resulting covariate balance as well as the prediction of treatment assignment. The method, therefore, avoids an iteration between model fitting and balance checking. The package also implements several extensions of the CBPS beyond the cross-sectional, binary treatment setting. The current version implements the CBPS for longitudinal settings so that it can be used in conjunction with marginal structural models (Imai and Ratkovic, 2013a), treatments with three- and four-valued treatment variables (Fong, 2013), and the situation with multiple distinct binary treatments administered simultaneously. In the future it will be extended to other settings including continuous treatments and the generalization of experimental and instrumental variable estimates.
Author: Christian Fong
Maintainer: Marc Ratkovic
DESCRIPTION | 16 -
MD5 | 30 +--
NAMESPACE | 1
R/CBPSBinary.R | 420 +++++++++++++++++++++++++-----------------
R/CBPSMain.R | 26 +-
R/CBPSMultiTreat.r | 500 ++++++++++++++++++++++++++++++++++++++-------------
man/CBPS.Rd | 32 ++-
man/DR.rd | 10 -
man/IPW.Rd | 11 -
man/balance.CBMB.Rd | 2
man/balance.CBMSM.Rd | 2
man/balance.CBPS.Rd | 21 +-
man/balance.Rd | 2
man/plot.CBPS.Rd | 2
man/summary.CBPS.Rd | 2
man/vcov.CBPS.Rd | 5
16 files changed, 721 insertions(+), 361 deletions(-)
Title: Statistical inference for parametric and semiparametric models
based on dependently truncated data
Diff between depend.truncation versions 2.0 dated 2012-04-04 and 2.1 dated 2014-03-08
More information about depend.truncation at CRAN
Description: The package performs parametric and semiparametric inferences for models based on dependently truncated data. Semi-parametric approaches are based on Chaieb, Rivest and Abdous (2006 Biometrika) and Emura, Wang and Hung (2011 Statistica Sinica). Parametric approaches are based on Emura and Konno (2012 Statistical Papers).
Author: Takeshi EMURA
Maintainer: Takeshi EMURA
depend.truncation-2.0/depend.truncation/R/CHAIEB.Clayton.SS.R |only
depend.truncation-2.0/depend.truncation/R/CHAIEB.Frank.SS.R |only
depend.truncation-2.0/depend.truncation/R/EMURA.Clayton.SS.R |only
depend.truncation-2.0/depend.truncation/R/EMURA.Frank.SS.R |only
depend.truncation-2.0/depend.truncation/R/NPMLE.Frank.SS.R |only
depend.truncation-2.0/depend.truncation/R/NPMLE.Indep.SS.R |only
depend.truncation-2.0/depend.truncation/R/NPMLE.Normal.SS.R |only
depend.truncation-2.0/depend.truncation/R/NPMLE.Plackett.SS.R |only
depend.truncation-2.0/depend.truncation/man/CHAIEB.Clayton.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/CHAIEB.Frank.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/EMURA.Clayton.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/EMURA.Frank.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/NPMLE.Frank.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/NPMLE.Indep.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/NPMLE.Normal.SS.Rd |only
depend.truncation-2.0/depend.truncation/man/NPMLE.Plackett.SS.Rd |only
depend.truncation-2.1/depend.truncation/DESCRIPTION | 19 ++---
depend.truncation-2.1/depend.truncation/MD5 | 38 +++++-----
depend.truncation-2.1/depend.truncation/NAMESPACE | 1
depend.truncation-2.1/depend.truncation/R/CHAIEB.Clayton.R |only
depend.truncation-2.1/depend.truncation/R/CHAIEB.Frank.R |only
depend.truncation-2.1/depend.truncation/R/EMURA.Clayton.R |only
depend.truncation-2.1/depend.truncation/R/EMURA.Frank.R |only
depend.truncation-2.1/depend.truncation/R/NPMLE.Frank.R |only
depend.truncation-2.1/depend.truncation/R/NPMLE.Indep.R |only
depend.truncation-2.1/depend.truncation/R/NPMLE.Normal.R |only
depend.truncation-2.1/depend.truncation/R/NPMLE.Plackett.R |only
depend.truncation-2.1/depend.truncation/man/CHAIEB.Clayton.Rd |only
depend.truncation-2.1/depend.truncation/man/CHAIEB.Frank.Rd |only
depend.truncation-2.1/depend.truncation/man/EMURA.Clayton.Rd |only
depend.truncation-2.1/depend.truncation/man/EMURA.Frank.Rd |only
depend.truncation-2.1/depend.truncation/man/NPMLE.Frank.Rd |only
depend.truncation-2.1/depend.truncation/man/NPMLE.Indep.Rd |only
depend.truncation-2.1/depend.truncation/man/NPMLE.Normal.Rd |only
depend.truncation-2.1/depend.truncation/man/NPMLE.Plackett.Rd |only
depend.truncation-2.1/depend.truncation/man/depend.truncation-package.Rd | 9 +-
36 files changed, 34 insertions(+), 33 deletions(-)
Permanent link
Title: Core methods and classes used by aroma.* packages part of The
Aroma Framework
Diff between aroma.core versions 2.11.0 dated 2013-10-17 and 2.12.1 dated 2014-03-08
Description: This package contains core methods and classes used by
higher-level aroma.* packages part of the Aroma Project, e.g.
aroma.affymetrix and aroma.cn. Its API is mostly of interest
to developers and is rarely used by end users directly.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson
aroma.core-2.11.0/aroma.core/R/999.DEPRECATED,downloadPackagePatch.R |only
aroma.core-2.11.0/aroma.core/R/999.DEPRECATED,patchPackage.R |only
aroma.core-2.11.0/aroma.core/R/profileCGH.plot.R |only
aroma.core-2.11.0/aroma.core/inst/NEWS |only
aroma.core-2.11.0/aroma.core/man/downloadPackagePatch.Rd |only
aroma.core-2.11.0/aroma.core/man/patchPackage.Rd |only
aroma.core-2.12.1/aroma.core/DESCRIPTION | 26 -
aroma.core-2.12.1/aroma.core/MD5 | 144 ++++------
aroma.core-2.12.1/aroma.core/NAMESPACE | 35 --
aroma.core-2.12.1/aroma.core/NEWS |only
aroma.core-2.12.1/aroma.core/R/998.AromaPackage.R | 38 --
aroma.core-2.12.1/aroma.core/R/999.DEPRECATED.R | 44 +--
aroma.core-2.12.1/aroma.core/R/AromaGenomeTextFile.R | 30 +-
aroma.core-2.12.1/aroma.core/R/AromaMicroarrayTabularBinaryFile.R | 21 -
aroma.core-2.12.1/aroma.core/R/AromaTabularBinaryFile.R | 4
aroma.core-2.12.1/aroma.core/R/AromaTransform.R | 125 +++++---
aroma.core-2.12.1/aroma.core/R/AromaUcscGenomeTextFile.R | 6
aroma.core-2.12.1/aroma.core/R/AromaUnitPscnBinarySet.R | 2
aroma.core-2.12.1/aroma.core/R/AromaUnitSignalBinaryFile.R | 4
aroma.core-2.12.1/aroma.core/R/AromaUnitTotalCnBinarySet.R | 2
aroma.core-2.12.1/aroma.core/R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 44 +++
aroma.core-2.12.1/aroma.core/R/ChromosomalModel.R | 3
aroma.core-2.12.1/aroma.core/R/ChromosomeExplorer.R | 13
aroma.core-2.12.1/aroma.core/R/CopyNumberChromosomalModel.R | 3
aroma.core-2.12.1/aroma.core/R/CopyNumberOutliers.R | 3
aroma.core-2.12.1/aroma.core/R/CopyNumberRegions.R | 3
aroma.core-2.12.1/aroma.core/R/Explorer.R | 15 -
aroma.core-2.12.1/aroma.core/R/RasterImage.R | 3
aroma.core-2.12.1/aroma.core/R/RawGenomicSignals.R | 4
aroma.core-2.12.1/aroma.core/R/RawGenomicSignals.segmentByCBS.R | 11
aroma.core-2.12.1/aroma.core/R/RawGenomicSignals.segmentByGLAD.R | 81 +++--
aroma.core-2.12.1/aroma.core/R/RawGenomicSignals.segmentByHaarSeg.R | 11
aroma.core-2.12.1/aroma.core/R/RawGenomicSignals.segmentByMPCBS.R | 11
aroma.core-2.12.1/aroma.core/R/RichDataFrame.R | 14
aroma.core-2.12.1/aroma.core/R/SegmentationDataSet.R | 6
aroma.core-2.12.1/aroma.core/R/SegmentedGenomicSignalsInterface.R | 30 +-
aroma.core-2.12.1/aroma.core/R/TextUnitNamesFile.R | 7
aroma.core-2.12.1/aroma.core/man/AromaCellTabularBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaGenomeTextFile.Rd | 64 ++--
aroma.core-2.12.1/aroma.core/man/AromaMicroarrayDataFile.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaMicroarrayDataSet.Rd | 5
aroma.core-2.12.1/aroma.core/man/AromaMicroarrayDataSetTuple.Rd | 2
aroma.core-2.12.1/aroma.core/man/AromaMicroarrayTabularBinaryFile.Rd | 42 +-
aroma.core-2.12.1/aroma.core/man/AromaPlatform.Rd | 2
aroma.core-2.12.1/aroma.core/man/AromaRepository.Rd | 2
aroma.core-2.12.1/aroma.core/man/AromaTabularBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaTabularBinarySet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaTransform.Rd | 2
aroma.core-2.12.1/aroma.core/man/AromaUnitCallFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitCallSet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitFracBCnBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitFracBCnBinarySet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitGenotypeCallFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitGenotypeCallSet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitPscnBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitPscnBinarySet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitSignalBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitSignalBinarySet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitTabularBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitTotalCnBinaryFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/AromaUnitTotalCnBinarySet.Rd | 4
aroma.core-2.12.1/aroma.core/man/AromaUnitTypesFile.Rd | 6
aroma.core-2.12.1/aroma.core/man/CbsModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/ChromosomalModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/ChromosomeExplorer.Rd | 2
aroma.core-2.12.1/aroma.core/man/CopyNumberChromosomalModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/CopyNumberSegmentationModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/Explorer.Rd | 2
aroma.core-2.12.1/aroma.core/man/GladModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/HaarSegModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/Non-documented_objects.Rd | 36 +-
aroma.core-2.12.1/aroma.core/man/RawCopyNumberModel.Rd | 2
aroma.core-2.12.1/aroma.core/man/SegmentedAlleleBFractions.Rd | 2
aroma.core-2.12.1/aroma.core/man/SegmentedCopyNumbers.Rd | 2
aroma.core-2.12.1/aroma.core/man/SegmentedGenomicSignalsInterface.Rd | 1
aroma.core-2.12.1/aroma.core/man/exportAromaUnitPscnBinarySet.Rd |only
aroma.core-2.12.1/aroma.core/man/getOutputDataSet.AromaTransform.Rd | 23 +
77 files changed, 556 insertions(+), 480 deletions(-)