Author: Douglas Bates
Diff between Matrix versions 0.999375-23 dated 2009-03-31 and 0.999375-25 dated 2009-04-19
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
Matrix-0.999375-23/Matrix/src/Makevars.win |only
Matrix-0.999375-23/Matrix/src/scripts/Win.mk |only
Matrix-0.999375-25/Matrix/ChangeLog | 43 +
Matrix-0.999375-25/Matrix/DESCRIPTION | 11
Matrix-0.999375-25/Matrix/Done | 1
Matrix-0.999375-25/Matrix/NAMESPACE | 35 -
Matrix-0.999375-25/Matrix/R/AllGeneric.R | 3
Matrix-0.999375-25/Matrix/R/Auxiliaries.R | 58 +
Matrix-0.999375-25/Matrix/R/Csparse.R | 3
Matrix-0.999375-25/Matrix/R/Matrix.R | 48 -
Matrix-0.999375-25/Matrix/R/Ops.R | 19
Matrix-0.999375-25/Matrix/R/Tsparse.R | 106 +--
Matrix-0.999375-25/Matrix/R/dgTMatrix.R | 11
Matrix-0.999375-25/Matrix/R/dgeMatrix.R | 4
Matrix-0.999375-25/Matrix/R/diagMatrix.R | 15
Matrix-0.999375-25/Matrix/R/dtpMatrix.R | 2
Matrix-0.999375-25/Matrix/R/kronecker.R | 6
Matrix-0.999375-25/Matrix/R/lgTMatrix.R | 3
Matrix-0.999375-25/Matrix/R/ngTMatrix.R | 3
Matrix-0.999375-25/Matrix/R/sparseMatrix.R | 20
Matrix-0.999375-25/Matrix/R/sparseVector.R | 24
Matrix-0.999375-25/Matrix/R/zzz.R | 22
Matrix-0.999375-25/Matrix/inst/doc/Comparisons.pdf |binary
Matrix-0.999375-25/Matrix/inst/doc/Design-issues.pdf |binary
Matrix-0.999375-25/Matrix/inst/doc/Intro2Matrix.pdf | 583 +++++++++----------
Matrix-0.999375-25/Matrix/inst/doc/Introduction.pdf |binary
Matrix-0.999375-25/Matrix/inst/doc/sparseModels.pdf |binary
Matrix-0.999375-25/Matrix/inst/test-tools.R | 79 --
Matrix-0.999375-25/Matrix/man/Matrix-class.Rd | 7
Matrix-0.999375-25/Matrix/man/bandSparse.Rd | 6
Matrix-0.999375-25/Matrix/man/dgeMatrix-class.Rd | 2
Matrix-0.999375-25/Matrix/man/lu.Rd | 16
Matrix-0.999375-25/Matrix/man/sparseMatrix-class.Rd | 3
Matrix-0.999375-25/Matrix/man/sparseMatrix.Rd | 5
Matrix-0.999375-25/Matrix/man/sparseVector-class.Rd | 2
Matrix-0.999375-25/Matrix/src/dgeMatrix.c | 2
Matrix-0.999375-25/Matrix/tests/Simple.R | 16
Matrix-0.999375-25/Matrix/tests/bind.Rout.save | 16
Matrix-0.999375-25/Matrix/tests/dg_Matrix.R | 5
Matrix-0.999375-25/Matrix/tests/indexing.R | 47 +
Matrix-0.999375-25/Matrix/tests/indexing.Rout.save | 411 +++----------
41 files changed, 736 insertions(+), 901 deletions(-)
Author: Nicholas L. Crookston
Diff between yaImpute versions 1.0-8 dated 2009-02-06 and 1.0-9 dated 2009-04-19
Title: yaImpute: An R Package for k-NN Imputation
Description: Performs popular nearest neighbor routines for imputation
DESCRIPTION | 8 +-
R/asciigridimpute.R | 30 ++++++----
R/yai.R | 2
inst/NEWS |only
man/asciigridimpute.Rd | 143 +++++++++++++++++++++++++------------------------
5 files changed, 99 insertions(+), 84 deletions(-)
Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto, Steve
Ellner, Bruce Kendall
Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.23-1 dated 2009-04-16 and 0.23-2 dated 2009-04-19
DESCRIPTION | 11 ++---- R/mif-methods.R | 2 - R/mif.R | 4 +- data/ou2.rda |binary inst/ChangeLog | 25 ++++++++++++++ inst/doc/Rplots.pdf | 4 +- inst/doc/compiled_code_in_pomp.Rnw | 1 inst/doc/compiled_code_in_pomp.pdf |binary inst/doc/intro_to_pomp.pdf |binary inst/examples/euler_sir.R | 5 +- inst/examples/euler_sir.c | 65 ++++++++++++++++++++++--------------- inst/include/pomp.h | 9 +++++ man/euler.Rd | 5 +- man/mif-class.Rd | 4 ++ man/mif-methods.Rd | 4 ++ man/mif.Rd | 20 ++++++----- src/euler.c | 21 +++++++++-- src/euler_sir.c | 65 ++++++++++++++++++++++--------------- src/ou2.c | 2 - src/pomp.h | 9 +++++ src/rmeasure.c | 4 ++ tests/sir.R | 5 +- tests/sir.Rout.save | 13 +++---- 23 files changed, 188 insertions(+), 90 deletions(-)
Author: Jonathan P. Weeks
Diff between plink versions 0.1-1 dated 2009-01-26 and 1.0.0 dated 2009-04-19
Title: IRT Separate Calibration Linking Methods
Description: This package uses item response theory methods to compute
linking constants and conduct chain linking of unidimensional
or multidimensional tests for multiple groups under a
nonequivalent groups common item design. The unidimensional
methods include the Mean/Mean, Mean/Sigma, Haebara, and
Stocking-Lord methods for dichotomous (1PL, 2PL and 3PL) and/or
polytomous (graded response, partial credit/generalized partial
credit, nominal, and multiple-choice model) items. The
multidimensional methods include the Reckase-Martineau method
and extensions of the Haebara and Stocking-Lord method using a
single dilation parameter, multiple dilation parameters, or the
Oshima, Davey, & Lee approach for multidimensional extensions
of all the unidimensional dichotomous and polytomous item
response models. The package also includes functions for
importing item and/or ability parameters from common IRT
software and ploting item characteristic/category curves or
surfaces and vector plots.
DESCRIPTION | 46 +-
NAMESPACE | 7
R/classes.R | 21
R/drm.R | 98 +++-
R/gpcm.R | 107 +++--
R/grm.R | 111 +++--
R/irt.pars.R | 65 +--
R/link.R | 93 ++--
R/mcm.R | 108 +++--
R/mixed.R | 105 +++-
R/nrm.R | 103 +++-
R/plink.R | 1019 ++++++++++++++++++++++++++++++++++--------------
R/plot.R | 269 +++++++++++-
R/read.bilog.R | 40 +
R/sep.pars.R | 499 ++++++++++++-----------
R/summary.R | 329 +++++++++------
R/weight.R | 168 +++++--
data/plink.RData |binary
inst/CITATION | 4
inst/NEWS | 67 +++
man/KB04.Rd | 12
man/TK07.Rd | 18
man/act.mcm.Rd | 11
man/act.nrm.Rd | 10
man/as.irt.pars.Rd | 213 ++--------
man/as.poly.mod.Rd | 28 -
man/as.weight.Rd | 179 ++++++--
man/combine.pars.Rd | 6
man/dgn.Rd | 19
man/drm-methods.Rd | 202 ++++++---
man/gpcm-methods.Rd | 173 +++++---
man/grm-methods.Rd | 151 ++++---
man/irt.pars-class.Rd | 9
man/irt.prob-class.Rd | 13
man/link-class.Rd | 40 +
man/link.con.Rd | 26 +
man/mcm-methods.Rd | 159 ++++---
man/md.mixed.Rd |only
man/mixed-methods.Rd | 72 ++-
man/nrm-methods.Rd | 105 +++-
man/plink-methods.Rd | 175 ++++++--
man/plink-package.Rd | 127 +++++
man/plot.irt.prob.Rd | 123 +++++
man/poly.mod-class.Rd | 7
man/read.bilog.Rd | 18
man/reading.Rd |only
man/reckase9.Rd |only
man/sep.pars-class.Rd | 30 -
man/sep.pars-methods.Rd | 235 ++---------
man/summary.irt.pars.Rd | 14
50 files changed, 3570 insertions(+), 1864 deletions(-)
Author: Tristen Hayfield
Diff between np versions 0.30-1 dated 2009-01-29 and 0.30-2 dated 2009-04-19
Title: Nonparametric kernel smoothing methods for mixed data types
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. We would
like to gratefully acknowledge support from the Natural
Sciences and Engineering Research Council of Canada
(NSERC:www.nserc.ca), the Social Sciences and Humanities
Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared
Hierarchical Academic Research Computing Network
(SHARCNET:www.sharcnet.ca).
CHANGELOG | 6
DESCRIPTION | 27
R/np.singleindex.bw.R | 18
R/np.smoothcoef.bw.R | 12
R/util.R | 5
R/zzz.R | 2
inst/doc/np.pdf | 1968 ++++++++++++++++--------------
inst/doc/np_faq.pdf | 3221 +++++++++++++++++++++++++++-----------------------
man/np-package.Rd | 2
man/np.cmstest.Rd | 4
man/np.smoothcoef.Rd | 2
src/statmods.c | 31
12 files changed, 2885 insertions(+), 2413 deletions(-)
Author: Andrew Gelman
Diff between mi versions 0.06-1 dated 2009-04-17 and 0.06-2 dated 2009-04-19
Title: Missing Data Imputation and Model Checking
Description: Missing-data imputation and model checking
CHANGELOG | 7 +++++++
DESCRIPTION | 8 ++++----
R/AllInternal.R | 11 +++++++++++
R/mi.R | 10 ++++------
R/mi.info.R | 40 ++++++++++++++++++++++------------------
5 files changed, 48 insertions(+), 28 deletions(-)
Author: Ji-Hyung Shin
Diff between luca versions 1.0-3 dated 2009-01-15 and 1.0-4 dated 2009-04-19
Title: Likelihood inference from case-control data Under Covariate
Assumptions (LUCA)
Description: Likelihood inference in case-control studies of a rare
disease under independence or simple dependence of genetic and
non-genetic covariates
DESCRIPTION | 18 ++++++++++++------
inst/ChangeLog | 5 +++++
man/luca.Rd | 54 +++++++++++++++++++++++++++++++-----------------------
3 files changed, 48 insertions(+), 29 deletions(-)
Author: John Fox, Michael Friendly, and Georges Monette
Title: Visualizing Tests in Multivariate Linear Models
Description: Represents sums-of-squares-and-products matrices for
linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions).
Diff between heplots versions 0.8-5 dated 2009-04-03 and 0.8-6 dated 2009-04-19
DESCRIPTION | 11 +++++------ R/heplot.mlm.R | 25 ++++++++++++------------- R/pairs.mlm.R | 25 +++++++++++++++++++------ R/termInfo.R |only data/VocabGrowth.rda |only demo |only inst/CHANGES | 6 +++++- man/VocabGrowth.Rd |only man/heplot-package.Rd | 4 ++-- man/heplot.Rd | 13 +++++++++---- man/heplots-internal.Rd | 3 ++- 11 files changed, 54 insertions(+), 33 deletions(-)
Author: Matthias Templ, Andreas Alfons
Title: Visualization and Imputation of Missing Values
Description: This package introduces new tools for the visualization of
missing values in R, which can be used for exploring the data
and the structure of the missing values. Depending on this
structure, they may help to identify the mechanism generating
the missings. A graphical user interface allows an easy
handling of the implemented plot methods.
Diff between VIM versions 1.2.4 dated 2009-01-06 and 1.3 dated 2009-04-19
VIM-1.2.4/VIM/R/bubbleMiss.R |only VIM-1.2.4/VIM/R/iimagMiss.R |only VIM-1.2.4/VIM/R/plot.aggr.R |only VIM-1.2.4/VIM/R/print.aggr.R |only VIM-1.2.4/VIM/R/summary.aggr.R |only VIM-1.2.4/VIM/R/utilities.R |only VIM-1.2.4/VIM/man/bubbleMiss.Rd |only VIM-1.2.4/VIM/man/iimagMiss.Rd |only VIM-1.2.4/VIM/man/plot.aggr.Rd |only VIM-1.2.4/VIM/man/utilities.Rd |only VIM-1.3/VIM/DESCRIPTION | 21 VIM-1.3/VIM/NAMESPACE |only VIM-1.3/VIM/R/TKRaggr.R |only VIM-1.3/VIM/R/TKRdevice.R |only VIM-1.3/VIM/R/TKRmarginmatrix.R |only VIM-1.3/VIM/R/TKRmatrixplot.R |only VIM-1.3/VIM/R/TKRparcoordMiss.R |only VIM-1.3/VIM/R/TKRpbox.R |only VIM-1.3/VIM/R/TKRscattmatrixMiss.R |only VIM-1.3/VIM/R/aggr.R | 310 +++++++- VIM-1.3/VIM/R/alphablend.R |only VIM-1.3/VIM/R/barMiss.R | 296 ++++++-- VIM-1.3/VIM/R/bgmap.R | 5 VIM-1.3/VIM/R/colormapMiss.R | 78 +- VIM-1.3/VIM/R/growdotMiss.R |only VIM-1.3/VIM/R/histMiss.R | 307 +++++--- VIM-1.3/VIM/R/initialise.R | 54 + VIM-1.3/VIM/R/mapMiss.R | 65 + VIM-1.3/VIM/R/marginmatrix.R |only VIM-1.3/VIM/R/marginplot.R | 243 ++++-- VIM-1.3/VIM/R/matrixplot.R |only VIM-1.3/VIM/R/pairsVIM.R |only VIM-1.3/VIM/R/parcoordMiss.R | 211 ++++-- VIM-1.3/VIM/R/pbox.R | 427 +++++++++--- VIM-1.3/VIM/R/prepare.R | 212 +++--- VIM-1.3/VIM/R/rugNA.R |only VIM-1.3/VIM/R/scattJitt.R | 174 +++- VIM-1.3/VIM/R/scattMiss.R | 171 +++- VIM-1.3/VIM/R/scattmatrixMiss.R | 221 +++++- VIM-1.3/VIM/R/spineMiss.R | 376 ++++++++-- VIM-1.3/VIM/R/utils.R |only VIM-1.3/VIM/R/vmGUImenu.R | 1188 ++++++++++++++++++---------------- VIM-1.3/VIM/R/zzz.R | 6 VIM-1.3/VIM/data/kola.background.rda |only VIM-1.3/VIM/man/VIM-package.Rd | 6 VIM-1.3/VIM/man/aggr.Rd | 123 ++- VIM-1.3/VIM/man/alphablend.Rd | 8 VIM-1.3/VIM/man/barMiss.Rd | 103 +- VIM-1.3/VIM/man/bgmap.Rd | 10 VIM-1.3/VIM/man/chorizonDL.Rd | 10 VIM-1.3/VIM/man/colormapMiss.Rd | 73 +- VIM-1.3/VIM/man/count.Rd |only VIM-1.3/VIM/man/growdotMiss.Rd |only VIM-1.3/VIM/man/histMiss.Rd | 99 +- VIM-1.3/VIM/man/initialise.Rd | 27 VIM-1.3/VIM/man/kola.background.Rd |only VIM-1.3/VIM/man/mapMiss.Rd | 28 VIM-1.3/VIM/man/marginmatrix.Rd |only VIM-1.3/VIM/man/marginplot.Rd | 64 + VIM-1.3/VIM/man/matrixplot.Rd |only VIM-1.3/VIM/man/pairsVIM.Rd |only VIM-1.3/VIM/man/parcoordMiss.Rd | 91 +- VIM-1.3/VIM/man/pbox.Rd | 109 ++- VIM-1.3/VIM/man/prepare.Rd | 63 - VIM-1.3/VIM/man/print.aggr.Rd | 12 VIM-1.3/VIM/man/print.summary.aggr.Rd |only VIM-1.3/VIM/man/rugNA.Rd |only VIM-1.3/VIM/man/scattJitt.Rd | 49 - VIM-1.3/VIM/man/scattMiss.Rd | 39 - VIM-1.3/VIM/man/scattmatrixMiss.Rd | 105 ++- VIM-1.3/VIM/man/sleep.Rd | 8 VIM-1.3/VIM/man/spineMiss.Rd | 111 ++- VIM-1.3/VIM/man/summary.aggr.Rd | 21 VIM-1.3/VIM/man/tao.Rd | 2 VIM-1.3/VIM/man/vmGUImenu.Rd | 49 - 75 files changed, 3783 insertions(+), 1792 deletions(-)
Author: John Maindonald
Title: Data Sets and Functions, supplementary to DAAG
Description: various data sets used in additonal exercises for the book
Maindonald, J.H. and Braun, W.J. (2nd edn 2007) "Data Analysis
and Graphics Using R", and for a 'Data Mining' course. Note
especially the datasets \code{nassCDS} (airbag and other
influences on US vehicle accident outcomes: 1997-2002),
\code{cricketer} (handedness, British first class cricketers
born 1840-1960 whose handedness could be determined),
\code{nswdemo} and related datasets (US Labor Training
Evaluation Data), \code{rockArt} (multivariate binary data on
Pacific rock art), \code{hotspots} (ages and distance from
Kilauea of larval hotspots; c.f. also \code{hotspots2006}),
\code{nihills} (record times for Northern Ireland mountain
races), \code{worldRecords} (record times for track and road
races), \code{progression} (progression of record times for
track races), \code{edcT} and \code{edcCO2} (temperature and
CO2 estimates from the EPICA Dome C ice core, covering 0 to 800
kyr BP), \code{grog} (Australian and NZ liquor consumption
patterns, 1998-2006), and \code{bomregions} (historical
Australian climate data).
Diff between DAAGxtras versions 0.7-5 dated 2009-03-29 and 0.7-6 dated 2009-04-19
DAAGxtras-0.7-5/DAAGxtras/data/cricketers.RData |only DAAGxtras-0.7-5/DAAGxtras/man/cricketers.Rd |only DAAGxtras-0.7-6/DAAGxtras/DESCRIPTION | 12 ++++++------ DAAGxtras-0.7-6/DAAGxtras/data/cricketer.RData |only DAAGxtras-0.7-6/DAAGxtras/data/earlycrcktr.RData |only DAAGxtras-0.7-6/DAAGxtras/man/DAAGxtras-package.Rd |only DAAGxtras-0.7-6/DAAGxtras/man/cricketer.Rd |only DAAGxtras-0.7-6/DAAGxtras/man/earlycrcktr.Rd |only 8 files changed, 6 insertions(+), 6 deletions(-)
Author: Adrian Raftery
Diff between BMA versions 3.09 dated 2009-02-03 and 3.10 dated 2009-04-19
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging for linear models,
generalizable linear models and survival models (cox
regression).
CHANGELOG | 4 ++++
DESCRIPTION | 31 ++++++++++++++++++-------------
man/bic.surv.Rd | 9 ++++++---
3 files changed, 28 insertions(+), 16 deletions(-)