Author: Beth Atkinson (atkinson@mayo.edu) for pedigree functions. Terry
Therneau (therneau@mayo.edu) for all other functions.
Title: mixed-effects Cox models, sparse matrices, and modeling data
from large pedigrees
Description: coxme: general mixed-effects Cox models; kinship: routines
to create and manipulate n by n matrices that describe the
genetic relationships between n persons; pedigree: create and
plot pedigrees; bdsmatrix: a class of objects for sparse
block-diagonal matrices (which is how kinship matrices are
stored); gchol: generalized cholesky decompositions
Diff between kinship versions 1.1.0-22 dated 2008-12-30 and 1.1.0-23 dated 2009-08-25
ChangeLog | 4 ++++ DESCRIPTION | 17 ++++++++++------- inst/doc/releasep.pdf |only man/coxme.Rd | 2 +- man/plot.pedigree.Rd | 2 +- man/solve.bdsmatrix.Rd | 2 +- man/solve.gchol.Rd | 2 +- man/solve.gchol.bdsmatrix.Rd | 2 +- 8 files changed, 19 insertions(+), 12 deletions(-)
Author: Virasakdi Chongsuvivatwong
Diff between epicalc versions 2.9.1.6 dated 2009-08-21 and 2.9.1.7 dated 2009-08-25
Title: Epidemiological calculator
Description: Functions making R easy for epidemiological calculation.
DESCRIPTION | 8 ++++----
R/epicalc.R | 22 ++++++++++++++++++++++
man/IudFollowup.rd | 2 +-
man/fillin.rd |only
4 files changed, 27 insertions(+), 5 deletions(-)
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon
and Jose M. Blanco-Moreno
Title: Functions for spatial point pattern analysis
Description: Some wrappers, functions and data sets for for spatial
point pattern analysis (mainly based on spatstat), used in the
book "Introduccion al Analisis Espacial de Datos en Ecologia y
Ciencias Ambientales: Metodos y Aplicaciones".
Diff between ecespa versions 1.1-1 dated 2008-11-17 and 1.1-2 dated 2009-08-25
DESCRIPTION | 32 +++++++++++++++++++------------- NAMESPACE |only man/00ecespa.Rd | 20 ++++++++++---------- man/Helianthemum.Rd | 4 ++-- man/K1K2.rd | 5 +++-- man/Kci.Rd | 4 ++-- man/Kinhom.log.rd | 6 +++--- man/Kmm.Rd | 19 ++++++++++--------- man/fig1.Rd | 12 ++++++------ 9 files changed, 55 insertions(+), 47 deletions(-)
Author: Florian Wickelmaier
Diff between eba versions 1.5-3 dated 2009-05-24 and 1.5-4 dated 2009-08-25
Title: Elimination-By-Aspects (EBA) Models
Description: Fitting and testing multi-attribute probabilistic choice
models, especially the Bradley-Terry-Luce (BTL) model (Bradley
& Terry, 1952; Luce, 1959), elimination-by-aspects (EBA) models
(Tversky, 1972), and preference tree (Pretree) models (Tversky
& Sattath, 1979).
ChangeLog | 8 +++++++-
DESCRIPTION | 8 ++++----
inst |only
man/strans.Rd | 13 +++++++------
4 files changed, 18 insertions(+), 11 deletions(-)
Author: M. Lado, A. Mendez, D. Olivieri, L. Rodriguez-Linares, X. Vila
Title: Heart rate variability analysis of ECG data
Description: This is a package for developing heart rate variability
studies of ECG records
Diff between RHRV versions 1.6.2 dated 2009-05-04 and 2.1 dated 2009-08-25
DESCRIPTION | 12 +-- R/AddEpisodes.R |only R/AnalyzeHRbyEpisodes.R |only R/BuildNIHR.R | 19 ++--- R/CalculatePowerBand.R | 45 +++++++----- R/CalculateSpectrogram.R | 17 ++-- R/CreateData.R | 35 --------- R/CreateFreqAnalysis.R |only R/CreateHRVData.R |only R/EditNIHR.R | 32 ++++---- R/FilterNIHR.R | 26 ++++-- R/GenerateEpisodes.R |only R/InterpolateNIHR.R | 60 ++++++++++++---- R/LoadApneaWFDB.R |only R/LoadBeatAscii.R | 22 ++++- R/LoadBeatWFDB.R | 14 ++- R/LoadEpisodesAscii.R | 76 +++++++++++++------- R/LoadHeaderWFDB.R | 9 +- R/PlotHR.R | 62 +++++++++++----- R/PlotNIHR.R | 58 ++++++++++----- R/PlotPowerBand.R | 149 ++++++++++++++++++++++++---------------- R/PlotSpectrogram.R | 10 +- R/ReadFromFile.R | 9 +- R/SplitHRbyEpisodes.R |only R/SplitPowerBandByEpisodes.R |only R/WriteToFile.R | 13 ++- man/AddEpisodes.Rd |only man/AnalyzeHRbyEpisodes.Rd |only man/BuildNIHR.Rd | 11 +- man/CalculatePowerBand.Rd | 54 ++++++-------- man/CalculateSpectrogram.Rd | 34 ++++----- man/CreateData.Rd | 8 +- man/CreateFreqAnalysis.Rd |only man/CreateHRVData.Rd |only man/EditNIHR.Rd | 8 +- man/FilterNIHR.Rd | 6 - man/GenerateEpisodes.Rd |only man/InterpolateNIHR.Rd | 8 +- man/LoadApneaWFDB.Rd |only man/LoadBeatAscii.Rd | 6 - man/LoadBeatWFDB.Rd | 25 +++--- man/LoadEpisodesAscii.Rd | 9 +- man/LoadHeaderWFDB.Rd | 6 - man/PlotHR.Rd | 8 +- man/PlotNIHR.Rd | 10 +- man/PlotPowerBand.Rd | 36 +++++---- man/PlotSpectrogram.Rd | 29 +++---- man/RHRV-package.Rd | 48 +++++++----- man/ReadFromFile.Rd | 4 - man/SplitHRbyEpisodes.Rd |only man/SplitPowerBandByEpisodes.Rd |only man/WriteToFile.Rd | 4 - 52 files changed, 565 insertions(+), 417 deletions(-)
Author: Ulrike Groemping
Title: Wrapper package for design of experiments functionality
Description: This package creates various kinds of designs for
(industrial) experiments. It uses, and sometimes enhances,
design generation routines from other packages. Initially,
response surface designs from package rsm and latin hypercube
samples from package lhs have been implemented.
Diff between DoE.wrapper versions 0.5 dated 2009-08-21 and 0.6 dated 2009-08-25
DESCRIPTION | 8 R/bbd.design.R | 2 R/ccd.augment.R | 1 R/ccd.design.R | 5 inst |only man/ccd.design.Rd | 6 tests/bbd.test.Rout.save | 3 tests/ccd.augment.test.R | 6 tests/ccd.augment.test.Rout.save | 715 +++++++++++++++++++++++++++------------ tests/qua.design.test.R |only tests/qua.design.test.Rout.save |only 11 files changed, 528 insertions(+), 218 deletions(-)
Author: Terry Therneau, original R port by Thomas Lumley
Title: Survival analysis, including penalised likelihood.
Description: survival analysis: descriptive statistics, two-sample
tests, parametric accelerated failure models, Cox model.
Delayed entry (truncation) allowed for all models; interval
censoring for parametric models. Case-cohort designs.
Diff between survival versions 2.35-4 dated 2009-04-01 and 2.35-5 dated 2009-08-25
survival-2.35-4/survival/R/model.frame.coxph.S |only survival-2.35-4/survival/R/model.frame.survreg.S |only survival-2.35-4/survival/R/model.newframe.S |only survival-2.35-5/survival/Changelog |only survival-2.35-5/survival/DESCRIPTION | 8 survival-2.35-5/survival/NAMESPACE | 2 survival-2.35-5/survival/R/Surv.S | 4 survival-2.35-5/survival/R/anova.coxph.S | 76 ++-- survival-2.35-5/survival/R/anova.coxphlist.S | 40 +- survival-2.35-5/survival/R/coxph.S | 39 -- survival-2.35-5/survival/R/coxph.control.S | 9 survival-2.35-5/survival/R/match.ratetable.S | 13 survival-2.35-5/survival/R/plot.cox.zph.S | 8 survival-2.35-5/survival/R/predict.coxph.S | 31 - survival-2.35-5/survival/R/predict.survreg.S | 46 +- survival-2.35-5/survival/R/ratetable.S | 4 survival-2.35-5/survival/R/survfit.coxph.null.S | 4 survival-2.35-5/survival/R/survfitCI.S | 34 - survival-2.35-5/survival/R/survreg.S | 36 + survival-2.35-5/survival/R/survreg.fit.S | 4 survival-2.35-5/survival/man/anova.coxph.Rd | 24 - survival-2.35-5/survival/man/coxph.Rd | 4 survival-2.35-5/survival/man/coxph.control.Rd | 3 survival-2.35-5/survival/man/predict.coxph.Rd | 8 survival-2.35-5/survival/man/predict.survreg.Rd | 9 survival-2.35-5/survival/man/ridge.Rd | 7 survival-2.35-5/survival/man/survfit.Rd | 286 +-------------- survival-2.35-5/survival/man/survfit.formula.Rd |only survival-2.35-5/survival/man/survival-internal.Rd | 42 +- survival-2.35-5/survival/man/survreg.Rd | 2 survival-2.35-5/survival/man/survreg.control.Rd | 4 survival-2.35-5/survival/src/survpenal.c | 2 survival-2.35-5/survival/src/survreg6.c | 5 survival-2.35-5/survival/src/survregc2.c | 2 survival-2.35-5/survival/tests/anova.R |only survival-2.35-5/survival/tests/anova.Rout.save |only survival-2.35-5/survival/tests/book6.R | 7 survival-2.35-5/survival/tests/book6.Rout.save | 10 survival-2.35-5/survival/tests/data.interval |only survival-2.35-5/survival/tests/factor.R |only survival-2.35-5/survival/tests/factor.Rout.save |only survival-2.35-5/survival/tests/fr_cancer.Rout.save | 14 survival-2.35-5/survival/tests/fr_colon.Rout.save | 216 +++++------ survival-2.35-5/survival/tests/fr_kidney.Rout.save | 107 ++--- survival-2.35-5/survival/tests/fr_lung.Rout.save | 4 survival-2.35-5/survival/tests/fr_ovarian.Rout.save | 10 survival-2.35-5/survival/tests/fr_rat1.Rout.save | 20 - survival-2.35-5/survival/tests/fr_rat2.R | 4 survival-2.35-5/survival/tests/fr_rat2.Rout.save | 36 - survival-2.35-5/survival/tests/fr_resid.Rout.save | 377 +++++++++----------- survival-2.35-5/survival/tests/infcox.Rout.save | 4 survival-2.35-5/survival/tests/ovarian.R | 2 survival-2.35-5/survival/tests/ovarian.Rout.save | 5 survival-2.35-5/survival/tests/r_sas.R | 2 survival-2.35-5/survival/tests/r_sas.Rout.save | 9 survival-2.35-5/survival/tests/r_user.R | 17 survival-2.35-5/survival/tests/r_user.Rout.save | 24 + survival-2.35-5/survival/tests/testci2.R |only survival-2.35-5/survival/tests/testci2.Rout.save |only survival-2.35-5/survival/tests/testreg.R | 24 - survival-2.35-5/survival/tests/testreg.Rout.save | 93 +++- 61 files changed, 803 insertions(+), 938 deletions(-)
Author: Michael Hahsler, Christian Buchta and Kurt Hornik
Title: Infrastructure for seriation
Description: Infrastructure for seriation with an implementation of
several seriation/sequencing techniques to reorder matrices,
dissimilarity matrices, and dendrograms. Also contains some
visualizations techniques based on seriation.
Diff between seriation versions 1.0-0 dated 2009-03-24 and 1.0-1 dated 2009-08-25
seriation-1.0-0/seriation/COPYRIGHT |only seriation-1.0-1/seriation/DESCRIPTION | 12 seriation-1.0-1/seriation/NAMESPACE | 5 seriation-1.0-1/seriation/R/dissplot.R | 631 +++++++++++++---------- seriation-1.0-1/seriation/R/permute.R | 17 seriation-1.0-1/seriation/inst/doc/seriation.pdf |binary seriation-1.0-1/seriation/man/dissplot.Rd | 90 ++- seriation-1.0-1/seriation/man/permute.Rd | 1 8 files changed, 453 insertions(+), 303 deletions(-)
Author: Julien Barnier
Diff between rgrs versions 0.2-13 dated 2009-08-13 and 0.2-14 dated 2009-08-25
Title: Functions to make R usage in social sciences easier (in french)
Description: This package provides functions for beginners and social
sciences students or researchers. Currently it includes
functions for cross-tabulation, weighting, results export, and
maps plotting. The documentation and help pages are written in
french.
DESCRIPTION | 10 +++++-----
R/carte.eff.R | 13 ++++++++++---
R/carte.prop.R | 15 +++++++++++----
R/carte.qual.R | 14 +++++++++++---
man/Cartographie.Rd | 25 ++++++++++++++++---------
man/Cartographie.legende.Rd |only
6 files changed, 53 insertions(+), 24 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.19 dated 2009-07-01 and 4.20 dated 2009-08-25
DESCRIPTION | 8 R/createGrid.R | 2 R/createModel.R | 12 R/misc.R | 23 R/predictionFunction.R | 2 R/predictors.R | 5 R/selection.R | 5 inst/CHANGES | 7 inst/doc/caretMisc.pdf | 3445 ++++++++++++++++++++++---------------------- inst/doc/caretSelection.pdf | 2624 ++++++++++++++++----------------- inst/doc/caretTrain.Rnw | 7 inst/doc/caretTrain.pdf |binary inst/doc/caretVarImp.pdf |binary man/train.Rd | 3 14 files changed, 3087 insertions(+), 3056 deletions(-)
Author: John Fox
Diff between car versions 1.2-14 dated 2009-04-23 and 1.2-15 dated 2009-08-25
Title: Companion to Applied Regression
Description: This package accompanies J. Fox, An R and S-PLUS Companion
to Applied Regression, Sage, 2002. The package contains mostly
functions for applied regression, linear models, and
generalized linear models, with an emphasis on regression
diagnostics, particularly graphical diagnostic methods. There
are also some utility functions. With some exceptions, I have
tried not to duplicate capabilities in the basic distribution
of R, nor in widely used packages. Where relevant, the
functions in car are consistent with na.action = na.omit or
na.exclude.
DESCRIPTION | 8 ++++----
R/scatterplot.R | 6 +++---
R/scatterplot.matrix.R | 8 ++++----
R/vif.R | 8 ++++----
inst/CHANGES | 5 +++++
man/car-package.Rd | 4 ++--
man/scatterplot.Rd | 6 ++++--
man/scatterplot.matrix.Rd | 5 +++--
man/vif.Rd | 5 +++--
9 files changed, 32 insertions(+), 23 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.7 dated 2009-08-19 and 0.8 dated 2009-08-25
DESCRIPTION | 8 ++-- NAMESPACE | 2 - R/add.response.R | 2 - R/export.design.R | 19 +++++++---- R/fac.design.R | 4 +- R/fix.design.R | 1 R/html.data.frame.R | 4 +- R/oa.design.R | 11 ++++++ R/plot.design.R | 2 - R/qua.design.R | 65 +++++++++++++++++++++------------------- R/utilities.R | 3 + inst/NEWS | 14 ++++++++ man/add.response.Rd | 8 ++-- man/arrays.Rd | 6 +-- man/class-design-methods.Rd | 16 ++++----- man/class-design.Rd | 36 +++++++++++++++------- man/contr.FrF2.Rd | 3 + man/cross.design.Rd | 8 ++-- man/export.design.Rd | 7 +++- man/fac.design.Rd | 13 +++++--- man/oa.design.Rd | 39 ++++++++++++++---------- man/param.design.Rd | 11 +++--- man/qua.design.Rd | 58 +++++++++++++++++++++++------------ man/represhape.Rd | 5 +-- man/utilities.Rd | 19 +++++++---- tests/test_qua.design.R |only tests/test_qua.design.Rout.save |only 27 files changed, 228 insertions(+), 136 deletions(-)
Author: Pedro Brasil
Diff between DiagnosisMed versions 0.2.2.1 dated 2009-06-19 and 0.2.2.2 dated 2009-08-25
Title: Diagnostic test accuracy evaluation for medical professionals.
Description: DiagnosisMed is a package to analyze data from diagnostic
test accuracy evaluating health conditions. It is being built
to be used by health professionals. This package is able to
estimate sensitivity and specificity from categorical and
continuous test results including some evaluations of
indeterminate results, or compare different categorical tests,
and estimate reasonble cut-offs of tests and display it in a
way commonly used by health professionals. No graphical
interface is avalible yet.
DESCRIPTION | 24 ++++++++++++------------
R/ROC.r | 45 +++++++++++++++++++++------------------------
2 files changed, 33 insertions(+), 36 deletions(-)