Author: Andrej-Nikolai Spiess
Diff between qpcR versions 1.1-7 dated 2008-12-16 and 1.1-8 dated 2009-03-27
Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of
various features that are essential in the analysis of
quantitative real-time polymerase chain reaction (qPCR).
qpcR-1.1-7/qpcR/man/qpcR.Rd |only
qpcR-1.1-8/qpcR/DESCRIPTION | 32 ++++++++++++++++++--------------
qpcR-1.1-8/qpcR/NAMESPACE | 6 +++---
qpcR-1.1-8/qpcR/R/REST.r |only
qpcR-1.1-8/qpcR/R/calib.R | 2 +-
qpcR-1.1-8/qpcR/R/calib2.r |only
qpcR-1.1-8/qpcR/R/confband.R | 7 ++++---
qpcR-1.1-8/qpcR/R/drmfit.r |only
qpcR-1.1-8/qpcR/R/expcomp.R | 2 +-
qpcR-1.1-8/qpcR/R/expfit.R | 4 ++--
qpcR-1.1-8/qpcR/R/modlist.R | 2 +-
qpcR-1.1-8/qpcR/R/pcrbatch.R | 2 +-
qpcR-1.1-8/qpcR/R/pcrfit.R | 2 +-
qpcR-1.1-8/qpcR/R/pcropt1.R | 2 +-
qpcR-1.1-8/qpcR/man/AICc.Rd | 2 +-
qpcR-1.1-8/qpcR/man/LR.Rd | 3 ---
qpcR-1.1-8/qpcR/man/PRESS.Rd | 2 +-
qpcR-1.1-8/qpcR/man/REST.rd |only
qpcR-1.1-8/qpcR/man/RMSE.Rd | 2 +-
qpcR-1.1-8/qpcR/man/RSS.Rd | 2 +-
qpcR-1.1-8/qpcR/man/Rsq.Rd | 2 +-
qpcR-1.1-8/qpcR/man/S27.Rd | 9 ++-------
qpcR-1.1-8/qpcR/man/akaike.weights.Rd | 2 +-
qpcR-1.1-8/qpcR/man/calib.Rd | 13 +++++++------
qpcR-1.1-8/qpcR/man/calib2.rd |only
qpcR-1.1-8/qpcR/man/confband.Rd | 2 +-
qpcR-1.1-8/qpcR/man/drmfit.rd |only
qpcR-1.1-8/qpcR/man/eff.Rd | 2 +-
qpcR-1.1-8/qpcR/man/efficiency.Rd | 10 +++++-----
qpcR-1.1-8/qpcR/man/evidence.Rd | 4 ++--
qpcR-1.1-8/qpcR/man/expcomp.Rd | 2 +-
qpcR-1.1-8/qpcR/man/expfit.Rd | 2 +-
qpcR-1.1-8/qpcR/man/mchoice.Rd | 2 +-
qpcR-1.1-8/qpcR/man/pcrGOF.Rd | 2 +-
qpcR-1.1-8/qpcR/man/pcrfit.Rd | 6 ++++--
qpcR-1.1-8/qpcR/man/pcropt1.Rd | 4 ++--
qpcR-1.1-8/qpcR/man/pcrplot.Rd | 4 ++--
qpcR-1.1-8/qpcR/man/pcrpred.Rd | 2 +-
qpcR-1.1-8/qpcR/man/ratiocalc.Rd | 3 ++-
qpcR-1.1-8/qpcR/man/repform.Rd | 5 ++---
qpcR-1.1-8/qpcR/man/reps.Rd | 4 ++--
qpcR-1.1-8/qpcR/man/reps2.Rd | 7 ++++---
qpcR-1.1-8/qpcR/man/reps3.Rd | 7 ++++---
qpcR-1.1-8/qpcR/man/resVar.Rd | 2 +-
qpcR-1.1-8/qpcR/man/rutledge.Rd | 5 ++---
qpcR-1.1-8/qpcR/man/sliwin.Rd | 2 +-
46 files changed, 88 insertions(+), 87 deletions(-)
Author: Torsten Hothorn, Kurt Hornik, Carolin Strobl and Achim Zeileis
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning. The
core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems,
including nominal, ordinal, numeric, censored as well as
multivariate response variables and arbitrary measurement
scales of the covariates. Based on conditional inference trees,
cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for
recursive partitioning based on parametric models (e.g. linear
models, GLMs or survival regression) employing parameter
instability tests for split selection. Extensible functionality
for visualizing tree-structured regression models is available.
Diff between party versions 0.9-995 dated 2009-02-23 and 0.9-996 dated 2009-03-27
CHANGES | 5 DESCRIPTION | 42 +-- R/ConditionalTree.R | 5 R/Plot.R | 4 R/RandomForest.R | 4 R/Utils.R | 11 inst/doc/MOB.pdf | 354 +++++++++++++++---------------- inst/doc/party.pdf |binary tests/Distributions.Rout.save | 2 tests/IndependenceTest-regtest.Rout.save | 10 tests/LinearStatistic-regtest.Rout.save | 2 tests/Node-regtest.Rout.save | 2 tests/Predict-regtest.Rout.save | 2 tests/RandomForest-regtest.Rout.save | 18 - tests/Splits-regtest.Rout.save | 2 tests/TestStatistic-regtest.Rout.save | 2 tests/TreeGrow-regtest.Rout.save | 17 - tests/Utils-regtest.Rout.save | 2 tests/bugfixes.Rout.save | 10 tests/codetools-checks.Rout.save | 16 - tests/mob.Rout.save | 20 - 21 files changed, 272 insertions(+), 258 deletions(-)
Author: Torsten Hothorn, Peter Buhlmann, Thomas Kneib, Matthias Schmid
and Benjamin Hofner
Title: Model-Based Boosting
Description: Functional gradient descent algorithms (boosting) for
optimizing general loss functions utilizing componentwise least
squares, either of parametric linear form or smoothing splines,
or regression trees as base learners for fitting generalized
linear, additive and interaction models to potentially
high-dimensional data.
Diff between mboost versions 1.0-6 dated 2009-01-09 and 1.1-0 dated 2009-03-27
mboost-1.0-6/mboost/svn-commit.tmp |only mboost-1.0-6/mboost/tests/setup.Rout.save |only mboost-1.1-0/mboost/DESCRIPTION | 28 +-- mboost-1.1-0/mboost/R/blackboost.R | 1 mboost-1.1-0/mboost/R/gamboost.R | 11 - mboost-1.1-0/mboost/R/glmboost.R | 2 mboost-1.1-0/mboost/R/helpers.R | 2 mboost-1.1-0/mboost/R/methods.R | 15 + mboost-1.1-0/mboost/R/xsp.R | 122 +++++++++------ mboost-1.1-0/mboost/inst/CHANGES | 15 + mboost-1.1-0/mboost/inst/CITATION |only mboost-1.1-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary mboost-1.1-0/mboost/inst/doc/mboost_illustrations.Rnw | 4 mboost-1.1-0/mboost/inst/doc/mboost_illustrations.pdf |binary mboost-1.1-0/mboost/man/baselearners.Rd | 5 mboost-1.1-0/mboost/man/gamboost.Rd | 5 mboost-1.1-0/mboost/man/methods.Rd | 10 - mboost-1.1-0/mboost/tests/bugfixes.R | 23 ++ mboost-1.1-0/mboost/tests/bugfixes.Rout.save | 37 +++- mboost-1.1-0/mboost/tests/codetools-checks.Rout.save | 6 mboost-1.1-0/mboost/tests/mboost_illustrations.R | 4 mboost-1.1-0/mboost/tests/mboost_illustrations.Rout.save | 8 mboost-1.1-0/mboost/tests/regtest-blackboost.Rout.save | 6 mboost-1.1-0/mboost/tests/regtest-gamboost.R | 24 +- mboost-1.1-0/mboost/tests/regtest-gamboost.Rout.save | 40 +--- mboost-1.1-0/mboost/tests/regtest-glmboost.Rout.save | 4 mboost-1.1-0/mboost/tests/regtest-hatmatrix.Rout.save | 4 mboost-1.1-0/mboost/to_do_list.txt | 1 28 files changed, 239 insertions(+), 138 deletions(-)
Author: Jan Graffelman
Diff between HardyWeinberg versions 1.2 dated 2008-04-22 and 1.3 dated 2009-03-27
Title: Graphical tests for Hardy-Weinberg equilibrium
Description: Package HardyWeinberg is a package for exploring
bi-allelic marker data. It focuses on the graphical
representation of the results of tests for Hardy-Weinberg
equlibrium in a ternary plot. Routines for several tests for
Hardy-Weinberg equilibrium are included in the package.
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg-008.eps |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg-008.pdf |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg.aux |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg.dvi |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg.log |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg.out |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/HardyWeinberg.tex |only
HardyWeinberg-1.2/HardyWeinberg/inst/doc/Rplots.ps |only
HardyWeinberg-1.3/HardyWeinberg/DESCRIPTION | 34
HardyWeinberg-1.3/HardyWeinberg/NAMESPACE | 2
HardyWeinberg-1.3/HardyWeinberg/R/CritSam.R | 5
HardyWeinberg-1.3/HardyWeinberg/R/HWCondProbAB.R |only
HardyWeinberg-1.3/HardyWeinberg/R/HWExact.R |only
HardyWeinberg-1.3/HardyWeinberg/R/HWTernaryPlot.R | 106
HardyWeinberg-1.3/HardyWeinberg/inst/doc/HardyWeinberg.Snw | 348
HardyWeinberg-1.3/HardyWeinberg/inst/doc/HardyWeinberg.pdf | 4186 +++++-----
HardyWeinberg-1.3/HardyWeinberg/inst/doc/Rplots.pdf |only
HardyWeinberg-1.3/HardyWeinberg/man/HWCondProbAB.Rd |only
HardyWeinberg-1.3/HardyWeinberg/man/HWExact.Rd |only
HardyWeinberg-1.3/HardyWeinberg/man/HWTernaryPlot.Rd | 25
HardyWeinberg-1.3/HardyWeinberg/man/HardyWeinberg-package.Rd | 8
21 files changed, 2525 insertions(+), 2189 deletions(-)
Author: Jerome Sueur
Diff between seewave versions 1.5.2 dated 2009-01-03 and 1.5.4 dated 2009-03-27
Title: Time wave analysis and graphical representation
Description: seewave provides functions for analysing, manipulating,
displaying, editing and synthesizing time waves (particularly
sound). This package processes time analysis (oscillograms and
envelopes), spectral content, resonance quality factor,
entropy, cross correlation and autocorrelation, zero-crossing,
dominant frequency, analytic signal, frequency coherence, 2D
and 3D spectrograms and many other analyses.
DESCRIPTION | 45
R/seewave.r | 8103 ++++++++++++++++++++++++------------------------
inst/doc/seewave_IO.pdf | 1888 +++++------
inst/doc/seewave_IO.rnw | 75
man/H.Rd | 2
man/afilter.Rd | 2
man/diffenv.Rd | 6
man/diffspec.Rd | 5
man/diffwave.Rd | 5
man/dynspec.rd | 2
man/rmnoise.Rd |only
man/seewave.package.Rd | 9
man/spectro.Rd | 2
man/spectro3D.Rd | 3
man/symba.Rd | 2
man/wf.Rd |only
16 files changed, 5277 insertions(+), 4872 deletions(-)
Author: Wacek Kusnierczyk
Diff between rbenchmark versions 0.1 dated 2009-03-20 and 0.2 dated 2009-03-27
Title: Benchmarking routine for R
Description: rbenchmark is inspired by the Perl module Benchmark, and
is intended to facilitate benchmarking of arbitrary R code. The
library consists of just one function, benchmark, which is a
simple wrapper around system.time. Given a specification of
the benchmarking process (counts of replications, evaluation
environment) and an arbitrary number of expressions, benchmark
evaluates each of the expressions in the specified environment,
replicating the evaluation as many times as specified, and
returning the results conveniently wrapped into a data frame.
DESCRIPTION | 8 ++++----
R/benchmark.R | 5 ++++-
man/benchmark-package.Rd | 6 +++---
man/benchmark.Rd | 2 +-
4 files changed, 12 insertions(+), 9 deletions(-)
Author: Thomas Lumley
Title: analysis of complex survey samples
Description: Summary statistics, generalised linear models, Cox models,
loglinear models, and general maximum pseudolikelihood
estimation for multistage stratified, cluster-sampled,
unequally weighted survey samples. Variances by Taylor series
linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase designs. Graphics.
Diff between survey versions 3.12 dated 2009-03-22 and 3.13 dated 2009-03-27
DESCRIPTION | 6 +-- NAMESPACE | 1 R/multistage.R | 1 R/survey.R | 23 ++++++++--- R/surveyrep.R | 2 + R/svykm.R | 92 +++++++++++++++++++++++++++++++++++++++-------- R/svyttest.R | 1 inst/CITATION | 4 +- inst/NEWS | 11 +++++ inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/phase1.pdf |binary inst/doc/survey.pdf |binary man/bootweights.Rd | 2 - man/svyby.Rd | 2 - man/svykm.Rd | 28 ++++++++++---- man/svymle.Rd | 2 - man/svyratio.Rd | 9 ++++ tests/domain.R | 2 - tests/domain.Rout.save | 22 +++++++---- tests/quantile.Rout.save | 4 +- 21 files changed, 165 insertions(+), 47 deletions(-)
Author: Sandy Eckel, Roger D. Peng
Title: A Set of Tools for Administering SHared Repositories
Description: A Set of Tools for Administering SHared Repositories
Diff between stashR versions 0.3-2 dated 2008-05-02 and 0.3-3 dated 2009-03-27
DESCRIPTION | 29 +++++++++++++++-------------- tests/tests.Rout.save | 20 +++++++++++--------- 2 files changed, 26 insertions(+), 23 deletions(-)
Author: William Revelle
Diff between psych versions 1.0-65 dated 2009-02-08 and 1.0-67 dated 2009-03-27
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and
experimental psychology. Functions are primarily for scale
construction using factor analysis, cluster analysis and
reliability analysis, although others provide basic descriptive
statistics. Functions for simulating particular item and test
structures are included. Several functions serve as a useful
front end for structural equation modeling. For more
information, see the personality-project.org/r webpage.
psych-1.0-65/psych/inst/doc/index.html |only
psych-1.0-65/psych/inst/psych.Rnw |only
psych-1.0-67/psych/CHANGES | 21
psych-1.0-67/psych/DESCRIPTION | 26
psych-1.0-67/psych/NAMESPACE | 3
psych-1.0-67/psych/R/ICLUST.R | 22
psych-1.0-67/psych/R/ICLUST.sort.R | 2
psych-1.0-67/psych/R/VSS.R | 3
psych-1.0-67/psych/R/alpha.R | 19
psych-1.0-67/psych/R/alpha.scale.R | 60
psych-1.0-67/psych/R/cluster.cor.R | 7
psych-1.0-67/psych/R/cluster.loadings.R | 39
psych-1.0-67/psych/R/corr.test.R |only
psych-1.0-67/psych/R/cortest.R | 5
psych-1.0-67/psych/R/cortest.mat.R | 4
psych-1.0-67/psych/R/cortest.normal.R | 4
psych-1.0-67/psych/R/count.pairwise.R | 31
psych-1.0-67/psych/R/describe.R | 31
psych-1.0-67/psych/R/describe.by.R | 41
psych-1.0-67/psych/R/error.bars.R | 21
psych-1.0-67/psych/R/error.bars.by.R | 52
psych-1.0-67/psych/R/error.crosses.R | 15
psych-1.0-67/psych/R/factor.congruence.R | 21
psych-1.0-67/psych/R/factor.rotate.R | 4
psych-1.0-67/psych/R/guttman.R | 41
psych-1.0-67/psych/R/mat.regress.R | 34
psych-1.0-67/psych/R/plot.psych.R | 4
psych-1.0-67/psych/R/print.psych.R | 184
psych-1.0-67/psych/R/r.test.R | 12
psych-1.0-67/psych/R/read.clipboard.lower.R | 4
psych-1.0-67/psych/R/score.items.R | 67
psych-1.0-67/psych/R/sim.congeneric.R | 5
psych-1.0-67/psych/R/sim.structural.R | 34
psych-1.0-67/psych/R/smc.R | 11
psych-1.0-67/psych/R/structure.graph.R | 5
psych-1.0-67/psych/R/structure.sem.R | 4
psych-1.0-67/psych/R/summary.psych.R | 43
psych-1.0-67/psych/data/bifactor.rda |binary
psych-1.0-67/psych/inst/NEWS | 17
psych-1.0-67/psych/inst/doc/all.bib |only
psych-1.0-67/psych/inst/doc/overview.Rnw |only
psych-1.0-67/psych/inst/doc/overview.pdf |only
psych-1.0-67/psych/inst/doc/psych_for_sem.Rnw |only
psych-1.0-67/psych/inst/doc/psych_for_sem.pdf |16827 +++---
psych-1.0-67/psych/inst/doc/psych_manual.pdf |65025 ++++++++++++++------------
psych-1.0-67/psych/man/00.psych-package.Rd | 13
psych-1.0-67/psych/man/ICLUST.Rd | 2
psych-1.0-67/psych/man/ICLUST.rgraph.Rd | 2
psych-1.0-67/psych/man/VSS.Rd | 6
psych-1.0-67/psych/man/alpha.Rd | 7
psych-1.0-67/psych/man/bifactor.Rd | 37
psych-1.0-67/psych/man/cluster.loadings.Rd | 9
psych-1.0-67/psych/man/corr.test.Rd |only
psych-1.0-67/psych/man/describe.Rd | 11
psych-1.0-67/psych/man/describe.by.Rd | 6
psych-1.0-67/psych/man/error.bars.Rd | 13
psych-1.0-67/psych/man/error.bars.by.Rd | 20
psych-1.0-67/psych/man/factor.congruence.Rd | 10
psych-1.0-67/psych/man/omega.Rd | 2
psych-1.0-67/psych/man/print.psych.Rd | 4
psych-1.0-67/psych/man/r.test.Rd | 23
psych-1.0-67/psych/man/read.clipboard.Rd | 11
psych-1.0-67/psych/man/score.items.Rd | 9
psych-1.0-67/psych/man/sim.Rd | 26
psych-1.0-67/psych/man/sim.structural.Rd | 2
psych-1.0-67/psych/man/smc.Rd | 7
psych-1.0-67/psych/man/structure.graph.Rd | 2
67 files changed, 45036 insertions(+), 37934 deletions(-)
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston and Andre
Williams
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification
and regression models
Diff between caret versions 4.08 dated 2009-02-19 and 4.10 dated 2009-03-27
DESCRIPTION | 23 + R/createGrid.R | 75 +++-- R/createModel.R | 63 ++++ R/misc.R | 82 +++++ R/predictionFunction.R | 91 +++++- R/probFunction.R | 2 R/selection.R | 10 inst/CHANGES | 19 + inst/doc/caretMisc.pdf | 701 +++++++++++++++++++++++------------------------ inst/doc/caretTrain.Rnw | 26 + inst/doc/caretTrain.pdf |binary inst/doc/caretVarImp.pdf |binary man/confusionMatrix.Rd | 2 man/train.Rd | 6 14 files changed, 695 insertions(+), 405 deletions(-)
Author: Markus Gesmann
Title: Mack-, Bootstrap and Munich-chain-ladder methods for insurance
claims reserving
Description: The package contains the Mack-, Munich-, and Bootstrap
chain-ladder methods which are used in insurance claims
reserving.
Diff between ChainLadder versions 0.1.2-9 dated 2009-02-01 and 0.1.2-10 dated 2009-03-27
DESCRIPTION | 31 +++-- NEWS | 13 ++ R/MackChainLadderFunctions.R | 246 +++++++++++++++++++++++------------------- R/zzz.R | 5 THANKS | 3 data/M3IR5.Rdata |only inst/Experimental/M3IR5.Rd |only inst/Experimental/M3IR5.Rdata |only inst/Experimental/chris.RData |only inst/Experimental/chris.Rd |only man/BootChainLadder.Rd | 4 man/MackChainLadder.Rd | 66 +++++++---- 12 files changed, 216 insertions(+), 152 deletions(-)