Title: ZeBook Working with dynamic models for agriculture and
environment
Diff between ZeBook versions 0.4 dated 2013-04-09 and 0.5 dated 2013-06-17
Description: R package accompanying the book Working with dynamic
models for agriculture and environment, by Daniel Wallach
(INRA), David Makowski (INRA), James W. Jones (U.of Florida),
Francois Brun (ACTA), in preparation for June 2013.
Author: Francois Brun (ACTA), David Makowski (INRA), Daniel Wallach
(INRA), James W. Jones (U.of Florida).
Maintainer: Francois Brun
ZeBook-0.4/ZeBook/R/grain.filling_data.r |only
ZeBook-0.4/ZeBook/data/grain.filling.rda |only
ZeBook-0.4/ZeBook/man/epirice.multi.simul.Rd |only
ZeBook-0.4/ZeBook/man/grain.filling.Rd |only
ZeBook-0.5/ZeBook/DESCRIPTION | 21 +
ZeBook-0.5/ZeBook/MD5 | 198 ++++++++++------
ZeBook-0.5/ZeBook/NAMESPACE | 26 ++
ZeBook-0.5/ZeBook/R/AIC.r | 4
ZeBook-0.5/ZeBook/R/Sunflower_Phomopsis_data.r | 2
ZeBook-0.5/ZeBook/R/WheatYieldGreece_data.r | 2
ZeBook-0.5/ZeBook/R/Wheat_GPC_data.r | 2
ZeBook-0.5/ZeBook/R/ZeBook.r | 21 +
ZeBook-0.5/ZeBook/R/carbon.model.r |only
ZeBook-0.5/ZeBook/R/carcass.EMI.model.r |only
ZeBook-0.5/ZeBook/R/carcass.model.r |only
ZeBook-0.5/ZeBook/R/carcass_data.r |only
ZeBook-0.5/ZeBook/R/chicks_data.r |only
ZeBook-0.5/ZeBook/R/cotton.model.r |only
ZeBook-0.5/ZeBook/R/epirice.model.r | 31 --
ZeBook-0.5/ZeBook/R/evaluation.criteria.r | 4
ZeBook-0.5/ZeBook/R/exponential.model.r |only
ZeBook-0.5/ZeBook/R/goodness.of.fit.r | 4
ZeBook-0.5/ZeBook/R/lactation.calf.model.r |only
ZeBook-0.5/ZeBook/R/lactation.machine.model.r |only
ZeBook-0.5/ZeBook/R/magarey.model.r | 43 ++-
ZeBook-0.5/ZeBook/R/maize.data_EuropeEU.r | 2
ZeBook-0.5/ZeBook/R/maize.model.r | 37 +-
ZeBook-0.5/ZeBook/R/population.age.model.r |only
ZeBook-0.5/ZeBook/R/prey.predator.model.r |only
ZeBook-0.5/ZeBook/R/sample.r | 8
ZeBook-0.5/ZeBook/R/seedweight.data_data.r |only
ZeBook-0.5/ZeBook/R/seedweight.model.r |only
ZeBook-0.5/ZeBook/R/verhulst.model.r | 10
ZeBook-0.5/ZeBook/R/watbal.model.r | 84 ++++++
ZeBook-0.5/ZeBook/R/watbal.simobsdata.r | 4
ZeBook-0.5/ZeBook/R/weather_EuropeEU_data.r | 12
ZeBook-0.5/ZeBook/R/weather_FranceWest_data.r | 4
ZeBook-0.5/ZeBook/R/weather_SouthAsia_data.r | 4
ZeBook-0.5/ZeBook/R/weed.model.r | 33 +-
ZeBook-0.5/ZeBook/data/carcass_data.rda |only
ZeBook-0.5/ZeBook/data/chicks_data.rda |only
ZeBook-0.5/ZeBook/data/datalist | 4
ZeBook-0.5/ZeBook/data/seedweight.data.rda |only
ZeBook-0.5/ZeBook/demo/00Index | 49 ++-
ZeBook-0.5/ZeBook/demo/ch04Simulation.epirice.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.exponential.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.maize.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.population.age.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.prey.predator.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.watbal.r |only
ZeBook-0.5/ZeBook/demo/ch05USA_Carcass.r |only
ZeBook-0.5/ZeBook/demo/ch05USA_Lactation.r |only
ZeBook-0.5/ZeBook/demo/ch08DLM_CarbonSoil.r | 7
ZeBook-0.5/ZeBook/demo/ch08DLM_WheatYieldGreece.r | 6
ZeBook-0.5/ZeBook/demo/ch08DLM_watbal.r |only
ZeBook-0.5/ZeBook/demo/ch10maize1data.r | 4
ZeBook-0.5/ZeBook/demo/ch10maize2evaluation.r | 3
ZeBook-0.5/ZeBook/demo/ch10maize5cparameterConcL.r | 52 +++-
ZeBook-0.5/ZeBook/demo/ch10maize5dparameterConcL_log.r |only
ZeBook-0.5/ZeBook/demo/ch10maizeB5aBayesEstimRUE.r | 2
ZeBook-0.5/ZeBook/demo/ch10maizeB5bBayesEstimAllparam.r | 2
ZeBook-0.5/ZeBook/demo/ch10maizeB7Bayes_functionsMH.r | 5
ZeBook-0.5/ZeBook/man/AICf.Rd | 2
ZeBook-0.5/ZeBook/man/ZeBook-package.Rd | 38 +--
ZeBook-0.5/ZeBook/man/carbonsoil.model.Rd |only
ZeBook-0.5/ZeBook/man/carbonsoil.update.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.model.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.model2.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.multi.Rd |only
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ZeBook-0.5/ZeBook/man/carcass.define.param.Rd |only
ZeBook-0.5/ZeBook/man/carcass.model.Rd |only
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ZeBook-0.5/ZeBook/man/chicks_data.Rd |only
ZeBook-0.5/ZeBook/man/cotton.model.Rd |only
ZeBook-0.5/ZeBook/man/epirice.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/epirice.model.Rd | 4
ZeBook-0.5/ZeBook/man/epirice.multi.simule.Rd |only
ZeBook-0.5/ZeBook/man/epirice.weather.Rd | 5
ZeBook-0.5/ZeBook/man/evaluation.criteria.Rd | 2
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ZeBook-0.5/ZeBook/man/exponential.model.bis.Rd |only
ZeBook-0.5/ZeBook/man/exponential.model.ie.Rd |only
ZeBook-0.5/ZeBook/man/goodness.of.fit.Rd | 5
ZeBook-0.5/ZeBook/man/lactation.calf.model.Rd |only
ZeBook-0.5/ZeBook/man/lactation.calf.model2.Rd |only
ZeBook-0.5/ZeBook/man/lactation.calf.simule.Rd |only
ZeBook-0.5/ZeBook/man/lactation.define.param.Rd |only
ZeBook-0.5/ZeBook/man/lactation.model.machine.Rd |only
ZeBook-0.5/ZeBook/man/lactation.model.machine2.Rd |only
ZeBook-0.5/ZeBook/man/magarey.define.param.Rd | 15 -
ZeBook-0.5/ZeBook/man/magarey.model2.Rd | 2
ZeBook-0.5/ZeBook/man/magarey.simule.Rd | 2
ZeBook-0.5/ZeBook/man/maize.RUEtemp.Rd | 4
ZeBook-0.5/ZeBook/man/maize.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/maize.model.Rd | 11
ZeBook-0.5/ZeBook/man/maize.model2.Rd | 5
ZeBook-0.5/ZeBook/man/maize.multisy240.Rd | 6
ZeBook-0.5/ZeBook/man/maize.simule.Rd | 6
ZeBook-0.5/ZeBook/man/maize.simule240.Rd | 10
ZeBook-0.5/ZeBook/man/maize.simule_multisy240.Rd | 11
ZeBook-0.5/ZeBook/man/maize.weather.Rd | 5
ZeBook-0.5/ZeBook/man/maize_cir.model.Rd | 5
ZeBook-0.5/ZeBook/man/maize_cir_rue.model.Rd | 4
ZeBook-0.5/ZeBook/man/maize_cir_rue_ear.model.Rd | 5
ZeBook-0.5/ZeBook/man/param.rtriangle.Rd | 2
ZeBook-0.5/ZeBook/man/param.runif.Rd | 2
ZeBook-0.5/ZeBook/man/population.age.matrix.model.Rd |only
ZeBook-0.5/ZeBook/man/population.age.model.Rd |only
ZeBook-0.5/ZeBook/man/population.age.model.ode.Rd |only
ZeBook-0.5/ZeBook/man/predator.prey.model.Rd |only
ZeBook-0.5/ZeBook/man/q.arg.fast.runif.Rd | 2
ZeBook-0.5/ZeBook/man/seedweight.data.Rd |only
ZeBook-0.5/ZeBook/man/seedweight.model.Rd |only
ZeBook-0.5/ZeBook/man/verhulst.model.Rd | 9
ZeBook-0.5/ZeBook/man/verhulst.update.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.define.param.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.model.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.model.arid.Rd |only
ZeBook-0.5/ZeBook/man/watbal.simobsdata.Rd | 2
ZeBook-0.5/ZeBook/man/watbal.update.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.weather.Rd | 6
ZeBook-0.5/ZeBook/man/weather_EuropeEU.Rd | 12
ZeBook-0.5/ZeBook/man/weather_FranceWest.Rd | 2
ZeBook-0.5/ZeBook/man/weather_SouthAsia.Rd | 2
ZeBook-0.5/ZeBook/man/weed.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/weed.model.Rd | 2
ZeBook-0.5/ZeBook/man/weed.simule.Rd | 6
ZeBook-0.5/ZeBook/man/weed.update.Rd | 2
129 files changed, 595 insertions(+), 323 deletions(-)
Title: Robust Library
Diff between robust versions 0.4-11 dated 2013-02-24 and 0.4-15 dated 2013-06-17
Description: A package of robust methods.
Author: Jiahui Wang, Ruben Zamar
Maintainer: Kjell Konis
robust-0.4-11/robust/R/covMLE.q |only
robust-0.4-11/robust/R/plot.covMLE.q |only
robust-0.4-11/robust/R/summary.covMLE.q |only
robust-0.4-11/robust/man/covMLE.Rd |only
robust-0.4-15/robust/DESCRIPTION | 18 -
robust-0.4-15/robust/MD5 | 63 ++---
robust-0.4-15/robust/NAMESPACE | 39 +--
robust-0.4-15/robust/R/covClassic.q |only
robust-0.4-15/robust/R/covRob.control.q | 85 ++-----
robust-0.4-15/robust/R/gen.data.q | 2
robust-0.4-15/robust/R/glm.methods.q | 4
robust-0.4-15/robust/R/globalVariables.q |only
robust-0.4-15/robust/R/library.q | 2
robust-0.4-15/robust/R/plot.covClassic.q |only
robust-0.4-15/robust/R/print.covMLE.q | 2
robust-0.4-15/robust/R/print.summary.covMLE.q | 5
robust-0.4-15/robust/R/robLev.q | 35 +-
robust-0.4-15/robust/R/summary.covClassic.q |only
robust-0.4-15/robust/README | 2
robust-0.4-15/robust/inst/tests_S/plots.covrob.t | 4
robust-0.4-15/robust/man/covClassic.Rd |only
robust-0.4-15/robust/man/covRob.Rd | 2
robust-0.4-15/robust/man/ddPlot.covfm.Rd | 2
robust-0.4-15/robust/man/distancePlot.covfm.Rd | 2
robust-0.4-15/robust/man/ellipsesPlot.covfm.Rd | 2
robust-0.4-15/robust/man/lmRob.control.Rd | 48 ++--
robust-0.4-15/robust/man/plot.covfm.Rd | 18 -
robust-0.4-15/robust/man/predict.glmRob.Rd | 6
robust-0.4-15/robust/man/screePlot.covfm.Rd | 2
robust-0.4-15/robust/man/summary.covfm.Rd | 16 -
robust-0.4-15/robust/src/glmrob.f | 188 ++++++++--------
robust-0.4-15/robust/src/lmrobfs.f | 4
robust-0.4-15/robust/src/lmrobml.f | 2
robust-0.4-15/robust/src/lmrobmm.f | 6
robust-0.4-15/robust/src/tdmean.f | 179 +++++++--------
robust-0.4-15/robust/src/tmlfor.f | 108 ++++-----
robust-0.4-15/robust/tests/Examples/robust-Ex.Rout.save | 59 ++---
37 files changed, 446 insertions(+), 459 deletions(-)
Title: Moment and Inverse Moment Bayes factors
Diff between mombf versions 1.4.1 dated 2013-04-05 and 1.5.2 dated 2013-06-17
Description: This package performs model selection based on non-local
priors, including MOM, eMOM and iMOM priors. Routines are
provided to compute Bayes factors, marginal densities and to
perform variable selection in regression setups. Routines to
evaluate prior densities, distribution functions, quantiles and
modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell
DESCRIPTION | 18 ++--
INDEX |only
MD5 | 54 ++++++++------
NAMESPACE | 11 ++
R/AllClasses.R | 3
R/AllGenerics.R | 9 ++
R/margpemom.R |only
R/margpimom.R | 8 +-
R/margpmom.R | 2
R/modelSelection.R | 33 ++++++++
R/msPriorSpec.R | 31 ++++++++
R/pplProbit.R | 15 ----
R/rmom.R | 41 +++++++++--
changeLog | 6 +
data/hald.rda |binary
inst/doc/mombf.R |only
inst/doc/mombf.Rnw | 8 +-
inst/doc/mombf.pdf |binary
man/dmom.Rd | 3
man/modelSelection.Rd | 22 +++--
man/msPriorSpec-class.Rd | 45 +++++++++++-
man/msfit-class.Rd |only
man/pmomLM.Rd | 30 ++++----
man/postProb.Rd |only
man/rnlp.Rd |only
src/cstat.cpp | 174 +++++++++++++++++++++++++++++++++++++++++------
src/cstat.h | 36 +++++++--
src/do_mombf.h | 2
src/modelSel.cpp | 115 ++++++++++++++++---------------
src/modelSel.h | 1
vignettes/mombf.Rnw | 8 +-
31 files changed, 501 insertions(+), 174 deletions(-)
Title: Regional frequency analysis using L-moments
Diff between lmomRFA versions 2.4 dated 2012-01-24 and 2.5 dated 2013-06-17
Description: Functions for regional frequency analysis using the
methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional
frequency analysis: an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
lmomRFA-2.4/lmomRFA/LICENSE |only
lmomRFA-2.5/lmomRFA/DESCRIPTION | 13 +--
lmomRFA-2.5/lmomRFA/MD5 | 51 ++++++-------
lmomRFA-2.5/lmomRFA/NAMESPACE | 1
lmomRFA-2.5/lmomRFA/NEWS | 25 ++++++
lmomRFA-2.5/lmomRFA/R/lmomRFA.r | 111 +++++++++++++++++++++++++++--
lmomRFA-2.5/lmomRFA/data/Appalach.rda |binary
lmomRFA-2.5/lmomRFA/data/Cascades.rda |binary
lmomRFA-2.5/lmomRFA/data/Maxwind.rda |binary
lmomRFA-2.5/lmomRFA/man/cluagg.Rd | 2
lmomRFA-2.5/lmomRFA/man/cluinf.Rd | 2
lmomRFA-2.5/lmomRFA/man/clukm.Rd | 2
lmomRFA-2.5/lmomRFA/man/evplot.rfd.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/lmomRFA-package.Rd | 2
lmomRFA-2.5/lmomRFA/man/regavlmom.Rd | 2
lmomRFA-2.5/lmomRFA/man/regdata.Rd | 2
lmomRFA-2.5/lmomRFA/man/regfit.Rd | 2
lmomRFA-2.5/lmomRFA/man/reglmr.Rd | 2
lmomRFA-2.5/lmomRFA/man/regquant.Rd | 2
lmomRFA-2.5/lmomRFA/man/regquantbounds.Rd | 8 --
lmomRFA-2.5/lmomRFA/man/regsamlmu.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/regsimh.Rd | 6 -
lmomRFA-2.5/lmomRFA/man/regsimq.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/regtst.Rd | 15 ++-
lmomRFA-2.5/lmomRFA/man/sitequant.Rd | 2
lmomRFA-2.5/lmomRFA/man/summary.regtst.Rd | 5 -
lmomRFA-2.5/lmomRFA/src/lmomRFA.f | 98 ++++++++-----------------
27 files changed, 232 insertions(+), 133 deletions(-)
Title: L-moments
Diff between lmom versions 1.6 dated 2012-01-24 and 2.0 dated 2013-06-17
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples;
parameter estimation; L-moment ratio diagram; plot vs.
quantiles of an extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
lmom-1.6/lmom/LICENSE |only
lmom-1.6/lmom/src/lmom.f |only
lmom-2.0/lmom/DESCRIPTION | 17
lmom-2.0/lmom/MD5 | 40 -
lmom-2.0/lmom/NAMESPACE | 2
lmom-2.0/lmom/NEWS | 24
lmom-2.0/lmom/R/lmom.r | 1225 ++++++++++++++++++++++++-------------
lmom-2.0/lmom/man/cdfln3.Rd | 6
lmom-2.0/lmom/man/evplot.Rd | 2
lmom-2.0/lmom/man/lmom-package.Rd | 73 +-
lmom-2.0/lmom/man/lmr-functions.Rd | 58 -
lmom-2.0/lmom/man/lmrd.Rd | 50 -
lmom-2.0/lmom/man/lmrdpoints.Rd | 2
lmom-2.0/lmom/man/lmrp.Rd | 154 ++--
lmom-2.0/lmom/man/pel-functions.Rd | 58 -
lmom-2.0/lmom/man/pelp.Rd | 128 ++-
lmom-2.0/lmom/man/samlmu.Rd | 80 +-
lmom-2.0/lmom/src/d1mach.f |only
lmom-2.0/lmom/src/dqagie.f |only
lmom-2.0/lmom/src/dqagse.f |only
lmom-2.0/lmom/src/dqelg.f |only
lmom-2.0/lmom/src/dqk15i.f |only
lmom-2.0/lmom/src/dqk21.f |only
lmom-2.0/lmom/src/dqpsrt.f |only
lmom-2.0/lmom/src/lmomc.c |only
lmom-2.0/lmom/src/lmoments.f |only
lmom-2.0/lmom/src/samlm.f |only
27 files changed, 1234 insertions(+), 685 deletions(-)
Title: Tests for random and fixed effects for linear mixed effect
models (lmer objects of lme4 package).
Diff between lmerTest versions 1.2-0 dated 2013-03-20 and 1.2-1 dated 2013-06-17
Description: The package provides different kinds of tests on lmer
objects(of lme4 package). Tests comprise type 3 F tests for
fixed effects, LRT tests for random effects, calculation of
population means for fixed factors with confidence intervals
and corresponding plots. Package also provides backward
elimination of non-significant effects
Author: Alexandra Kuznetsova, Per Bruun Brockhoff, Rune Haubo Bojesen
Christensen
Maintainer: Alexandra Kuznetsova
DESCRIPTION | 8 +-
MD5 | 12 +--
R/utils.R | 10 +-
man/lmer.Rd | 3
man/merLmerTest-class.Rd | 1
man/step.Rd | 3
tests/Examples/lmerTest-Ex.Rout.save | 125 +++++++++++++++++++++++------------
7 files changed, 106 insertions(+), 56 deletions(-)
Title: Two functions for Generalized SARIMA time series simulation
Diff between gsarima versions 0.1-3 dated 2013-01-17 and 0.1-4 dated 2013-06-17
Description: Write SARIMA models in (finite) AR representation and
simulate generalized multiplicative seasonal autoregressive
moving average (time) series with Normal / Gaussian, Poisson or
negative binomial distribution.
Author: Olivier Briet
Maintainer: Olivier Briet
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
man/arrep.Rd | 8 +++++---
man/garsim.Rd | 29 ++++++++++++++++++++---------
man/gsarima-package.Rd | 8 ++++++--
5 files changed, 40 insertions(+), 22 deletions(-)
Title: Baseline identification and peak decomposition for x-ray
diffractograms
Diff between diffractometry versions 0.1-03 dated 2011-03-11 and 0.1-7 dated 2013-06-17
More information about diffractometry at CRAN
Description: Residual-based baseline identification and peak
decomposition for x-ray diffractograms as introduced in
Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger.
Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger
DESCRIPTION | 9
MD5 |only
R/baselinefit.r | 12 -
R/fitint.r | 601 +++++++++++++++++++++++++--------------------------
man/diffractogram.Rd | 4
man/pkdecomp.Rd | 4
man/pkdecompint.Rd | 2
src/Cbaselinefit.c | 25 +-
src/Fbaselinefit.f | 37 ++-
9 files changed, 358 insertions(+), 336 deletions(-)
Permanent link
Title: Bolstad functions
Diff between Bolstad versions 0.2-24 dated 2013-04-30 and 0.2-25 dated 2013-06-17
Description: A set of R functions and data sets for the book
Introduction to Bayesian Statistics, Bolstad, W.M. (2007), John
Wiley & Sons ISBN 0-471-27020-2
Author: James Curran
Maintainer: James Curran
DESCRIPTION | 8 +++---
MD5 | 40 +++++++++++++++++----------------
NAMESPACE | 1
R/binobp.r | 8 ++++--
R/binodp.r | 50 +++++++++++++++++++++++++----------------
R/binogcp.r | 8 ++++--
R/binomixp.r | 6 ++++-
R/normdp.r | 7 ++++-
R/normgcp.r | 8 +++++-
R/normnp.r | 9 +++++--
R/nvaricp.r | 8 +++++-
R/plot.Bolstad.r |only
R/poisdp.r | 6 ++++-
R/poisgamp.r | 62 ++++++++++++++++++++++++++++++----------------------
R/poisgcp.r | 26 +++++++++++++--------
R/xdesign.r | 37 ++++++++++++-------------------
man/binobp.Rd | 10 ++++----
man/binodp.Rd | 3 +-
man/plot.Bolstad.Rd |only
man/poisgamp.Rd | 7 +++--
man/poisgcp.Rd | 3 +-
man/xdesign.Rd | 13 +++++++---
22 files changed, 188 insertions(+), 132 deletions(-)
Title: Interactive manipulation of R expressions
Diff between twiddler versions 0.4-0 dated 2012-09-13 and 0.5-0 dated 2013-06-17
Description: Twiddler is an interactive tool that automatically creates
a Tcl/Tk GUI for manipulating variables in any R expression.
See the documentation of the function twiddle to get started.
Author: Oliver Flasch, Olaf Mersmann
Maintainer: Oliver Flasch
twiddler-0.4-0/twiddler/man/print-dot-twiddlerControl.Rd |only
twiddler-0.4-0/twiddler/man/twiddle-sub-print.Rd |only
twiddler-0.5-0/twiddler/DESCRIPTION | 17 +-
twiddler-0.5-0/twiddler/MD5 | 26 +--
twiddler-0.5-0/twiddler/NAMESPACE | 10 -
twiddler-0.5-0/twiddler/R/twiddler.R | 7
twiddler-0.5-0/twiddler/man/combo.Rd | 32 ++-
twiddler-0.5-0/twiddler/man/entry.Rd | 47 +++--
twiddler-0.5-0/twiddler/man/filer.Rd | 34 ++--
twiddler-0.5-0/twiddler/man/knob.Rd | 58 ++++--
twiddler-0.5-0/twiddler/man/print.twiddlerControl.Rd |only
twiddler-0.5-0/twiddler/man/shortenString.Rd | 23 +-
twiddler-0.5-0/twiddler/man/toggle.Rd | 29 ++-
twiddler-0.5-0/twiddler/man/twiddle_print.Rd |only
twiddler-0.5-0/twiddler/man/twiddler.Rd | 125 +++++++++------
twiddler-0.5-0/twiddler/man/unboundVariables.Rd | 23 +-
16 files changed, 275 insertions(+), 156 deletions(-)
Title: R functions for robust statistics
Diff between robeth versions 2.2 dated 2011-08-20 and 2.6 dated 2013-06-17
Description: Locations problems, M-estimates of coefficients and scale
in linear regression, Weights for bounded influence regression,
Covariance matrix of the coefficient estimates, Asymptotic
relative efficiency of regression M-estimates, Robust testing
in linear models, High breakdown point regression, M-estimates
of covariance matrices, M-estimates for discrete generalized
linear models.
Author: Alfio Marazzi
Maintainer: A. Randriamiharisoa
DESCRIPTION | 9 -
MD5 | 212 ++++++++++++++++++-------------------
NAMESPACE | 12 +-
R/Fn.Exp.f.R | 4
R/QD2coef.f.R | 6 -
R/QD2funC.f.R | 6 -
R/Qn.Exp.f.R | 6 -
R/Random.R | 8 -
R/Regtau.f.R | 4
R/RegtauW.f.R | 4
R/airefq.R | 10 -
R/cerfd.R | 4
R/cfrcov.R | 2
R/cimedv.R | 2
R/cyfalg.R | 10 -
R/cygalg.R | 20 +--
R/cynalg.R | 14 +-
R/dfcomn.R | 18 +--
R/dfrpar.R | 20 +--
R/dfvals.R | 90 +++++++--------
R/dotpd.R | 6 -
R/exchd.R | 2
R/gaussd.R | 4
R/gintac.R | 4
R/gyastp.R | 11 +
R/gymain.R | 11 +
R/h12d.R | 6 -
R/machd.R | 2
R/mchld.R | 2
R/mffd.R | 6 -
R/mfyd.R | 6 -
R/minvd.R | 2
R/mlyd.R | 4
R/msf1d.R | 6 -
R/msfd.R | 6 -
R/mssd.R | 6 -
R/mtt1d.R | 4
R/mtt2d.R | 4
R/mtt3d.R | 6 -
R/mtyd.R | 4
R/nrm2d.R | 4
R/precd.R | 2
R/probin.R |only
R/rimtrd.R | 8 -
R/rybifr.R | 2
R/scald.R | 2
R/swapd.R | 4
R/to.double.R | 1
R/ucv_1.R | 2
R/upcv_1.R | 2
R/wcv_1.R | 2
R/wimedv.R | 2
R/wpcv_1.R | 2
R/www_1.R | 2
R/wyfalg.R | 12 +-
R/wyfcol.R | 20 +--
R/wygalg.R | 18 +--
R/wynalg.R | 14 +-
R/xsyd.R | 8 -
R/zemll.R |only
man/QD2coef.f.Rd | 3
man/Regtau.f.Rd | 3
man/RegtauW.f.Rd | 3
man/airef0.Rd | 4
man/airefq.Rd | 5
man/cifact.Rd | 7 -
man/cyfalg.Rd | 4
man/cygalg.Rd | 5
man/cynalg.Rd | 5
man/dfcomn.Rd | 19 ++-
man/gintac.Rd | 4
man/gyastp.Rd | 5
man/gycstp.Rd | 3
man/gymain.Rd | 9 +
man/gytstp.Rd | 5
man/hylmse.Rd | 4
man/hyltse.Rd | 4
man/hysest.Rd | 6 -
man/hysestw.Rd | 6 -
man/kiedcu.Rd | 3
man/ktaskw.Rd | 3
man/lyhalg.Rd | 4
man/lyhdle.Rd | 3
man/lymnwt.Rd | 3
man/lytau2.Rd | 4
man/lywalg.Rd | 13 +-
man/messagena.Rd |only
man/mfragr.Rd | 4
man/mirtsr.Rd | 5
man/mymvlm.Rd | 5
man/ribet0.Rd | 3
man/ribetu.Rd | 3
man/riclls.Rd | 3
man/robeth.package.Rd | 38 +++---
man/rybifr.Rd | 4
man/ryhalg.Rd | 7 +
man/rynalg.Rd | 6 -
man/rysalg.Rd | 6 -
man/rysigm.Rd | 4
man/rywalg.Rd | 6 -
man/tauare.Rd | 4
man/wimedv.Rd | 3
man/wyfalg.Rd | 5
man/wyfcol.Rd | 5
man/wygalg.Rd | 5
man/wynalg.Rd | 5
man/zemll.Rd |only
src/fastcens.f | 78 +++++++++++++
src/robeth.f | 285 ++++++++++++++++++++++++++++++++++++--------------
109 files changed, 809 insertions(+), 482 deletions(-)
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-8 dated 2013-05-28 and 1.0-9 dated 2013-06-17
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/lmmpower.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Multivariate Permutation Tests
Diff between flip versions 2.1 dated 2013-05-07 and 2.2 dated 2013-06-17
Description: It implements many univariate and multivariate permutation
(and rotation) tests. Allowed tests: the t one and two samples,
ANOVA, linear models, Chi Squared test, rank tests (i.e.
Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar.
Test on Linear Models are performed also in presence of
covariates (i.e. nuisance parameters). The permutation and the
rotation methods to get the null distribution of the test
statistics are available. It also implements methods for
multiplicity control such as Westfall-Young minP procedure and
Closed Testing (Marcus, 1976). Moreover, it allows to test for
fixed effects in mixed effects models.
Author: Livio Finos, with contributions by Dario Basso, Aldo Solari and
Jelle Goeman
Maintainer: Livio Finos
flip-2.1/flip/R/rotation.R |only
flip-2.2/flip/DESCRIPTION | 18 +++---
flip-2.2/flip/MD5 | 34 ++++++-----
flip-2.2/flip/NAMESPACE | 6 +-
flip-2.2/flip/R/Padjust.R | 13 +++-
flip-2.2/flip/R/between.R |only
flip-2.2/flip/R/dependence.R | 52 +++++++----------
flip-2.2/flip/R/estimateSu.R |only
flip-2.2/flip/R/flip-object.R | 97 ++++++++++++++++-----------------
flip-2.2/flip/R/flip.R | 8 +-
flip-2.2/flip/R/flipMix.R |only
flip-2.2/flip/R/obs2coeffWithin.R |only
flip-2.2/flip/R/permSpace.R | 4 -
flip-2.2/flip/R/symmetry.R | 39 ++++++++++++-
flip-2.2/flip/R/utilities.R | 90 +++++++++++++++++-------------
flip-2.2/flip/changelog.txt | 7 ++
flip-2.2/flip/man/flip.Rd | 39 +++++++++----
flip-2.2/flip/man/flip.object-class.Rd | 40 ++++++++++++-
flip-2.2/flip/man/flipMix.Rd |only
flip-2.2/flip/man/multiplicity.Rd | 11 ++-
flip-2.2/flip/man/permutationSpace.Rd | 1
21 files changed, 286 insertions(+), 173 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 2.3-0 dated 2013-05-12 and 2.4-0 dated 2013-06-17
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer
DESCRIPTION | 8 -
MD5 | 46 +++---
NAMESPACE | 2
NEWS | 42 ++++++
R/catmeth.R | 6
R/forest.meta.R | 330 ++++++++++++++++++++++++++++++++++++-------------
R/metabin.R | 124 +++++++++++++++---
R/metacont.R | 72 +++++++++-
R/metacor.R | 87 ++++++++++++
R/metagen.R | 91 ++++++++++++-
R/metaprop.R | 82 ++++++++++--
R/print.meta.R | 8 -
R/print.summary.meta.R | 83 ++++++++----
R/read.rm5.R | 17 --
R/summary.meta.R | 73 ++++++++++
R/trimfill.default.R | 1
R/trimfill.meta.R | 1
man/forest.meta.Rd | 32 +++-
man/metabin.Rd | 32 ++++
man/metacont.Rd | 26 +++
man/metacor.Rd | 28 +++-
man/metagen.Rd | 38 ++++-
man/metaprop.Rd | 38 ++++-
man/print.meta.Rd | 47 +++++-
24 files changed, 1051 insertions(+), 263 deletions(-)
Title: A Monte Carlo permutation method for multiple test correlation
Diff between MCPerm versions 1.1.3 dated 2013-01-28 and 1.1.4 dated 2013-06-17
Description: A Monte Carlo permutation method for multiple test
correlation.
Author: Lanying Zhang and Yongshuai Jiang
Maintainer: Yongshuai Jiang
MCPerm-1.1.3/MCPerm/R/MCPerm-internal.R |only
MCPerm-1.1.3/MCPerm/R/permuteData.R |only
MCPerm-1.1.3/MCPerm/data/exampleData.rda |only
MCPerm-1.1.3/MCPerm/man/exampleData.Rd |only
MCPerm-1.1.3/MCPerm/man/permuteData.Rd |only
MCPerm-1.1.4/MCPerm/DESCRIPTION | 13 -
MCPerm-1.1.4/MCPerm/MD5 | 95 ++++++++++--
MCPerm-1.1.4/MCPerm/R/HW.test.R |only
MCPerm-1.1.4/MCPerm/R/I2.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/I2.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.Hist.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.CDC.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.Hist.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.boxplot.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.qqnorm.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.boxplot.R |only
MCPerm-1.1.4/MCPerm/R/Q.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/Q.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.QQ.R |only
MCPerm-1.1.4/MCPerm/R/VS.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.QQ.R |only
MCPerm-1.1.4/MCPerm/R/VS.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.KS.R |only
MCPerm-1.1.4/MCPerm/R/VS.QQ.R |only
MCPerm-1.1.4/MCPerm/R/meta.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/meta.R |only
MCPerm-1.1.4/MCPerm/R/meta.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/pearson_scatter.R |only
MCPerm-1.1.4/MCPerm/R/permuteGenotype.R | 49 +-----
MCPerm-1.1.4/MCPerm/R/permuteGenotypeCount.R |only
MCPerm-1.1.4/MCPerm/R/print.PermMeta.R |only
MCPerm-1.1.4/MCPerm/data/MetaGenotypeCount.rda |only
MCPerm-1.1.4/MCPerm/data/MetaGenotypeData.rda |only
MCPerm-1.1.4/MCPerm/data/genotypeData.rda |only
MCPerm-1.1.4/MCPerm/man/Armitage.MCPerm.Rd | 35 ++--
MCPerm-1.1.4/MCPerm/man/Armitage.Rd | 39 ++---
MCPerm-1.1.4/MCPerm/man/Armitage.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/HW.test.Rd |only
MCPerm-1.1.4/MCPerm/man/I2.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/I2.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/MCPerm-package.Rd | 172 +++++++++++++----------
MCPerm-1.1.4/MCPerm/man/MetaGenotypeCount.Rd |only
MCPerm-1.1.4/MCPerm/man/MetaGenotypeData.Rd |only
MCPerm-1.1.4/MCPerm/man/OR.MCPerm.Rd | 39 ++---
MCPerm-1.1.4/MCPerm/man/OR.Rd | 35 ++--
MCPerm-1.1.4/MCPerm/man/OR.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/PermMeta.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.boxplot.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.qqnorm.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.boxplot.Rd |only
MCPerm-1.1.4/MCPerm/man/Q.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/Q.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.KS.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/chisq.MCPerm.Rd | 46 +++---
MCPerm-1.1.4/MCPerm/man/chisq.TradPerm.Rd | 47 +++---
MCPerm-1.1.4/MCPerm/man/fisher.MCPerm.Rd | 50 +++---
MCPerm-1.1.4/MCPerm/man/fisher.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/genotypeData.Rd |only
MCPerm-1.1.4/MCPerm/man/genotypeStat.Rd | 50 +++---
MCPerm-1.1.4/MCPerm/man/meta.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/meta.Rd |only
MCPerm-1.1.4/MCPerm/man/meta.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/pearson_scatter.Rd |only
MCPerm-1.1.4/MCPerm/man/permuteGenotype.Rd | 63 ++------
MCPerm-1.1.4/MCPerm/man/permuteGenotypeCount.Rd |only
MCPerm-1.1.4/MCPerm/man/print.PermMeta.Rd |only
81 files changed, 469 insertions(+), 411 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.4 dated 2013-06-13 and 0.8.5.1 dated 2013-06-17
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 10 ++--
MD5 | 20 ++++-----
NAMESPACE | 2
R/fscaret.R | 36 ++++++++--------
R/funcReg.all.R | 2
R/regVarImp.R | 104 ++++++++++++-------------------------------------
man/fscaret-package.Rd | 5 +-
man/fscaret.Rd | 14 ++++++
man/impCalc.Rd | 7 ++-
man/regVarImp.Rd | 12 ++++-
man/timeout.Rd | 1
11 files changed, 95 insertions(+), 118 deletions(-)
Title: Analysis of music and speech
Diff between tuneR versions 0.4-1 dated 2012-08-28 and 0.4-2 dated 2013-06-17
Description: Collection of tools to analyze music, extract features
like MFCCs, handling wave files, read mp3, transcription, ...
Also contains functions ported from the rastamat Matlab
package.
Author: Uwe Ligges
Maintainer: Uwe Ligges
tuneR-0.4-1/tuneR/R/levinson.R |only
tuneR-0.4-1/tuneR/R/zzz.R |only
tuneR-0.4-1/tuneR/man/levinson.Rd |only
tuneR-0.4-2/tuneR/DESCRIPTION | 13 +++++++------
tuneR-0.4-2/tuneR/MD5 | 13 +++++--------
tuneR-0.4-2/tuneR/NAMESPACE | 2 +-
tuneR-0.4-2/tuneR/R/Wave.R | 1 -
tuneR-0.4-2/tuneR/R/plot-Wave.R | 27 +++++++++++++++++----------
tuneR-0.4-2/tuneR/man/plot-Wave.Rd | 7 +++++--
9 files changed, 35 insertions(+), 28 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Diff between evtree versions 0.1-2 dated 2012-04-11 and 0.1-3 dated 2013-06-17
Description: Commonly used classification and regression tree methods
like the CART algorithm are recursive partitioning methods that
build the model in a forward stepwise search. Although this
approach is known to be an efficient heuristic, the results of
recursive tree methods are only locally optimal, as splits are
chosen to maximize homogeneity at the next step only. An
alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary
algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully
computed in C++ while the partykit package is leveraged to
represent the resulting trees in R, providing unified
infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre], Achim Zeileis [aut], Karl-Peter
Pfeiffer [aut]
Maintainer: Thomas Grubinger
DESCRIPTION | 18 -
MD5 | 51 ++
NEWS | 5
R/evtree.R | 2
data/BBBClub.rda |binary
data/ContraceptiveChoice.RData |binary
data/GermanCredit.RData |binary
data/MAGICGammaTelescope.RData |binary
data/StatlogHeart.RData |binary
inst/doc/evtree.R |only
inst/doc/evtree.Rnw | 650 ++++++++++++++++++++++++++++++-------
inst/doc/evtree.pdf |binary
tests/Examples/evtree-Ex.Rout.save | 11
vignettes/.install_extras | 2
vignettes/evtree.Rnw | 650 ++++++++++++++++++++++++++++++-------
vignettes/evtree.bib | 71 +++-
vignettes/results_j48 |only
vignettes/results_parameter |only
18 files changed, 1192 insertions(+), 268 deletions(-)
Title: Robust Linear Mixed Effects Models
Diff between robustlmm versions 1.0 dated 2013-03-08 and 1.1 dated 2013-06-17
Description: Robust mixed effects modeling by robustification of
scoring equations using the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller
DESCRIPTION | 8
MD5 | 149
NAMESPACE | 162 -
R/AllClass.R | 1574 ++++-----
R/AllGeneric.R | 80
R/DAS-scale.R | 1010 +++---
R/accessors.R | 796 ++--
R/fit.effects.R | 90
R/fromLme4.R | 464 +-
R/helpers.R | 1264 +++----
R/lmer.R | 78
R/multiroot.R | 204 -
R/mutators.R | 226 -
R/psiFunc2.R | 544 +--
R/rlmer.R | 799 ++---
R/zero.theta.R | 120
README.md | 50
ToDo | 34
inst/doc/ggplot.theme.R | 26
inst/doc/plots.R | 353 +-
inst/doc/rlmer.pdf |binary
inst/doc/sleepstudy.R | 66
man/VarCorr.Rd | 102
man/cPsi.Rd | 24
man/compare.Rd | 50
man/fixef.Rd | 64
man/getInfo.Rd | 58
man/getME.Rd | 227 -
man/lmerNoFit.Rd | 46
man/nobs-methods.Rd | 30
man/print.xtable.comparison.table.Rd | 80
man/psi2propII.Rd | 34
man/psiFuncCached.Rd | 70
man/psi_func_cached-class.Rd | 150
man/residuals.rlmerMod.Rd | 42
man/rho.b.Rd | 30
man/rho.e.Rd | 30
man/rlmer.Rd | 215 -
man/rlmerMod-class.Rd | 86
man/sigma.Rd | 30
man/smoothPsi.Rd | 48
man/theta.Rd | 26
man/wgt.Rd | 74
man/xtable.comparison.table.Rd | 78
tests/DAS-scale.R | 416 +-
tests/compare-methods.R | 242 -
tests/compare-methods.Rout.save | 941 ++---
tests/expectations.R | 92
tests/genericFunctions.R | 124
tests/getME.R | 30
tests/getME.Rout.save | 763 ++--
tests/psi-rho-funs.R | 186 -
tests/rlmerMod.R | 196 -
tests/subset.R |only
tests/tau.R | 164 -
tests/testMatrices.R | 374 +-
vignettes/cache/03451c9f666591b6ac41dc9a9ed06ce40b992c72 |binary
vignettes/cache/3eedbad1dba67d608f15fff9c8483ecb74f5b750 |binary
vignettes/cache/5d35c874f80664a261be32f6c0cc9ad6cf912ab0 |binary
vignettes/cache/6b459128b6f80b01986ff6c4115e7dfb52f962fb |binary
vignettes/cache/6c12e8730fa7df924a4b57a4258f7d876dd3cc7f |binary
vignettes/cache/e514dc7b17af4b19dcabad5cf474029c569fca86 |binary
vignettes/efficiency-table-B-optimal.tex | 44
vignettes/efficiency-table-lqq-locationScale.tex | 40
vignettes/efficiency-table-lqq.tex | 44
vignettes/efficiency-table.tex | 28
vignettes/figs |only
vignettes/rlmer.Rnw | 2394 +++++++--------
vignettes/rlmer.bib | 882 ++---
vignettes/rlmer.tex |only
vignettes/tuning-constants-table.tex | 28
71 files changed, 8364 insertions(+), 8315 deletions(-)
Title: Power and Sample size based on two one-sided t-tests (TOST) for
(bio)equivalence studies
Diff between PowerTOST versions 1.1-03 dated 2013-05-03 and 1.1-05 dated 2013-06-17
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies. See
function known.designs() for study designs covered. Moreover
the package contains functions for power and sample size based
on 'expected' power in case of uncertain (estimated)
variability. ----- Added are functions for the power and
sample size for the ratio of two means with normally
distributed data on the original scale (based on Fieller's
confidence ('fiducial') interval). ----- Contains further
functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but
eventually useful if the question of 'non-superiority' must be
evaluated. The power and sample size calculations based on
non-inferiority test may also performed via 'expected' power in
case of uncertain (estimated) variability. ----- Contains
functions power.scABEL() and sampleN.scABEL() to calculate
power and sample size for the BE decision via scaled (widened)
BE acceptance limits based on simulations. Contains functions
power.RSABE() and sampleN.RSABE() to calculate power and sample
size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations. Contains
further functions power.NTIDFDA() and sampleN.NTIDFDA() to
calculate power and sample size for the BE decision via the FDA
procedure for NTID's based on simulations.
Author: Detlew Labes
Maintainer: Detlew Labes
PowerTOST-1.1-03/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.02.pdf |only
PowerTOST-1.1-05/PowerTOST/DESCRIPTION | 19 +-
PowerTOST-1.1-05/PowerTOST/MD5 | 32 ++--
PowerTOST-1.1-05/PowerTOST/NAMESPACE | 2
PowerTOST-1.1-05/PowerTOST/NEWS | 18 ++
PowerTOST-1.1-05/PowerTOST/R/SampleSize.R | 22 ++-
PowerTOST-1.1-05/PowerTOST/R/power_RSABE_NTID.R |only
PowerTOST-1.1-05/PowerTOST/R/power_scABEL.R | 6
PowerTOST-1.1-05/PowerTOST/R/samplesize_RSABE.R | 69 +++++++---
PowerTOST-1.1-05/PowerTOST/R/samplesize_RSABE_NTID.R |only
PowerTOST-1.1-05/PowerTOST/R/samplesize_scABEL.R | 68 +++++++--
PowerTOST-1.1-05/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.03.pdf |only
PowerTOST-1.1-05/PowerTOST/man/PowerTOST-package.Rd | 19 ++
PowerTOST-1.1-05/PowerTOST/man/power.NTIDFDA.Rd |only
PowerTOST-1.1-05/PowerTOST/man/power.RSABE.Rd | 12 -
PowerTOST-1.1-05/PowerTOST/man/power.scABEL.Rd | 17 +-
PowerTOST-1.1-05/PowerTOST/man/sampleN.NTIDFDA.Rd |only
PowerTOST-1.1-05/PowerTOST/man/sampleN.RSABE.Rd | 33 ++--
PowerTOST-1.1-05/PowerTOST/man/sampleN.TOST.Rd | 3
PowerTOST-1.1-05/PowerTOST/man/sampleN.scABEL.Rd | 22 +--
20 files changed, 226 insertions(+), 116 deletions(-)
Title: Calculations and visualizations related to Geometric
Morphometrics
Diff between Morpho versions 0.23.3 dated 2013-03-21 and 0.24.1 dated 2013-06-17
Description: A toolset for Geometric Morphometrics and mesh processing.
Author: Stefan Schlager
Maintainer: Stefan Schlager
Morpho-0.23.3/Morpho/R/crestlines.r |only
Morpho-0.23.3/Morpho/R/face.r |only
Morpho-0.23.3/Morpho/R/minClost.r |only
Morpho-0.23.3/Morpho/R/unbias.r |only
Morpho-0.23.3/Morpho/src/gauss_displace.f90 |only
Morpho-0.23.3/Morpho/src/minClost.f90 |only
Morpho-0.24.1/Morpho/DESCRIPTION | 8 +--
Morpho-0.24.1/Morpho/MD5 | 70 ++++++++++++++--------------
Morpho-0.24.1/Morpho/NAMESPACE | 6 +-
Morpho-0.24.1/Morpho/R/adnormals.r | 24 +++++++++
Morpho-0.24.1/Morpho/R/bindArr.r |only
Morpho-0.24.1/Morpho/R/covDist.r |only
Morpho-0.24.1/Morpho/R/histGroup.r | 17 ++++--
Morpho-0.24.1/Morpho/R/kendalldist.r |only
Morpho-0.24.1/Morpho/R/mcNNindex.r | 4 +
Morpho-0.24.1/Morpho/R/name2.r | 2
Morpho-0.24.1/Morpho/R/pls2B.r | 32 ++++++++++--
Morpho-0.24.1/Morpho/R/procAOV.r | 13 +++--
Morpho-0.24.1/Morpho/R/procSym.r | 18 +++++--
Morpho-0.24.1/Morpho/R/regdist.r | 4 -
Morpho-0.24.1/Morpho/R/regdist.raw.r | 10 +---
Morpho-0.24.1/Morpho/R/scaleproc.r | 4 +
Morpho-0.24.1/Morpho/man/CVA.Rd | 35 ++++++++------
Morpho-0.24.1/Morpho/man/Morpho-package.Rd | 12 ++--
Morpho-0.24.1/Morpho/man/adnormals.Rd | 23 ++++++++-
Morpho-0.24.1/Morpho/man/covDist.Rd |only
Morpho-0.24.1/Morpho/man/deformGrid.Rd | 4 +
Morpho-0.24.1/Morpho/man/groupPCA.Rd | 6 +-
Morpho-0.24.1/Morpho/man/histGroup.Rd | 11 +++-
Morpho-0.24.1/Morpho/man/internal.Rd | 16 ------
Morpho-0.24.1/Morpho/man/mesh2ply.Rd | 4 +
Morpho-0.24.1/Morpho/man/meshDist.Rd | 4 +
Morpho-0.24.1/Morpho/man/name2factor.Rd | 6 +-
Morpho-0.24.1/Morpho/man/pls2B.Rd |only
Morpho-0.24.1/Morpho/man/procSym.Rd | 13 ++++-
Morpho-0.24.1/Morpho/man/regdist.raw.Rd | 8 ++-
Morpho-0.24.1/Morpho/man/relaxLM.Rd | 6 +-
Morpho-0.24.1/Morpho/man/rotonto.Rd | 6 +-
Morpho-0.24.1/Morpho/man/tobedoc.Rd | 3 -
Morpho-0.24.1/Morpho/man/typprob.Rd | 2
Morpho-0.24.1/Morpho/man/warpmovie3d.Rd | 6 +-
Morpho-0.24.1/Morpho/src/facenormals.f90 |only
42 files changed, 240 insertions(+), 137 deletions(-)
Title: Bolstad functions
Diff between Bolstad2 versions 1.0-27 dated 2011-11-18 and 1.0-28 dated 2013-06-17
Description: A set of R functions and data sets for the book
Understanding Computational Bayesian Statistics, Bolstad, W.M.
(2009), John Wiley & Sons ISBN 978-0470046098
Author: James M. Curran
Maintainer: James M. Curran
DESCRIPTION | 17 +++--
MD5 | 12 +--
R/BayesCPH.r | 180 +++++++++++++++++++++++++++---------------------------
R/BayesLogistic.r | 14 ++--
R/BayesPois.r | 180 +++++++++++++++++++++++++++---------------------------
R/bivnormMH.r | 16 ++--
R/hierMeanReg.r | 174 ++++++++++++++++++++++++++--------------------------
7 files changed, 298 insertions(+), 295 deletions(-)
Title: A collection of miscellaneous tools for reproducible research
with R.
Diff between repmis versions 0.2.5 dated 2013-04-24 and 0.2.6 dated 2013-06-17
Description: A collection of miscellaneous tools for reproducible
research with R. Currently the package includes tools to load R
packages and automatically generate BibTeX files citing them as
well as load plain-text data stored on Dropbox, GitHub, and
from other sources.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 12 ++---
MD5 | 24 +++++------
NAMESPACE | 5 --
NEWS | 6 ++
R/InstallOldPackages.R | 15 +++----
R/LoadandCite.R | 96 +++++++++++++++++++++++++++++++++++++++-------
R/source_DropboxData.R | 4 -
R/source_GitHubData.R | 4 -
R/source_data.R | 7 +--
README.md | 5 +-
man/InstallOldPackages.Rd | 9 ++--
man/LoadandCite.Rd | 32 ++++++++-------
man/source_data.Rd | 3 -
13 files changed, 153 insertions(+), 69 deletions(-)
Title: Relaxation of glmnet models (as in relaxed lasso, Meinshausen
2007)
Diff between relaxnet versions 0.2-1 dated 2013-05-13 and 0.3-1 dated 2013-06-17
Description: Extends the glmnet package with "relaxation", done by
running glmnet once on the entire predictor matrix, then again
on each different subset of variables from along the
regularization path. Relaxation may lead to improved prediction
accuracy for truly sparse data generating models, as well as
fewer false positives (i.e. fewer noncontributing predictors in
the final model). Penalty may be lasso (alpha = 1) or elastic
net (0 < alpha < 1). For this version, family may be "gaussian"
or "binomial" only. Takes advantage of fast fortran code from
the glmnet package.
Author: Stephan Ritter, Alan Hubbard
Maintainer: Stephan Ritter
ChangeLog |only
DESCRIPTION | 20 ++++----
MD5 | 15 +++---
NAMESPACE | 3 +
R/cv.alpha.relaxnet.R | 125 +++++++++++++++++++++++++++++++++++++-------------
R/cv.relaxnet.R | 110 ++++++++++++++++++++++++++++++++++++--------
R/predict.relaxnet.R | 37 ++++++++++++--
R/relaxnet.R | 5 +-
man/cv.relaxnet.Rd | 15 ++++++
9 files changed, 260 insertions(+), 70 deletions(-)
Title: Dynamic Deterministic Effects Propagation Networks: Infer
signalling networks for timecourse RPPA data.
Diff between ddepn versions 2.1.2 dated 2012-06-21 and 2.1.4 dated 2013-06-17
Description: DDEPN (Dynamic Deterministic Effects Propagation
Networks): Infer signalling networks for timecourse data. Given
a matrix of high-throughput genomic or proteomic timecourse
data, generated after external perturbation of the biological
system, DDEPN models the time-dependent propagation of active
and passive states depending on a network structure. Optimal
network structures given the experimental data are
reconstructed. Two network inference algorithms can be used:
inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA,
a Genetic Algorithm network optimisation. Inclusion of prior
biological knowledge can be done using different network prior
models.
Author: Christian Bender
Maintainer: Christian Bender
DESCRIPTION | 14 +++++-----
MD5 | 45 ++++++++++++++++-----------------
R/ddepn.R | 7 +++--
R/perform.hmmsearch.R | 4 ++
R/samplephi.R | 2 -
data/hcc1954.RData |binary
data/hcc1954raw.RData |binary
data/kegggraphs.RData |binary
inst/doc/ddepn.R |only
inst/doc/ddepn.pdf |binary
man/adjacencyMatrix_to_logicalRules.Rd | 9 ++++--
man/create_signetwork.Rd | 29 ++++++++++++++-------
man/ddepn.Rd | 21 ++++++++++-----
man/getfirstphi.Rd | 3 +-
man/makedata.Rd | 8 +++--
man/mcmc_ddepn.Rd | 15 ++++++-----
man/netga.Rd | 10 +++----
man/plot_edgeconfidences.Rd | 3 +-
man/plot_profiles.Rd | 5 ++-
man/plotdetailed.Rd | 11 +++++---
man/plotdetailed_Rgraphviz.Rd | 6 ++--
man/posterior.Rd | 3 +-
man/samplephi.Rd | 8 +++--
man/signalnetwork.Rd | 3 +-
24 files changed, 127 insertions(+), 79 deletions(-)
Title: Constrained, covariance-matching constrained and universal point
or block kriging
Diff between constrainedKriging versions 0.1.9 dated 2012-12-24 and 0.2.0 dated 2013-06-17
More information about constrainedKriging at CRAN
Description: The constrainedKriging package provides functions for
efficient computations of nonlinear spatial predictions with
local change of support. The package supplies functions for
tow-dimensional spatial interpolation by constrained,
covariance-matching constrained and universal (external drift)
kriging for points or block of any shape for data with a
nonstationary mean function and an isotropic weakly stationary
variogram. The linear spatial interpolation methods,
constrained and covariance-matching constrained kriging,
provide approximately unbiased prediction for nonlinear target
values under change of support. The constrainedKriging package
extends the range of geostatistical tools available in R and
provides a veritable alternative to conditional simulation for
nonlinear spatial prediction problems with local change of
support.
Author: Christoph Hofer
Maintainer: Christoph Hofer
constrainedKriging-0.1.9/constrainedKriging/LICENCE |only
constrainedKriging-0.2.0/constrainedKriging/DESCRIPTION | 9 -
constrainedKriging-0.2.0/constrainedKriging/MD5 | 20 +--
constrainedKriging-0.2.0/constrainedKriging/R/covmodlist.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.point.block.cov.R | 58 +++++-----
constrainedKriging-0.2.0/constrainedKriging/R/f.point.rec.covmat.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.polygons.preCKrige.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.preCKrige.check.and.test.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/z#f.build.pixel.R |only
constrainedKriging-0.2.0/constrainedKriging/inst/ChangeLog.txt | 8 +
constrainedKriging-0.2.0/constrainedKriging/src/covariancefunctions.h | 30 ++++-
constrainedKriging-0.2.0/constrainedKriging/src/point_block_cov.c | 6 +
12 files changed, 90 insertions(+), 49 deletions(-)
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