Title: Probability-Scale Residuals and Residual Correlations
Diff between PResiduals versions 0.2-0 dated 2014-08-22 and 0.2-1 dated 2015-03-03
Description: Computes probability-scale residuals and residual correlations
for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont
DESCRIPTION | 25 ++++-----
MD5 | 42 ++++++++-------
NAMESPACE | 7 ++
R/GKGamma.R | 1
R/PResiduals-package.R | 14 ++---
R/cobot.R | 11 ++--
R/cocobot.R | 6 +-
R/countbot.R |only
R/diagn.R | 1
R/presid.R | 123 +++++++++++++++++++++++++++++++++++++++++-----
R/print.cobot.R | 1
R/print.cocobot.R | 1
data/PResidData.rda |binary
man/GKGamma.Rd | 3 -
man/PResidData.Rd | 5 +
man/PResiduals-package.Rd | 16 +++--
man/cobot.Rd | 11 ----
man/cocobot.Rd | 2
man/countbot.Rd |only
man/diagn.Rd | 3 -
man/presid.Rd | 25 +++------
man/print.cobot.Rd | 3 -
man/print.cocobot.Rd | 3 -
23 files changed, 196 insertions(+), 107 deletions(-)
Title: Advanced Tables for Markdown/HTML
Diff between htmlTable versions 1.1 dated 2015-02-07 and 1.2 dated 2015-03-03
Description: Tables with state-of-the-art layout elements such as
row spanners, column spanners, table spanners, zebra striping,
and more. While allowing advanced layout, the underlying CSS structure is
simple in order to maximize compatibility with wordprocessors such as
MS Word or LibreOffice.
The package also contains a few text formatting functions that help outputting
text compatible with HTML/LaTeX.
Author: Max Gordon
Maintainer: Max Gordon
DESCRIPTION | 19
MD5 | 28
NAMESPACE | 1
NEWS | 6
R/htmlTable.R | 16
R/htmlTable_helpers.R | 7
build/vignette.rds |binary
inst/doc/general.Rmd | 2
inst/doc/general.html | 46
inst/doc/tables.R | 27
inst/doc/tables.Rmd | 40
inst/doc/tables.html | 1273 +++++++++++++++++++++++-
tests/testthat/test-htmlTable_rgroup_tspanner.R | 11
vignettes/general.Rmd | 2
vignettes/tables.Rmd | 40
15 files changed, 1426 insertions(+), 92 deletions(-)
Title: Performs the Processing and Normalisation of Nanostring miRNA
and mRNA Data
Diff between NAPPA versions 2.0 dated 2014-07-16 and 2.0.1 dated 2015-03-03
Description: Enables the processing and normalisation of the standard mRNA data output from the Nanostring nCounter software.
Author: Chris Harbron, Mark Wappett
Maintainer: Mark Wappett
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
build/vignette.rds |binary
inst/doc/NAPPA.pdf |binary
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Mixed Effects Cox Models
Diff between coxme versions 2.2-3 dated 2012-05-15 and 2.2-4 dated 2015-03-03
Description: Cox proportional hazards models containing Gaussian random
effects, also known as frailty models.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau
coxme-2.2-3/coxme/COPYRIGHT |only
coxme-2.2-3/coxme/Readme |only
coxme-2.2-3/coxme/noweb/noweb.R |only
coxme-2.2-3/coxme/noweb/noweb.sty |only
coxme-2.2-3/coxme/noweb/nwmac.tex |only
coxme-2.2-4/coxme/DESCRIPTION | 25 +-
coxme-2.2-4/coxme/MD5 | 186 +++++++++--------
coxme-2.2-4/coxme/NAMESPACE | 18 -
coxme-2.2-4/coxme/R/anova.coxme.R | 5
coxme-2.2-4/coxme/R/bdsmatrix.R | 2
coxme-2.2-4/coxme/R/coxme.R | 18 +
coxme-2.2-4/coxme/R/coxme.control.R | 17 +
coxme-2.2-4/coxme/R/coxme.fit.R | 83 +++++--
coxme-2.2-4/coxme/R/coxme.varcheck.R | 9
coxme-2.2-4/coxme/R/coxmeFull.R | 23 --
coxme-2.2-4/coxme/R/coxmeMlist.R | 19 -
coxme-2.2-4/coxme/R/lmekin.R | 19 +
coxme-2.2-4/coxme/R/lmekin.control.R | 20 +
coxme-2.2-4/coxme/R/predict.coxme.R |only
coxme-2.2-4/coxme/R/print.coxme.R | 4
coxme-2.2-4/coxme/R/print.lmekin.R | 5
coxme-2.2-4/coxme/R/ranef.R | 23 ++
coxme-2.2-4/coxme/build |only
coxme-2.2-4/coxme/cleanup |only
coxme-2.2-4/coxme/cleanup.win |only
coxme-2.2-4/coxme/inst/COPYRIGHTS |only
coxme-2.2-4/coxme/inst/NEWS.Rd | 43 +++
coxme-2.2-4/coxme/inst/doc/coxme.R |only
coxme-2.2-4/coxme/inst/doc/coxme.pdf |binary
coxme-2.2-4/coxme/inst/doc/laplace.R |only
coxme-2.2-4/coxme/inst/doc/laplace.Rnw | 6
coxme-2.2-4/coxme/inst/doc/laplace.pdf |binary
coxme-2.2-4/coxme/inst/doc/lmekin.R |only
coxme-2.2-4/coxme/inst/doc/lmekin.Rnw | 10
coxme-2.2-4/coxme/inst/doc/lmekin.pdf |binary
coxme-2.2-4/coxme/inst/doc/variance.R |only
coxme-2.2-4/coxme/inst/doc/variance.Rnw | 12 -
coxme-2.2-4/coxme/inst/doc/variance.pdf |binary
coxme-2.2-4/coxme/man/VarCorr.Rd |only
coxme-2.2-4/coxme/man/coxme.Rd | 11 -
coxme-2.2-4/coxme/man/coxme.control.Rd | 51 ++++
coxme-2.2-4/coxme/man/coxme.object.Rd |only
coxme-2.2-4/coxme/man/fixed.effects.Rd |only
coxme-2.2-4/coxme/man/fixef.lmekin.Rd | 32 ++
coxme-2.2-4/coxme/man/lmekin.Rd | 39 ++-
coxme-2.2-4/coxme/man/lmekin.control.Rd |only
coxme-2.2-4/coxme/man/lmekin.object.Rd | 12 -
coxme-2.2-4/coxme/man/logLik.coxme.Rd |only
coxme-2.2-4/coxme/man/predict.coxme.Rd |only
coxme-2.2-4/coxme/man/print.coxme.Rd | 14 +
coxme-2.2-4/coxme/man/ranef.Rd |only
coxme-2.2-4/coxme/noweb/Makefile | 19 -
coxme-2.2-4/coxme/noweb/Readme | 13 -
coxme-2.2-4/coxme/noweb/all.nw | 323 +++++++++++++++++-------------
coxme-2.2-4/coxme/noweb/basic.Rnw | 6
coxme-2.2-4/coxme/noweb/bdsmatrix.Rnw | 4
coxme-2.2-4/coxme/noweb/build.Rnw | 19 -
coxme-2.2-4/coxme/noweb/fit.Rnw | 89 +++++---
coxme-2.2-4/coxme/noweb/formula.Rnw | 17 -
coxme-2.2-4/coxme/noweb/lmekin.Rnw | 29 +-
coxme-2.2-4/coxme/noweb/main.Rnw | 54 +----
coxme-2.2-4/coxme/noweb/ranef.Rnw | 28 ++
coxme-2.2-4/coxme/noweb/varfun.Rnw | 32 +-
coxme-2.2-4/coxme/noweb/varfun2.Rnw | 43 ++-
coxme-2.2-4/coxme/src/agfit6b.c | 1
coxme-2.2-4/coxme/src/bdsmatrix.h |only
coxme-2.2-4/coxme/src/bdsmatrix_stub.h |only
coxme-2.2-4/coxme/src/coxfit6a.c | 1
coxme-2.2-4/coxme/src/coxfit6c.c | 2
coxme-2.2-4/coxme/src/coxmeS.h | 17 -
coxme-2.2-4/coxme/tests/bdstest.R | 10
coxme-2.2-4/coxme/tests/bdstest.Rout.save | 23 +-
coxme-2.2-4/coxme/tests/brdat.rda |only
coxme-2.2-4/coxme/tests/brfit.R |only
coxme-2.2-4/coxme/tests/lmekin1.R | 16 +
coxme-2.2-4/coxme/tests/lmekin1.Rout.save | 30 +-
coxme-2.2-4/coxme/tests/lmekin2.R | 8
coxme-2.2-4/coxme/tests/lmekin2.Rout.save | 21 +
coxme-2.2-4/coxme/tests/nest1.Rout.save | 2
coxme-2.2-4/coxme/tests/nest2.Rout.save | 2
coxme-2.2-4/coxme/tests/refine.Rout.save | 2
coxme-2.2-4/coxme/tests/refine1.R | 2
coxme-2.2-4/coxme/tests/refine1.Rout.save | 15 -
coxme-2.2-4/coxme/tests/refine2.R | 2
coxme-2.2-4/coxme/tests/refine2.Rout.save | 15 -
coxme-2.2-4/coxme/tests/refine3.Rout.save | 2
coxme-2.2-4/coxme/tests/shrink.Rout.save | 2
coxme-2.2-4/coxme/tests/slope1.Rout.save | 2
coxme-2.2-4/coxme/tests/slope2.R | 6
coxme-2.2-4/coxme/tests/slope2.Rout.save | 19 -
coxme-2.2-4/coxme/tests/slope3.Rout.save | 2
coxme-2.2-4/coxme/tests/slope4.R | 2
coxme-2.2-4/coxme/tests/slope4.Rout.save | 15 -
coxme-2.2-4/coxme/tests/strata1.Rout.save | 2
coxme-2.2-4/coxme/tests/test0.R | 7
coxme-2.2-4/coxme/tests/test0.Rout.save | 22 +-
coxme-2.2-4/coxme/tests/test1.Rout.save | 2
coxme-2.2-4/coxme/tests/test2.R | 17 -
coxme-2.2-4/coxme/tests/test2.Rout.save | 30 +-
coxme-2.2-4/coxme/tests/test3.Rout.save | 2
coxme-2.2-4/coxme/tests/test4.Rout.save | 2
coxme-2.2-4/coxme/tests/twoterm.R | 2
coxme-2.2-4/coxme/tests/twoterm.Rout.save | 17 -
coxme-2.2-4/coxme/vignettes/figures |only
coxme-2.2-4/coxme/vignettes/laplace.Rnw | 6
coxme-2.2-4/coxme/vignettes/lmekin.Rnw | 10
coxme-2.2-4/coxme/vignettes/variance.Rnw | 12 -
107 files changed, 1028 insertions(+), 704 deletions(-)
Title: MCMC Algorithms for the Coalescent
Diff between coalescentMCMC versions 0.4 dated 2013-12-04 and 0.4-1 dated 2015-03-03
More information about coalescentMCMC at CRAN
Description: Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters.
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis
DESCRIPTION | 15 ++++++---------
MD5 | 26 ++++++++++++++------------
NAMESPACE | 6 ++++--
NEWS | 16 ++++++++++++++++
R/coalescentMCMC.R | 31 +++++++++++++++++++++----------
R/sim.coalescent.R |only
R/treeOperators.R | 8 ++++----
build/vignette.rds |binary
inst/doc/CoalescentModels.pdf |binary
inst/doc/Running_coalescentMCMC.R | 29 +++++++++++++++--------------
inst/doc/Running_coalescentMCMC.Rnw | 10 +++++-----
inst/doc/Running_coalescentMCMC.pdf |binary
man/coalesceMCMC.Rd | 7 ++++---
man/sim.coalescent.Rd |only
vignettes/Running_coalescentMCMC.Rnw | 10 +++++-----
15 files changed, 94 insertions(+), 64 deletions(-)
Permanent link
Title: Companion to Applied Regression
Diff between car versions 2.0-24 dated 2015-02-01 and 2.0-25 dated 2015-03-03
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 16
MD5 | 19
NAMESPACE | 540 ++++++++++----------
NEWS | 1288 ++++++++++++++++++++++++-------------------------
R/Anova.R | 6
R/Boot.R | 601 +++++++++++-----------
R/linearHypothesis.R | 3
inst/doc/embedding.pdf |binary
man/Anova.Rd | 653 ++++++++++++------------
man/car-internal.Rd |only
man/car-package.Rd | 72 +-
11 files changed, 1611 insertions(+), 1587 deletions(-)
Title: Agricultural Datasets
Diff between agridat versions 1.10 dated 2014-11-26 and 1.11 dated 2015-03-03
Description: Datasets from books, papers, and websites related to agriculture.
Example analyses are included. Includes functions for plotting field
designs and GGE biplots.
Author: Kevin Wright
Maintainer: Kevin Wright
agridat-1.10/agridat/data/piepho.cooksfoot.txt.gz |only
agridat-1.10/agridat/man/piepho.cooksfoot.Rd |only
agridat-1.11/agridat/DESCRIPTION | 23
agridat-1.11/agridat/MD5 | 407 +++++------
agridat-1.11/agridat/NAMESPACE | 4
agridat-1.11/agridat/NEWS | 153 ++--
agridat-1.11/agridat/R/gge.r | 565 ++++++++++------
agridat-1.11/agridat/build/vignette.rds |binary
agridat-1.11/agridat/data/besag.beans.txt.gz |only
agridat-1.11/agridat/data/besag.triticale.txt.gz |only
agridat-1.11/agridat/data/burgueno.alpha.txt.gz |only
agridat-1.11/agridat/data/burgueno.rowcol.txt.gz |only
agridat-1.11/agridat/data/burgueno.unreplicated.txt.gz |only
agridat-1.11/agridat/data/datalist | 9
agridat-1.11/agridat/data/piepho.cocksfoot.txt.gz |only
agridat-1.11/agridat/data/steptoe.morex.geno.rda |only
agridat-1.11/agridat/data/steptoe.morex.pheno.txt.gz |only
agridat-1.11/agridat/inst/doc/agridat_examples.Rnw | 6
agridat-1.11/agridat/inst/doc/agridat_examples.pdf |binary
agridat-1.11/agridat/man/aastveit.barley.Rd | 6
agridat-1.11/agridat/man/adugna.sorghum.Rd | 3
agridat-1.11/agridat/man/agridat.Rd | 60 +
agridat-1.11/agridat/man/allcroft.lodging.Rd | 22
agridat-1.11/agridat/man/archbold.apple.Rd | 5
agridat-1.11/agridat/man/ars.earlywhitecorn96.Rd | 11
agridat-1.11/agridat/man/australia.soybean.Rd | 2
agridat-1.11/agridat/man/baker.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/batchelor.uniformity.Rd | 26
agridat-1.11/agridat/man/beall.webworms.Rd | 1
agridat-1.11/agridat/man/beaven.barley.Rd | 1
agridat-1.11/agridat/man/besag.bayesian.Rd | 33
agridat-1.11/agridat/man/besag.beans.Rd |only
agridat-1.11/agridat/man/besag.elbatan.Rd | 63 +
agridat-1.11/agridat/man/besag.endive.Rd | 1
agridat-1.11/agridat/man/besag.met.Rd | 2
agridat-1.11/agridat/man/besag.triticale.Rd |only
agridat-1.11/agridat/man/blackman.wheat.Rd | 1
agridat-1.11/agridat/man/bliss.borers.Rd | 47 -
agridat-1.11/agridat/man/bond.diallel.Rd | 2
agridat-1.11/agridat/man/box.cork.Rd | 1
agridat-1.11/agridat/man/brandle.rape.Rd | 13
agridat-1.11/agridat/man/brandt.switchback.Rd | 2
agridat-1.11/agridat/man/bridges.cucmber.Rd | 1
agridat-1.11/agridat/man/broadbalk.wheat.Rd | 2
agridat-1.11/agridat/man/burgueno.alpha.Rd |only
agridat-1.11/agridat/man/burgueno.rowcol.Rd |only
agridat-1.11/agridat/man/burgueno.unreplicated.Rd |only
agridat-1.11/agridat/man/butron.maize.Rd | 1
agridat-1.11/agridat/man/byers.apple.Rd | 25
agridat-1.11/agridat/man/caribbean.maize.Rd | 2
agridat-1.11/agridat/man/carlson.germination.Rd | 35
agridat-1.11/agridat/man/carmer.density.Rd | 36 -
agridat-1.11/agridat/man/cate.potassium.Rd | 1
agridat-1.11/agridat/man/cleveland.soil.Rd | 2
agridat-1.11/agridat/man/cochran.bib.Rd | 7
agridat-1.11/agridat/man/cochran.crd.Rd | 1
agridat-1.11/agridat/man/cochran.eelworms.Rd | 2
agridat-1.11/agridat/man/cochran.factorial.Rd | 10
agridat-1.11/agridat/man/cochran.latin.Rd | 3
agridat-1.11/agridat/man/cochran.wireworms.Rd | 2
agridat-1.11/agridat/man/connolly.potato.Rd | 1
agridat-1.11/agridat/man/cornelius.maize.Rd | 2
agridat-1.11/agridat/man/corsten.interaction.Rd | 2
agridat-1.11/agridat/man/cox.stripsplit.Rd | 10
agridat-1.11/agridat/man/crossa.wheat.Rd | 33
agridat-1.11/agridat/man/crowder.seeds.Rd | 13
agridat-1.11/agridat/man/cullis.earlygen.Rd | 2
agridat-1.11/agridat/man/darwin.maize.Rd | 2
agridat-1.11/agridat/man/denis.missing.Rd | 3
agridat-1.11/agridat/man/denis.ryegrass.Rd | 2
agridat-1.11/agridat/man/desplot.Rd | 5
agridat-1.11/agridat/man/digby.jointregression.Rd | 3
agridat-1.11/agridat/man/diggle.cow.Rd | 9
agridat-1.11/agridat/man/durban.competition.Rd | 1
agridat-1.11/agridat/man/durban.rowcol.Rd | 3
agridat-1.11/agridat/man/durban.splitplot.Rd | 3
agridat-1.11/agridat/man/eden.potato.Rd | 4
agridat-1.11/agridat/man/engelstad.nitro.Rd | 8
agridat-1.11/agridat/man/fan.stability.Rd | 14
agridat-1.11/agridat/man/federer.diagcheck.Rd | 18
agridat-1.11/agridat/man/federer.tobacco.Rd | 3
agridat-1.11/agridat/man/fisher.latin.Rd | 1
agridat-1.11/agridat/man/foulley.calving.Rd | 4
agridat-1.11/agridat/man/fox.wheat.Rd | 1
agridat-1.11/agridat/man/garber.mulit.uniformity.Rd | 3
agridat-1.11/agridat/man/gathmann.bt.Rd | 3
agridat-1.11/agridat/man/gauch.soy.Rd | 28
agridat-1.11/agridat/man/gge.Rd | 17
agridat-1.11/agridat/man/gilmour.serpentine.Rd | 2
agridat-1.11/agridat/man/gilmour.slatehall.Rd | 1
agridat-1.11/agridat/man/gomez.fractionalfactorial.Rd | 14
agridat-1.11/agridat/man/gomez.groupsplit.Rd | 3
agridat-1.11/agridat/man/gomez.multilocsplitplot.Rd | 3
agridat-1.11/agridat/man/gomez.nitrogen.Rd | 2
agridat-1.11/agridat/man/gomez.rice.uniformity.Rd | 30
agridat-1.11/agridat/man/gomez.seedrate.Rd | 10
agridat-1.11/agridat/man/gomez.splitplot.subsample.Rd | 1
agridat-1.11/agridat/man/gomez.splitsplit.Rd | 2
agridat-1.11/agridat/man/gomez.stripplot.Rd | 1
agridat-1.11/agridat/man/gomez.stripsplitplot.Rd | 2
agridat-1.11/agridat/man/gotway.hessianfly.Rd | 2
agridat-1.11/agridat/man/goulden.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/goulden.latin.Rd | 1
agridat-1.11/agridat/man/graybill.heteroskedastic.Rd | 3
agridat-1.11/agridat/man/gumpertz.pepper.Rd | 1
agridat-1.11/agridat/man/hanks.sprinkler.Rd | 3
agridat-1.11/agridat/man/harris.multi.uniformity.Rd | 2
agridat-1.11/agridat/man/harris.wateruse.Rd | 11
agridat-1.11/agridat/man/harrison.priors.Rd | 20
agridat-1.11/agridat/man/hayman.tobacco.Rd | 1
agridat-1.11/agridat/man/hazell.vegetables.Rd | 2
agridat-1.11/agridat/man/heady.fertilizer.Rd | 1
agridat-1.11/agridat/man/henderson.milkfat.Rd | 2
agridat-1.11/agridat/man/hernandez.nitrogen.Rd | 6
agridat-1.11/agridat/man/hessling.argentina.Rd | 22
agridat-1.11/agridat/man/hildebrand.systems.Rd | 2
agridat-1.11/agridat/man/holland.arthropods.Rd | 2
agridat-1.11/agridat/man/holshouser.splitstrip.Rd | 8
agridat-1.11/agridat/man/hughes.grapes.Rd | 8
agridat-1.11/agridat/man/hunter.corn.Rd | 2
agridat-1.11/agridat/man/ilri.sheep.Rd | 3
agridat-1.11/agridat/man/immer.sugarbeet.uniformity.Rd | 3
agridat-1.11/agridat/man/ivins.herbs.Rd | 1
agridat-1.11/agridat/man/jansen.strawberry.Rd | 1
agridat-1.11/agridat/man/jenkyn.mildew.Rd | 2
agridat-1.11/agridat/man/john.alpha.Rd | 16
agridat-1.11/agridat/man/johnson.blight.Rd | 2
agridat-1.11/agridat/man/kalamkar.potato.uniformity.Rd | 1
agridat-1.11/agridat/man/kang.maize.Rd | 1
agridat-1.11/agridat/man/kang.peanut.Rd | 3
agridat-1.11/agridat/man/karcher.turfgrass.Rd | 1
agridat-1.11/agridat/man/keen.potatodamage.Rd | 23
agridat-1.11/agridat/man/kempton.barley.uniformity.Rd | 2
agridat-1.11/agridat/man/kempton.competition.Rd | 3
agridat-1.11/agridat/man/kempton.rowcol.Rd | 2
agridat-1.11/agridat/man/kempton.slatehall.Rd | 8
agridat-1.11/agridat/man/lambert.soiltemp.Rd | 2
agridat-1.11/agridat/man/lasrosas.corn.Rd | 18
agridat-1.11/agridat/man/lavoranti.eucalyptus.Rd | 2
agridat-1.11/agridat/man/lee.potatoblight.Rd | 6
agridat-1.11/agridat/man/li.millet.uniformity.Rd | 2
agridat-1.11/agridat/man/lonnquist.maize.Rd | 4
agridat-1.11/agridat/man/lucas.switchback.Rd | 1
agridat-1.11/agridat/man/lyon.potato.uniformity.Rd | 2
agridat-1.11/agridat/man/lyons.wheat.Rd | 2
agridat-1.11/agridat/man/mcconway.turnip.Rd | 9
agridat-1.11/agridat/man/mcleod.barley.Rd | 2
agridat-1.11/agridat/man/mead.cauliflower.Rd | 5
agridat-1.11/agridat/man/mead.cowpeamaize.Rd | 13
agridat-1.11/agridat/man/mead.germination.Rd | 2
agridat-1.11/agridat/man/mead.strawberry.Rd | 2
agridat-1.11/agridat/man/mercer.mangold.uniformity.Rd | 2
agridat-1.11/agridat/man/mercer.wheat.uniformity.Rd | 3
agridat-1.11/agridat/man/minnesota.barley.weather.Rd | 25
agridat-1.11/agridat/man/minnesota.barley.yield.Rd | 3
agridat-1.11/agridat/man/nass.corn.Rd | 3
agridat-1.11/agridat/man/nebraska.farmincome.Rd | 58 -
agridat-1.11/agridat/man/odland.soy.uniformity.Rd | 2
agridat-1.11/agridat/man/ortiz.tomato.Rd | 8
agridat-1.11/agridat/man/pacheco.soybean.Rd | 23
agridat-1.11/agridat/man/patterson.switchback.Rd | 2
agridat-1.11/agridat/man/pearce.apple.Rd | 2
agridat-1.11/agridat/man/pearl.kernels.Rd | 1
agridat-1.11/agridat/man/perry.springwheat.Rd | 3
agridat-1.11/agridat/man/piepho.cocksfoot.Rd |only
agridat-1.11/agridat/man/ratkowsky.onions.Rd | 96 +-
agridat-1.11/agridat/man/ridout.appleshoots.Rd | 6
agridat-1.11/agridat/man/rothamsted.brussels.Rd | 2
agridat-1.11/agridat/man/ryder.groundnut.Rd | 3
agridat-1.11/agridat/man/salmon.bunt.Rd | 42 -
agridat-1.11/agridat/man/senshu.rice.Rd | 2
agridat-1.11/agridat/man/shafii.rapeseed.Rd | 2
agridat-1.11/agridat/man/sinclair.clover.Rd | 2
agridat-1.11/agridat/man/smith.corn.uniformity.Rd | 2
agridat-1.11/agridat/man/snedecor.asparagus.Rd | 5
agridat-1.11/agridat/man/snijders.fusarium.Rd | 2
agridat-1.11/agridat/man/steel.soybean.Rd | 2
agridat-1.11/agridat/man/stephens.sorghum.uniformity.Rd | 2
agridat-1.11/agridat/man/steptoe.morex.pheno.Rd |only
agridat-1.11/agridat/man/stirret.borers.Rd | 10
agridat-1.11/agridat/man/streibig.competition.Rd | 2
agridat-1.11/agridat/man/stroup.nin.Rd | 2
agridat-1.11/agridat/man/stroup.splitplot.Rd | 3
agridat-1.11/agridat/man/student.barley.Rd | 2
agridat-1.11/agridat/man/talbot.potato.Rd | 34
agridat-1.11/agridat/man/theobald.barley.Rd | 1
agridat-1.11/agridat/man/theobald.covariate.Rd | 1
agridat-1.11/agridat/man/thompson.cornsoy.Rd | 3
agridat-1.11/agridat/man/turner.herbicide.Rd | 15
agridat-1.11/agridat/man/vargas.txe.Rd | 2
agridat-1.11/agridat/man/vargas.wheat1.Rd | 79 +-
agridat-1.11/agridat/man/vargas.wheat2.Rd | 1
agridat-1.11/agridat/man/verbyla.lupin.Rd | 20
agridat-1.11/agridat/man/vold.longterm.Rd | 18
agridat-1.11/agridat/man/vsn.lupin3.Rd | 3
agridat-1.11/agridat/man/wallace.iowaland.Rd | 17
agridat-1.11/agridat/man/walsh.cottonprice.Rd | 2
agridat-1.11/agridat/man/wassom.brome1.uniformity.Rd | 1
agridat-1.11/agridat/man/waynick.soil.Rd | 2
agridat-1.11/agridat/man/wedderburn.barley.Rd | 1
agridat-1.11/agridat/man/weiss.incblock.Rd | 21
agridat-1.11/agridat/man/weiss.lattice.Rd | 1
agridat-1.11/agridat/man/welch.bermudagrass.Rd | 16
agridat-1.11/agridat/man/wiebe.wheat.uniformity.Rd | 2
agridat-1.11/agridat/man/williams.barley.uniformity.Rd | 3
agridat-1.11/agridat/man/williams.cotton.uniformity.Rd | 3
agridat-1.11/agridat/man/williams.trees.Rd | 3
agridat-1.11/agridat/man/yan.winterwheat.Rd | 1
agridat-1.11/agridat/man/yang.barley.Rd | 4
agridat-1.11/agridat/man/yates.missing.Rd | 4
agridat-1.11/agridat/man/yates.oats.Rd | 15
agridat-1.11/agridat/man/zuidhof.broiler.Rd | 3
agridat-1.11/agridat/vignettes/agridat_examples.Rnw | 6
213 files changed, 1659 insertions(+), 1060 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 1.3 dated 2015-01-06 and 1.5-0 dated 2015-03-03
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch
sirt-1.3/sirt/R/lllsa.R |only
sirt-1.3/sirt/R/rm.facets.IC.R |only
sirt-1.5-0/sirt/DESCRIPTION | 18 +-
sirt-1.5-0/sirt/MD5 | 209 ++++++++++++------------
sirt-1.5-0/sirt/NAMESPACE | 6
sirt-1.5-0/sirt/R/IRT.irfprob.sirt.R | 3
sirt-1.5-0/sirt/R/IRT.likelihood_sirt.R | 3
sirt-1.5-0/sirt/R/IRT.posterior_sirt.R | 4
sirt-1.5-0/sirt/R/anova_sirt.R | 4
sirt-1.5-0/sirt/R/detect.R | 4
sirt-1.5-0/sirt/R/dif.logisticregression.R | 3
sirt-1.5-0/sirt/R/dif.variance.R | 9 -
sirt-1.5-0/sirt/R/logLik_sirt.R | 3
sirt-1.5-0/sirt/R/pcm.fit.R | 5
sirt-1.5-0/sirt/R/plot.rm.sdt.R |only
sirt-1.5-0/sirt/R/prob.guttman.R | 20 --
sirt-1.5-0/sirt/R/rasch.conquest.R | 4
sirt-1.5-0/sirt/R/rasch.mml.raschtype.R | 53 ++----
sirt-1.5-0/sirt/R/rasch.mml2.R | 128 +++++++++++---
sirt-1.5-0/sirt/R/rasch.mml2.missing1.R | 28 ++-
sirt-1.5-0/sirt/R/rm.hrm.calcprobs.R |only
sirt-1.5-0/sirt/R/rm.hrm.est.tau.item.R |only
sirt-1.5-0/sirt/R/rm.sdt.R | 184 ++++++++++++++++-----
sirt-1.5-0/sirt/R/rm.sdt_alg.R | 130 ++------------
sirt-1.5-0/sirt/R/rm.smooth.distribution.R | 9 -
sirt-1.5-0/sirt/R/summary.rasch.mml2.R | 4
sirt-1.5-0/sirt/R/summary.rm.sdt.R | 19 +-
sirt-1.5-0/sirt/data/data.activity.itempars.rda |binary
sirt-1.5-0/sirt/data/data.big5.qgraph.rda |binary
sirt-1.5-0/sirt/data/data.big5.rda |binary
sirt-1.5-0/sirt/data/data.bs07a.rda |only
sirt-1.5-0/sirt/data/data.eid.rda |binary
sirt-1.5-0/sirt/data/data.ess2005.rda |binary
sirt-1.5-0/sirt/data/data.g308.rda |binary
sirt-1.5-0/sirt/data/data.inv4gr.rda |binary
sirt-1.5-0/sirt/data/data.liking.science.rda |binary
sirt-1.5-0/sirt/data/data.long.rda |binary
sirt-1.5-0/sirt/data/data.math.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.LSAT6.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.act15.rda |binary
sirt-1.5-0/sirt/data/data.mcdonald.rape.rda |binary
sirt-1.5-0/sirt/data/data.mixed1.rda |binary
sirt-1.5-0/sirt/data/data.ml1.rda |binary
sirt-1.5-0/sirt/data/data.ml2.rda |binary
sirt-1.5-0/sirt/data/data.noharm18.rda |binary
sirt-1.5-0/sirt/data/data.noharmExC.rda |binary
sirt-1.5-0/sirt/data/data.pars1.2pl.rda |binary
sirt-1.5-0/sirt/data/data.pars1.rasch.rda |binary
sirt-1.5-0/sirt/data/data.pirlsmissing.rda |binary
sirt-1.5-0/sirt/data/data.pisaMath.rda |binary
sirt-1.5-0/sirt/data/data.pisaPars.rda |binary
sirt-1.5-0/sirt/data/data.pisaRead.rda |binary
sirt-1.5-0/sirt/data/data.ratings1.rda |binary
sirt-1.5-0/sirt/data/data.ratings2.rda |binary
sirt-1.5-0/sirt/data/data.ratings3.rda |binary
sirt-1.5-0/sirt/data/data.raw1.rda |binary
sirt-1.5-0/sirt/data/data.read.rda |binary
sirt-1.5-0/sirt/data/data.reck21.rda |binary
sirt-1.5-0/sirt/data/data.reck61DAT1.rda |binary
sirt-1.5-0/sirt/data/data.reck61DAT2.rda |binary
sirt-1.5-0/sirt/data/data.reck73C1a.rda |binary
sirt-1.5-0/sirt/data/data.reck73C1b.rda |binary
sirt-1.5-0/sirt/data/data.reck75C2.rda |binary
sirt-1.5-0/sirt/data/data.reck78ExA.rda |binary
sirt-1.5-0/sirt/data/data.reck79ExB.rda |binary
sirt-1.5-0/sirt/data/data.si01.rda |binary
sirt-1.5-0/sirt/data/data.si02.rda |binary
sirt-1.5-0/sirt/data/data.si03.rda |binary
sirt-1.5-0/sirt/data/data.si04.rda |binary
sirt-1.5-0/sirt/data/data.si05.rda |binary
sirt-1.5-0/sirt/data/data.si06.rda |binary
sirt-1.5-0/sirt/data/data.timss.rda |binary
sirt-1.5-0/sirt/data/data.timss07.G8.RUS.rda |binary
sirt-1.5-0/sirt/inst/NEWS | 169 ++++++++++++-------
sirt-1.5-0/sirt/man/R2conquest.Rd | 32 ++-
sirt-1.5-0/sirt/man/R2noharm.Rd | 5
sirt-1.5-0/sirt/man/data.big5.Rd | 15 -
sirt-1.5-0/sirt/man/data.bs.Rd |only
sirt-1.5-0/sirt/man/data.eid.Rd | 28 ++-
sirt-1.5-0/sirt/man/data.ess2005.Rd | 8
sirt-1.5-0/sirt/man/data.g308.Rd | 3
sirt-1.5-0/sirt/man/data.inv4gr.Rd | 3
sirt-1.5-0/sirt/man/data.liking.science.Rd | 3
sirt-1.5-0/sirt/man/data.long.Rd | 5
sirt-1.5-0/sirt/man/data.math.Rd | 6
sirt-1.5-0/sirt/man/data.mixed1.Rd | 4
sirt-1.5-0/sirt/man/data.ml.Rd | 13 -
sirt-1.5-0/sirt/man/data.noharm.Rd | 13 -
sirt-1.5-0/sirt/man/data.pars1.rasch.Rd | 13 -
sirt-1.5-0/sirt/man/data.pirlsmissing.Rd | 5
sirt-1.5-0/sirt/man/data.pisaMath.Rd | 4
sirt-1.5-0/sirt/man/data.pisaPars.Rd | 5
sirt-1.5-0/sirt/man/data.pisaRead.Rd | 7
sirt-1.5-0/sirt/man/data.ratings1.Rd | 23 --
sirt-1.5-0/sirt/man/data.raw1.Rd | 3
sirt-1.5-0/sirt/man/data.read.Rd | 85 ++++-----
sirt-1.5-0/sirt/man/data.si.Rd | 36 ----
sirt-1.5-0/sirt/man/data.timss.Rd | 5
sirt-1.5-0/sirt/man/invariance.alignment.Rd | 2
sirt-1.5-0/sirt/man/linking.haberman.Rd | 2
sirt-1.5-0/sirt/man/mirt.wrapper.Rd | 3
sirt-1.5-0/sirt/man/noharm.sirt.Rd | 2
sirt-1.5-0/sirt/man/prob.guttman.Rd | 24 ++
sirt-1.5-0/sirt/man/rasch.copula.Rd | 2
sirt-1.5-0/sirt/man/rasch.mirtlc.Rd | 5
sirt-1.5-0/sirt/man/rasch.mml.Rd | 47 ++++-
sirt-1.5-0/sirt/man/rm.sdt.Rd | 90 ++++++++--
sirt-1.5-0/sirt/man/sirt-package.Rd | 186 ++++++++++-----------
sirt-1.5-0/sirt/src/rm_smirt_mml2_code.cpp | 8
109 files changed, 929 insertions(+), 785 deletions(-)
Title: Entrez in R
Diff between rentrez versions 0.4 dated 2015-02-08 and 0.4.1 dated 2015-03-03
Description: Rentrez provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
NEWS | 6 ++++++
R/entrez_citmatch.r | 2 +-
inst/doc/rentrez_tutorial.html | 4 ++--
man/entrez_citmatch.Rd | 2 +-
6 files changed, 18 insertions(+), 12 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Diff between coda versions 0.16-1 dated 2012-11-06 and 0.17-1 dated 2015-03-03
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut]
Maintainer: Martyn Plummer
coda-0.16-1/coda/AUTHORS |only
coda-0.16-1/coda/misc |only
coda-0.17-1/coda/CHANGELOG | 23 ++++++++++++++++---
coda-0.17-1/coda/DESCRIPTION | 41 +++++++++++++++++++++-------------
coda-0.17-1/coda/MD5 | 26 +++++++++------------
coda-0.17-1/coda/NAMESPACE | 5 +++-
coda-0.17-1/coda/R/mcmc.R | 4 +--
coda-0.17-1/coda/R/mcmclist.R | 2 -
coda-0.17-1/coda/R/trellisplots.R | 2 -
coda-0.17-1/coda/R/util.R | 15 +++---------
coda-0.17-1/coda/data/line.rda |binary
coda-0.17-1/coda/inst/AUTHORS |only
coda-0.17-1/coda/man/effectiveSize.Rd | 7 +++--
coda-0.17-1/coda/man/mcmc.Rd | 3 +-
14 files changed, 75 insertions(+), 53 deletions(-)
Title: Plugin de R-Commander para el Manual 'EACSPIR'
Diff between RcmdrPlugin.EACSPIR versions 0.2-1 dated 2014-02-07 and 0.2-2 dated 2015-03-03
More information about RcmdrPlugin.EACSPIR at CRAN
Description: Este paquete proporciona una interfaz grafica de usuario (GUI) para algunos de los procedimientos estadisticos detallados en un curso de 'Estadistica aplicada a las Ciencias Sociales mediante el programa informatico R' (EACSPIR). LA GUI se ha desarrollado como un Plugin del programa R-Commander.
Author: Maribel Pero
Maintainer: David Leiva
DESCRIPTION | 12 +++++------
MD5 | 10 ++++-----
NAMESPACE | 2 -
R/RcmdrPlugin.EACSPIR.R | 31 ++++++++++++++++++++----------
inst/etc/menus.txt | 38 ++++++++++++++++++-------------------
man/RcmdrPlugin.EACSPIR-package.Rd | 4 +--
6 files changed, 54 insertions(+), 43 deletions(-)
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-10 0.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-30 1.7
2013-11-14 1.6
2013-02-12 1.5
2012-06-14 1.4
2012-04-25 1.3
2012-03-30 1.2
2012-03-27 1.1
2012-03-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-22 2.13
2012-01-05 2.10
2012-01-03 2.9
2010-07-30 2.7
2010-07-24 2.6
2010-02-05 2.4
2010-02-03 2.3
2008-10-09 2.2
2008-09-19 2.1
2008-06-27 1.3
2008-05-20 1.2
2007-11-20 1.1
2007-11-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-17 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-26 2.5.6
2013-05-18 2.5.3
2012-11-06 2.5.2
2012-10-29 2.5.1
2012-06-25 2.02
2012-06-04 2.00-3
2012-03-07 0.71
2012-02-16 0.66
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-29 1.2
2012-11-03 1.1
2012-01-12 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-21 0.1.0
2013-11-13 0.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-11 0.2.1
2014-11-29 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-31 1.0.3.2
2014-01-31 1.0.3.1
2014-01-04 1.0.2.0
2013-12-18 1.0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-30 0.5.3
2014-11-21 0.5.2
2014-09-04 0.4
Title: Color Space Manipulation
Diff between colorspace versions 1.2-4 dated 2013-09-30 and 1.2-5 dated 2015-03-03
Description: Carries out mapping between assorted color spaces including
RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),
CIELAB and polar CIELAB. Qualitative, sequential, and
diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut],
Paul Murrell [aut],
Kurt Hornik [aut],
Jason C. Fisher [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 11 ++++++-----
MD5 | 17 +++++++++--------
NAMESPACE | 1 +
NEWS | 5 +++++
R/choose_palette.R | 16 ++++++----------
build |only
data/USSouthPolygon.rda |binary
inst/doc/hcl-colors.pdf |binary
man/choose_palette.Rd | 6 ++++--
tests/Examples/colorspace-Ex.Rout.save | 11 ++++++++---
10 files changed, 39 insertions(+), 28 deletions(-)
Title: Toolkit to Identify Candidate Synthetic Lethality
Diff between BiSEp versions 2.0 dated 2014-10-25 and 2.0.1 dated 2015-03-03
Description: Enables the user to infer potential synthetic lethal relationships
by analysing relationships between bimodally distributed gene pairs in big
gene expression datasets. Enables the user to visualise these candidate
synthetic lethal relationships.
Author: Mark Wappett
Maintainer: Mark Wappett
DESCRIPTION | 20 ++++++++++++--------
MD5 | 20 ++++++++++----------
NAMESPACE | 3 +--
R/FURE.R | 6 +++---
build/vignette.rds |binary
data/BISEP_dat.RData |binary
data/BISEP_data.RData |binary
data/FURE_data.RData |binary
data/INPUT_data.RData |binary
data/MUT_data.RData |binary
inst/doc/BiSEp.pdf |binary
11 files changed, 26 insertions(+), 23 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-31 0.9.11
2014-10-28 0.9
2014-08-26 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-27 0.0.6
2014-04-25 0.0.5
2014-02-23 0.0.4
2014-01-05 0.0.3
2013-11-07 0.0.2
2013-09-25 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-09 1.0.1
2014-11-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-20 1.05
2013-08-02 1.04
2011-12-02 1.03
2010-11-29 1.02
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-10 0.1.1
2014-11-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-11 0.2-2
2013-12-10 0.2-1
2013-04-16 0.2-0
2012-10-08 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-11 1.4-3
2012-07-12 1.4-2
2012-06-27 1.4-1
2012-05-09 1.4
2012-02-04 1.3
2011-11-13 1.2
2011-09-21 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-17 0.3.7
2014-07-11 0.3.3
2014-05-17 0.3
Title: Simulation of Event Histories for Multi-State Models
Diff between simMSM versions 1.1.4 dated 2015-02-02 and 1.1.41 dated 2015-03-03
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions, and dependencies on the past of the history. Random generation of event histories is performed using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
DESCRIPTION | 10 ++---
MD5 | 4 +-
R/tolongformat.R | 106 +++++++++++++++++++++++++++----------------------------
3 files changed, 60 insertions(+), 60 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-08 0.7.2.125
2014-04-07 0.7.2.124
Title: eXtreme Gradient Boosting
Diff between xgboost versions 0.3-2 dated 2014-09-07 and 0.3-3 dated 2015-03-03
Description: Xgboost is short for eXtreme Gradient Boosting, which is an
efficient and scalable implementation of gradient boosting framework.
This package is an R wrapper of xgboost. The package includes efficient
linear model solver and tree learning algorithms. The package can automatically
do parallel computation with OpenMP, and it can be more than 10 times faster
than existing gradient boosting packages such as gbm. It supports various
objective functions, including regression, classification and ranking. The
package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen
Maintainer: Tong He
DESCRIPTION | 26 +-
MD5 | 194 +++++++++++++-------
NAMESPACE | 40 ++++
R/getinfo.xgb.DMatrix.R | 9
R/predict.xgb.Booster.R | 45 ++++
R/predict.xgb.Booster.handle.R |only
R/slice.xgb.DMatrix.R | 14 +
R/utils.R | 70 +++++--
R/xgb.DMatrix.R | 2
R/xgb.cv.R | 78 ++++++--
R/xgb.dump.R | 58 +++++-
R/xgb.importance.R |only
R/xgb.load.R | 8
R/xgb.model.dt.tree.R |only
R/xgb.plot.importance.R |only
R/xgb.plot.tree.R |only
R/xgb.save.R | 5
R/xgb.save.raw.R |only
R/xgb.train.R | 89 +++++++--
R/xgboost.R | 42 ++--
README.md | 3
build |only
data/agaricus.test.rda |binary
data/agaricus.train.rda |binary
demo/00Index | 2
demo/basic_walkthrough.R | 34 ++-
demo/boost_from_prediction.R | 2
demo/create_sparse_matrix.R |only
demo/cross_validation.R | 8
demo/custom_objective.R | 25 ++
demo/generalized_linear_model.R | 2
demo/predict_first_ntree.R | 2
demo/predict_leaf_indices.R |only
inst |only
man/agaricus.test.Rd | 7
man/agaricus.train.Rd | 5
man/getinfo.Rd | 7
man/predict-xgb.Booster-method.Rd | 14 +
man/predict-xgb.Booster.handle-method.Rd |only
man/setinfo.Rd | 7
man/slice.Rd | 7
man/xgb.DMatrix.Rd | 6
man/xgb.DMatrix.save.Rd | 3
man/xgb.cv.Rd | 23 +-
man/xgb.dump.Rd | 33 ++-
man/xgb.importance.Rd |only
man/xgb.load.Rd | 5
man/xgb.model.dt.tree.Rd |only
man/xgb.plot.importance.Rd |only
man/xgb.plot.tree.Rd |only
man/xgb.save.Rd | 5
man/xgb.save.raw.Rd |only
man/xgb.train.Rd | 86 ++++++--
man/xgboost.Rd | 33 ++-
src/Makevars | 6
src/Makevars.win | 4
src/src/data.h | 3
src/src/gbm/gblinear-inl.hpp | 42 +++-
src/src/gbm/gbm.cpp | 1
src/src/gbm/gbm.h | 54 +++++
src/src/gbm/gbtree-inl.hpp | 162 +++++++++++++++-
src/src/io/io.cpp | 51 +++++
src/src/io/page_dmatrix-inl.hpp |only
src/src/io/page_fmatrix-inl.hpp |only
src/src/io/simple_dmatrix-inl.hpp | 15 +
src/src/io/simple_fmatrix-inl.hpp | 27 +-
src/src/learner/evaluation-inl.hpp | 51 ++++-
src/src/learner/evaluation.h | 11 -
src/src/learner/learner-inl.hpp | 241 +++++++++++++++++++++----
src/src/learner/objective-inl.hpp | 30 ++-
src/src/sync |only
src/src/tree/model.h | 31 ++-
src/src/tree/param.h | 32 +++
src/src/tree/updater.cpp | 13 +
src/src/tree/updater.h | 10 +
src/src/tree/updater_basemaker-inl.hpp |only
src/src/tree/updater_colmaker-inl.hpp | 297 +++++++++++++++++++++++++------
src/src/tree/updater_distcol-inl.hpp |only
src/src/tree/updater_histmaker-inl.hpp |only
src/src/tree/updater_prune-inl.hpp | 6
src/src/tree/updater_refresh-inl.hpp | 93 +++++----
src/src/tree/updater_skmaker-inl.hpp |only
src/src/tree/updater_sync-inl.hpp |only
src/src/utils/base64.h |only
src/src/utils/bitmap.h |only
src/src/utils/group_data.h |only
src/src/utils/io.h | 110 ++++++++++-
src/src/utils/matrix_csr.h | 137 ++++++++++++++
src/src/utils/quantile.h |only
src/src/utils/thread.h |only
src/src/utils/thread_buffer.h |only
src/src/xgboost_main.cpp | 125 ++++++++++---
src/subtree |only
src/wrapper/xgboost_wrapper.cpp | 56 ++++-
src/wrapper/xgboost_wrapper.h | 38 +++
src/xgboost_R.cpp | 54 +++--
src/xgboost_R.h | 21 +-
vignettes/discoverYourData.Rmd |only
vignettes/vignette.css |only
vignettes/xgboost.Rnw | 7
vignettes/xgboostPresentation.Rmd |only
101 files changed, 2196 insertions(+), 531 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Diff between Rssa versions 0.11 dated 2014-02-05 and 0.13 dated 2015-03-03
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov
DESCRIPTION | 14 -
MD5 | 91 +++++-----
NAMESPACE | 50 +++--
R/autossa.R |only
R/cadzow.R | 20 +-
R/chankel.R | 10 -
R/common.R | 38 ++--
R/forecast.R | 65 +++++--
R/gapfill.R |only
R/hankel.R | 165 ++++++++++++++++--
R/hbhankel.R | 119 ++++++++-----
R/igapfill.R | 190 ++++++++++++++++++---
R/mhankel.R | 28 +--
R/ossa.R | 193 +++++++++++++++-------
R/parest.R | 140 ++++++++++++++-
R/plot.R | 96 ++++++----
R/plot2.R | 71 +++++---
R/plotn.R |only
R/pssa.R | 62 +++++--
R/ssa.R | 207 ++++++++++++++++-------
R/toeplitz.R | 42 +++-
R/wcor.R | 138 +++++----------
data/Barbara.rda |only
inst/CITATION | 5
man/Barbara.rd |only
man/autossa.Rd |only
man/cadzow.Rd | 5
man/calcv.Rd | 4
man/clplot.Rd |only
man/clusterify.Rd | 37 +---
man/decompose.Rd | 4
man/fossa.Rd | 18 +-
man/gapfill.Rd |only
man/grouping.auto.Rd |only
man/hankel.Rd | 11 +
man/igapfill.Rd |only
man/iossa.Rd | 57 +++++-
man/lrr.Rd | 11 -
man/parest.Rd | 11 +
man/plot.Rd | 25 ++
man/plot.reconstruct.Rd | 35 +++
man/rforecast.Rd | 16 +
man/ssa-data.Rd | 11 +
man/ssa.Rd | 33 +++
man/summarize.gaps.Rd |only
man/vforecast.Rd | 3
man/wcor.Rd | 29 +--
man/wnorm.Rd | 6
src/fft_plan.h | 4
src/hankel.c | 224 +++++++++++++++++++------
src/hbhankel.c | 421 ++++++++++++++++++++++++++++++------------------
src/masks.c |only
src/masks.h |only
53 files changed, 1916 insertions(+), 793 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Diff between mgcv versions 1.8-4 dated 2014-11-27 and 1.8-5 dated 2015-03-03
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood
Maintainer: Simon Wood
ChangeLog | 42 +
DESCRIPTION | 17
MD5 | 109 ++--
NAMESPACE | 2
R/bam.r | 42 +
R/efam.r | 92 ++-
R/fast-REML.r | 2
R/gam.fit3.r | 13
R/gam.fit4.r | 26 -
R/gamlss.r | 16
R/gamm.r | 38 +
R/jagam.r | 14
R/mgcv.r | 43 +
R/misc.r | 7
R/mvam.r | 2
R/plots.r | 10
R/smooth.r | 26 -
R/soap.r | 4
R/sparse.r | 6
inst/po |only
man/Beta.Rd | 12
man/gam.Rd | 5
man/jagam.Rd | 4
man/mgcv-parallel.Rd | 17
man/plot.gam.Rd | 4
man/predict.bam.Rd | 3
man/single.index.Rd |only
man/vis.gam.Rd | 2
man/ziplss.Rd | 2
po/R-de.po | 1213 ++++++++++++++++++++++++++++++++++++++++----------
po/R-fr.po | 1223 ++++++++++++++++++++++++++++++++++++++++-----------
po/R-ko.po |only
po/R-mgcv.pot | 61 ++
po/R-pl.po | 688 ++++++++++++++++++++--------
po/R-po.po | 1150 ++++++++++++++++++++++++++++++++++++++---------
po/de.po | 128 -----
po/fr.po | 135 -----
po/ko.po |only
po/mgcv.pot | 116 ----
po/pl.po | 127 -----
po/po.po | 131 -----
src/coxph.c | 10
src/gdi.c | 54 +-
src/general.h | 21
src/init.c | 1
src/magic.c | 9
src/mat.c | 200 ++++++--
src/matrix.c | 35 -
src/mgcv.c | 8
src/mgcv.h | 20
src/qp.c | 5
src/tprs.c | 47 -
52 files changed, 4130 insertions(+), 1812 deletions(-)
Title: Random Fields (and Bridges) Simulations
Diff between FieldSim versions 3.1.3 dated 2010-07-30 and 3.2.1 dated 2015-03-03
Description: Tools for random fields and bridges simulations.
Author: Alexandre Brouste
Maintainer: Alexandre Brouste
FieldSim-3.1.3/FieldSim/R/AllClasses.R |only
FieldSim-3.1.3/FieldSim/R/constructcovf.R |only
FieldSim-3.1.3/FieldSim/R/constructgrid.R |only
FieldSim-3.1.3/FieldSim/inst |only
FieldSim-3.1.3/FieldSim/man/constructcovf.Rd |only
FieldSim-3.1.3/FieldSim/man/constructgrid.Rd |only
FieldSim-3.1.3/FieldSim/man/visualize.Rd |only
FieldSim-3.2.1/FieldSim/COPYING | 2
FieldSim-3.2.1/FieldSim/DESCRIPTION | 23 -
FieldSim-3.2.1/FieldSim/MD5 |only
FieldSim-3.2.1/FieldSim/NAMESPACE | 24 -
FieldSim-3.2.1/FieldSim/R/C2D.R | 30 --
FieldSim-3.2.1/FieldSim/R/fieldsim.R | 96 ++++---
FieldSim-3.2.1/FieldSim/R/global.R |only
FieldSim-3.2.1/FieldSim/R/locquadvar.R |only
FieldSim-3.2.1/FieldSim/R/manifold.R | 350 +++++++++++++++++---------
FieldSim-3.2.1/FieldSim/R/midpoint.R |only
FieldSim-3.2.1/FieldSim/R/process.R |only
FieldSim-3.2.1/FieldSim/R/quadvar.R | 98 ++++---
FieldSim-3.2.1/FieldSim/R/quadvaraux.R |only
FieldSim-3.2.1/FieldSim/R/setAtlas_under.R |only
FieldSim-3.2.1/FieldSim/R/setCovf_under.R |only
FieldSim-3.2.1/FieldSim/R/visualize.R | 63 ++--
FieldSim-3.2.1/FieldSim/man/fieldsim.Rd | 64 ++--
FieldSim-3.2.1/FieldSim/man/manifold-class.Rd | 13
FieldSim-3.2.1/FieldSim/man/midpoint.Rd |only
FieldSim-3.2.1/FieldSim/man/plot-methods.Rd |only
FieldSim-3.2.1/FieldSim/man/plot.Rd |only
FieldSim-3.2.1/FieldSim/man/process-class.Rd |only
FieldSim-3.2.1/FieldSim/man/process-method.Rd |only
FieldSim-3.2.1/FieldSim/man/quadvar.Rd | 31 +-
FieldSim-3.2.1/FieldSim/man/setAtlas.Rd |only
FieldSim-3.2.1/FieldSim/man/setManifold.Rd | 33 +-
FieldSim-3.2.1/FieldSim/man/setProcess.Rd |only
FieldSim-3.2.1/FieldSim/man/setValues.Rd |only
FieldSim-3.2.1/FieldSim/man/show-methods.Rd |only
36 files changed, 506 insertions(+), 321 deletions(-)
Title: Import SPSS, Stata and SAS Files
Diff between haven versions 0.1.0 dated 2015-03-01 and 0.1.1 dated 2015-03-03
Description: Import foreign statistical formats into R via the embedded
ReadStat C library (https://github.com/WizardMac/ReadStat). Package includes
preliminary support for writing Stata and SPSS formats.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph]
Maintainer: Hadley Wickham
DESCRIPTION | 12 +++++------
MD5 | 10 ++++-----
inst/doc/datetimes.html | 4 +--
src/readstat.h | 2 -
src/readstat_dta_write.c | 16 +++++++--------
src/readstat_sav_write.c | 49 +++++++++++++++++++++++++++++++----------------
6 files changed, 55 insertions(+), 38 deletions(-)
Title: Biological Structure Analysis
Diff between bio3d versions 2.2-1 dated 2015-02-27 and 2.2-2 dated 2015-03-03
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/atom.select.pdb.R | 17 ++++++++++-------
man/bio3d.package.Rd | 4 ++--
tests/testthat/test-atom.select.R | 13 ++++++++++++-
5 files changed, 31 insertions(+), 17 deletions(-)