Title: Acoustic template detection in R
Diff between monitoR versions 1.0 dated 2014-03-27 and 1.0.1 dated 2014-03-31
Description: Acoustic template detection and monitoring database interface.
Author: Sasha D. Hafner
Maintainer: Sasha D. Hafner
ChangeLog |only
DESCRIPTION | 11 +++----
MD5 | 55 +++++++++++++++++++++------------------
NAMESPACE | 1
R/Classes.R | 54 +++++++++++++++++---------------------
R/Methods-plot.R | 5 ---
R/binMatch.R | 3 --
R/bindEvents.R | 3 --
R/changeSampRate.R | 4 --
R/collapseClips.R | 5 ---
R/corMatch.R | 3 --
R/dBweight.R |only
R/fileCopyRename.R | 4 --
R/getDetections.R | 4 +-
R/makeBinTemplate.R | 5 ---
R/makeCorTemplate.R | 6 ----
R/mp3Subsamp.R | 3 --
R/readMP3.R | 3 --
R/stft.R |only
R/timeAlign.R | 3 --
R/viewSpec.R | 5 ---
R/windows.R |only
inst/CITATION |only
inst/doc/monitoR_QuickStart.R | 4 ++
inst/doc/monitoR_QuickStart.Rnw | 15 +++++++---
inst/doc/monitoR_QuickStart.pdf |binary
man/findPeaks.Rd | 2 -
man/internals.Rd | 18 ++++++++++++
man/monitoR-package.Rd | 7 ++--
man/templateMatching.Rd | 8 ++---
vignettes/monitoR_QuickStart.Rnw | 15 +++++++---
31 files changed, 125 insertions(+), 121 deletions(-)
Title: The Analysis of Biological Data
Diff between abd versions 0.2-5 dated 2013-04-02 and 0.2-6 dated 2014-03-31
Description: The abd package contains data sets and sample code for The
Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009;
Roberts & Company Publishers). Some examples utilize the manipulate package,
which is available within RStudio (http://www.rstudio.com).
Author: Kevin M. Middleton
Maintainer: Kevin M. Middleton
DESCRIPTION | 17 +-
MD5 | 298 ++++++++++++++++++++---------------------
NAMESPACE | 3
R/datasets.R | 4
data/AlgaeCO2.rda |binary
data/Antilles.rda |binary
data/Aspirin.rda |binary
data/BeeGenes.rda |binary
data/BeeLifespans.rda |binary
data/Beetles.rda |binary
data/BirdSexRatio.rda |binary
data/Blackbirds.rda |binary
data/BodyFatHeatLoss.rda |binary
data/BrainExpression.rda |binary
data/BrookTrout.rda |binary
data/BrookTrout2.rda |binary
data/Cavalry.rda |binary
data/Chickadees.rda |binary
data/ChimpBrains.rda |binary
data/Cichlids.rda |binary
data/CichlidsGnRH.rda |binary
data/Clearcuts.rda |binary
data/CocaineDopamine.rda |binary
data/Convictions.rda |binary
data/ConvictionsAndIncome.rda |binary
data/Crickets.rda |binary
data/DEET.rda |binary
data/DaphniaLongevity.rda |binary
data/DaphniaResistance.rda |binary
data/DayOfBirth.rda |binary
data/DesertBirds.rda |binary
data/Dioecy.rda |binary
data/Dolphins.rda |binary
data/DungBeetles.rda |binary
data/Earthworms.rda |binary
data/Earwigs.rda |binary
data/Eelgrass.rda |binary
data/ElVerde.rda |binary
data/ElectricFish.rda |binary
data/EndangeredSpecies.rda |binary
data/FingerRatio.rda |binary
data/Fireflies.rda |binary
data/FireflyFlash.rda |binary
data/FlyTestes.rda |binary
data/FlycatcherPatch.rda |binary
data/GeneRegulation.rda |binary
data/GlidingSnakes.rda |binary
data/GodwitArrival.rda |binary
data/Grassland.rda |binary
data/GreatTitMalaria.rda |binary
data/Greenspace.rda |binary
data/Guppies.rda |binary
data/Hemoglobin.rda |binary
data/HippocampusLesions.rda |binary
data/HornedLizards.rda |binary
data/HumanBodyTemp.rda |binary
data/HumanGeneLengths.rda |binary
data/Hurricanes.rda |binary
data/Iguanas.rda |binary
data/IntertidalAlgae.rda |binary
data/JetLagKnees.rda |binary
data/KenyaFinches.rda |binary
data/LanguageBrains.rda |binary
data/LarvalFish.rda |binary
data/Lefthanded.rda |binary
data/LionCubs.rda |binary
data/LionNoses.rda |binary
data/LiverPreparation.rda |binary
data/LizardBite.rda |binary
data/LizardSprint.rda |binary
data/Lobsters.rda |binary
data/LodgepolePines.rda |binary
data/LupusMice.rda |binary
data/Lynx.rda |binary
data/MarineReserve.rda |binary
data/MassExtinctions.rda |binary
data/MoleRats.rda |binary
data/Mosquitoes.rda |binary
data/MouseEmpathy.rda |binary
data/NeanderthalBrains.rda |binary
data/NematodeLifespan.rda |binary
data/NeotropicalTrees.rda |binary
data/Newts.rda |binary
data/NoSmokingDay.rda |binary
data/NorthSeaCod.rda |binary
data/OstrichTemp.rda |binary
data/Penguins.rda |binary
data/PlantPersistence.rda |binary
data/Pollen.rda |binary
data/Powerball.rda |binary
data/PrimateMetabolism.rda |binary
data/PrimateWBC.rda |binary
data/ProgesteroneExercise.rda |binary
data/Pseudoscorpions.rda |binary
data/Pufferfish.rda |binary
data/Rattlesnakes.rda |binary
data/Rigormortis.rda |binary
data/RopeTrick.rda |binary
data/SagebrushCrickets.rda |binary
data/SalmonColor.rda |binary
data/Seedlings.rda |binary
data/Selection.rda |binary
data/SexualSelection.rda |binary
data/ShadParasites.rda |binary
data/ShrinkingSeals.rda |binary
data/ShuttleDisaster.rda |binary
data/Silversword.rda |binary
data/SleepAndPerformance.rda |binary
data/SockeyeFemales.rda |binary
data/Sparrows.rda |binary
data/SpiderColonies.rda |binary
data/SpiderSpeed.rda |binary
data/Stalkies1.rda |binary
data/Stalkies2.rda |binary
data/SticklebackPlates.rda |binary
data/SticklebackPreference.rda |binary
data/Sumo.rda |binary
data/SyrupSwimming.rda |binary
data/TeenDeaths.rda |binary
data/Telomeres.rda |binary
data/TimeOfDeath.rda |binary
data/Toads.rda |binary
data/Tobacco.rda |binary
data/Tobacco2.rda |binary
data/ToothAge.rda |binary
data/TreeSeedlings.rda |binary
data/Trematodes.rda |binary
data/Trillium.rda |binary
data/Truffles.rda |binary
data/TsetseLearning.rda |binary
data/TwoKids.rda |binary
data/VampireBites.rda |binary
data/VasopressinVoles.rda |binary
data/Vines.rda |binary
data/VoleDispersal.rda |binary
data/WalkingStickFemurs.rda |binary
data/WalkingStickHeads.rda |binary
data/WeddellSeals.rda |binary
data/WillsDebates.rda |binary
data/WillsPresidents.rda |binary
data/WolfTeeth.rda |binary
data/Wolves.rda |binary
data/WorldCup.rda |binary
data/WrasseSexes.rda |binary
data/YeastGenes.rda |binary
data/ZebraFinchBeaks.rda |binary
data/ZebraFinches.rda |binary
data/ZooMortality.rda |binary
data/Zooplankton.rda |binary
data/dataInfo.rda |binary
150 files changed, 163 insertions(+), 159 deletions(-)
Title: Simulating from the Polya posterior
Diff between polyapost versions 1.1-2 dated 2012-03-21 and 1.1-5 dated 2014-03-31
Description: Generate dependent samples from a non-full dimensional
polytope via a Markov Chain sampler
Author: Glen Meeden
Maintainer: Glen Meeden
polyapost-1.1-2/polyapost/inst/doc/Makefile |only
polyapost-1.1-2/polyapost/inst/doc/pp1.tex |only
polyapost-1.1-2/polyapost/inst/doc/ref.bib |only
polyapost-1.1-5/polyapost/DESCRIPTION | 9 +++++----
polyapost-1.1-5/polyapost/MD5 | 9 +++++----
polyapost-1.1-5/polyapost/build |only
polyapost-1.1-5/polyapost/inst/doc/pp1.R |only
polyapost-1.1-5/polyapost/vignettes |only
8 files changed, 10 insertions(+), 8 deletions(-)
Title: Multivariate and univariate meta-analysis and meta-regression
Diff between mvmeta versions 0.3.5 dated 2013-12-11 and 0.4.2 dated 2014-03-31
Description: The package mvmeta consists of a collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression in R.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini
mvmeta-0.3.5/mvmeta/R/internal.R |only
mvmeta-0.3.5/mvmeta/R/mvmeta.igls.R |only
mvmeta-0.3.5/mvmeta/R/mvmeta.ml.fn.R |only
mvmeta-0.3.5/mvmeta/R/mvmeta.ml.gr.R |only
mvmeta-0.3.5/mvmeta/R/mvmeta.reml.fn.R |only
mvmeta-0.3.5/mvmeta/R/mvmeta.reml.gr.R |only
mvmeta-0.3.5/mvmeta/inst/changeLog |only
mvmeta-0.3.5/mvmeta/man/mvmeta.ml.fn.Rd |only
mvmeta-0.4.2/mvmeta/DESCRIPTION | 10
mvmeta-0.4.2/mvmeta/MD5 | 133 ++++--
mvmeta-0.4.2/mvmeta/NAMESPACE | 27 -
mvmeta-0.4.2/mvmeta/R/blup.R | 4
mvmeta-0.4.2/mvmeta/R/blup.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/checkPD.R |only
mvmeta-0.4.2/mvmeta/R/coef.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/extractAIC.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/fbtr.R |only
mvmeta-0.4.2/mvmeta/R/glsfit.R |only
mvmeta-0.4.2/mvmeta/R/gradchol.ml.R |only
mvmeta-0.4.2/mvmeta/R/gradchol.reml.R |only
mvmeta-0.4.2/mvmeta/R/initpar.R |only
mvmeta-0.4.2/mvmeta/R/inputcov.R |only
mvmeta-0.4.2/mvmeta/R/iter.igls.R |only
mvmeta-0.4.2/mvmeta/R/logLik.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/mkS.R |only
mvmeta-0.4.2/mvmeta/R/mlfull.fn.R |only
mvmeta-0.4.2/mvmeta/R/mlprof.fn.R |only
mvmeta-0.4.2/mvmeta/R/mlprof.gr.R |only
mvmeta-0.4.2/mvmeta/R/model.frame.mvmeta.R | 4
mvmeta-0.4.2/mvmeta/R/model.matrix.mvmeta.R | 4
mvmeta-0.4.2/mvmeta/R/mvSim.R |only
mvmeta-0.4.2/mvmeta/R/mvmeta.R | 33 +
mvmeta-0.4.2/mvmeta/R/mvmeta.control.R | 18
mvmeta-0.4.2/mvmeta/R/mvmeta.fit.R | 34 +
mvmeta-0.4.2/mvmeta/R/mvmeta.fixed.R | 15
mvmeta-0.4.2/mvmeta/R/mvmeta.ml.R | 91 ++--
mvmeta-0.4.2/mvmeta/R/mvmeta.mm.R | 28 -
mvmeta-0.4.2/mvmeta/R/mvmeta.reml.R | 91 ++--
mvmeta-0.4.2/mvmeta/R/mvmeta.vc.R | 181 ++++-----
mvmeta-0.4.2/mvmeta/R/mvmetaSim.R | 35 -
mvmeta-0.4.2/mvmeta/R/na.exclude.data.frame.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/na.omit.data.frame.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/nobs.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/onAttach.R |only
mvmeta-0.4.2/mvmeta/R/par2Psi.R |only
mvmeta-0.4.2/mvmeta/R/predict.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/print.mvmeta.R | 70 +--
mvmeta-0.4.2/mvmeta/R/print.qtest.mvmeta.R | 12
mvmeta-0.4.2/mvmeta/R/print.summary.mvmeta.R | 250 ++++++-------
mvmeta-0.4.2/mvmeta/R/qtest.R | 4
mvmeta-0.4.2/mvmeta/R/qtest.mvmeta.R | 25 -
mvmeta-0.4.2/mvmeta/R/remlfull.fn.R |only
mvmeta-0.4.2/mvmeta/R/remlprof.fn.R |only
mvmeta-0.4.2/mvmeta/R/remlprof.gr.R |only
mvmeta-0.4.2/mvmeta/R/simulate.mvmeta.R | 8
mvmeta-0.4.2/mvmeta/R/sumlist.R |only
mvmeta-0.4.2/mvmeta/R/summary.mvmeta.R | 132 +++---
mvmeta-0.4.2/mvmeta/R/vcov.mvmeta.R | 6
mvmeta-0.4.2/mvmeta/R/vechMat.R | 9
mvmeta-0.4.2/mvmeta/R/xpndMat.R | 7
mvmeta-0.4.2/mvmeta/data/fibrinogen.rda |only
mvmeta-0.4.2/mvmeta/data/hsls.rda |only
mvmeta-0.4.2/mvmeta/data/hyp.rda |only
mvmeta-0.4.2/mvmeta/data/p53.rda |only
mvmeta-0.4.2/mvmeta/data/smoking.rda |only
mvmeta-0.4.2/mvmeta/inst/ChangeLog |only
mvmeta-0.4.2/mvmeta/man/berkey98.Rd | 103 ++---
mvmeta-0.4.2/mvmeta/man/fibrinogen.Rd |only
mvmeta-0.4.2/mvmeta/man/hsls.Rd |only
mvmeta-0.4.2/mvmeta/man/hyp.Rd |only
mvmeta-0.4.2/mvmeta/man/inputcov.Rd |only
mvmeta-0.4.2/mvmeta/man/logLik.mvmeta.Rd | 1
mvmeta-0.4.2/mvmeta/man/mlprof.fn.Rd |only
mvmeta-0.4.2/mvmeta/man/model.frame.mvmeta.Rd | 8
mvmeta-0.4.2/mvmeta/man/mvmeta-package.Rd | 16
mvmeta-0.4.2/mvmeta/man/mvmeta.Rd | 364 ++++++++++---------
mvmeta-0.4.2/mvmeta/man/mvmeta.control.Rd | 126 +++---
mvmeta-0.4.2/mvmeta/man/mvmeta.fixed.Rd | 155 ++++----
mvmeta-0.4.2/mvmeta/man/mvmeta.ml.Rd | 186 +++++----
mvmeta-0.4.2/mvmeta/man/mvmeta.mm.Rd | 161 ++++----
mvmeta-0.4.2/mvmeta/man/mvmeta.vc.Rd | 183 ++++-----
mvmeta-0.4.2/mvmeta/man/mvmetaCovStruct.Rd |only
mvmeta-0.4.2/mvmeta/man/mvmetaObject.Rd | 12
mvmeta-0.4.2/mvmeta/man/mvmetaSim.Rd | 21 -
mvmeta-0.4.2/mvmeta/man/p53.Rd |only
mvmeta-0.4.2/mvmeta/man/qtest.mvmeta.Rd | 4
mvmeta-0.4.2/mvmeta/man/smoking.Rd |only
mvmeta-0.4.2/mvmeta/man/vechMat.Rd | 13
88 files changed, 1388 insertions(+), 1244 deletions(-)
Title: Treemap visualization
Diff between treemap versions 2.1-1 dated 2013-12-05 and 2.2 dated 2014-03-31
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes
DESCRIPTION | 20 +-----
MD5 | 48 ++++++++-------
NAMESPACE | 5 +
NEWS | 5 +
R/createRec.R | 4 -
R/datasets.R | 4 -
R/itreemap.R | 88 +++++++++++++++++-----------
R/pkg.R | 6 -
R/random_hierarchical_data.R |only
R/tmDrawRect.R | 7 +-
R/tmPlot.R | 2
R/tmSetHCLoptions.R | 2
R/treecolors.R |only
R/treefunctions.R | 14 ++--
R/treegraph.R | 53 ++++++++++++-----
R/treemap.R | 23 ++++---
R/treepalette.R | 16 +++--
man/GNI2010.Rd | 10 +--
man/business.Rd | 25 +++-----
man/itreemap.Rd | 21 +++---
man/random.hierarchical.data.Rd |only
man/tmPlot.Rd | 6 -
man/treecolors.Rd |only
man/treegraph.Rd | 77 ++++++++++++++++++++-----
man/treemap-package.Rd | 23 ++++---
man/treemap.Rd | 122 ++++++++++++++++++++--------------------
man/treepalette.Rd | 38 ++++++------
27 files changed, 371 insertions(+), 248 deletions(-)
Title: Sparse and Regularized Discriminant Analysis
Diff between sparsediscrim versions 0.1.0 dated 2013-05-25 and 0.2 dated 2014-03-31
Description: A collection of sparse and regularized discriminant analysis
methods intended for small-sample, high-dimensional data sets. The package
features the High-Dimensional Regularized Discriminant Analysis classifier.
Author: John A. Ramey
Maintainer: John A. Ramey
DESCRIPTION | 26 +----
LICENSE |only
MD5 | 114 ++++++++++++++--------
NAMESPACE | 43 ++++++++
NEWS | 41 +++++++
R/dlda.r | 15 --
R/dqda.r | 15 --
R/estimates.r | 2
R/hdrda.r | 200 +++++++++++++++++++++++++++++----------
R/helper-cov.r | 3
R/helper.r | 16 +++
R/lda-pseudo.r |only
R/lda-schafer.r |only
R/lda-thomaz.r |only
R/mdeb.r |only
R/mdmeb.r |only
R/mdmp.r |only
R/sdlda.r | 18 +--
R/sdqda.r | 17 +--
R/smdlda.r |only
R/smdqda.r |only
README.md | 34 ++++--
inst |only
man/center_data.Rd | 10 -
man/cov_autocorrelation.Rd | 23 ++--
man/cov_block_autocorrelation.Rd | 46 ++++----
man/cov_eigen.Rd | 31 ++----
man/cov_intraclass.Rd | 32 +++---
man/cov_list.Rd | 12 +-
man/cov_mle.Rd | 22 ++--
man/cov_pool.Rd | 12 +-
man/cov_shrink_diag.Rd | 45 ++++----
man/cv_partition.Rd | 35 +++---
man/diag_estimates.Rd | 77 +++++++--------
man/dlda.Rd | 138 ++++++++++++--------------
man/dqda.Rd | 139 ++++++++++++---------------
man/generate_blockdiag.Rd | 66 ++++++------
man/generate_intraclass.Rd | 63 +++++-------
man/h.Rd | 16 +--
man/hdrda.Rd | 150 ++++++++++++++++-------------
man/hdrda_cv.Rd | 24 ++--
man/lda_pseudo.Rd |only
man/lda_schafer.Rd |only
man/lda_thomaz.Rd |only
man/mdeb.Rd |only
man/mdmeb.Rd |only
man/mdmp.Rd |only
man/no_intercept.Rd | 17 +--
man/quadform.Rd | 24 ++--
man/quadform_inv.Rd | 26 ++---
man/rda_cov.Rd | 18 +--
man/rda_weights.Rd | 18 +--
man/regdiscrim_estimates.Rd | 67 ++++++-------
man/risk_stein.Rd | 28 ++---
man/sdlda.Rd | 166 +++++++++++++++-----------------
man/sdqda.Rd | 165 +++++++++++++++-----------------
man/smdlda.Rd |only
man/smdqda.Rd |only
man/solve_chol.Rd |only
man/tong_mean_shrinkage.Rd | 19 +--
man/update_hdrda.Rd | 20 ++-
man/var_shrinkage.Rd | 19 +--
62 files changed, 1135 insertions(+), 937 deletions(-)
Title: DBI/RJDBC interface to h2 Database
Diff between RH2 versions 0.1-2.10 dated 2013-02-07 and 0.1-2.12 dated 2014-03-31
Description: DBI/RJDBC interface to h2 database. h2 version 1.3.170 is included.
Author: G. Grothendieck. Author of h2 is Thomas Mueller.
Maintainer: "David M. Kaplan"
RH2-0.1-2.10/RH2/R/dot.R |only
RH2-0.1-2.12/RH2/DESCRIPTION | 14 +++----
RH2-0.1-2.12/RH2/MD5 | 13 +++----
RH2-0.1-2.12/RH2/NEWS | 10 +++++
RH2-0.1-2.12/RH2/R/class.R | 48 ++++++++++++++++-----------
RH2-0.1-2.12/RH2/inst/NOTE | 5 +-
RH2-0.1-2.12/RH2/inst/THANKS | 2 +
RH2-0.1-2.12/RH2/man/H2Connection-methods.Rd | 2 -
8 files changed, 58 insertions(+), 36 deletions(-)
Title: Network meta-analysis with R
Diff between netmeta versions 0.4-1 dated 2014-03-21 and 0.4-2 dated 2014-03-31
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker
Maintainer: Guido Schwarzer
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 7 +++++++
R/netmeasures.R | 2 +-
4 files changed, 15 insertions(+), 8 deletions(-)
Title: Geological timescale plot
Diff between geoscale versions 1.0 dated 2013-05-13 and 1.1 dated 2014-03-31
Description: Function for adding the geological timescale to bivariate plots.
Author: Mark A. Bell
Maintainer: Mark A. Bell
geoscale-1.0/geoscale/data/timescale.txt.gz |only
geoscale-1.0/geoscale/man/timescale.Rd |only
geoscale-1.1/geoscale/DESCRIPTION | 15 -
geoscale-1.1/geoscale/MD5 | 14 -
geoscale-1.1/geoscale/R/geoscale.plot.R | 197 ++++++++++++++------------
geoscale-1.1/geoscale/data/biozones.txt.gz |binary
geoscale-1.1/geoscale/data/timescales.RData |only
geoscale-1.1/geoscale/man/geoscale-package.Rd | 8 -
geoscale-1.1/geoscale/man/geoscale.plot.Rd | 101 ++++++-------
geoscale-1.1/geoscale/man/timescales.Rd |only
10 files changed, 178 insertions(+), 157 deletions(-)
Title: Normal Mixture Modeling for Model-Based Clustering,
Classification, and Density Estimation
Diff between mclust versions 4.2 dated 2013-07-19 and 4.3 dated 2014-03-31
Description: Normal Mixture Modeling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley, Adrian Raftery and Luca Scrucca
Maintainer: Luca Scrucca
mclust-4.2/mclust/inst/doc/mclust-weights.R |only
mclust-4.2/mclust/inst/doc/mclust.R |only
mclust-4.3/mclust/DESCRIPTION | 8
mclust-4.3/mclust/MD5 | 54
mclust-4.3/mclust/R/densityMclust.R | 409
mclust-4.3/mclust/R/icl.R | 69
mclust-4.3/mclust/R/mclust.R | 8701 +++++++-------
mclust-4.3/mclust/R/mclustda.R | 1054 -
mclust-4.3/mclust/R/mclustdr.R | 638 -
mclust-4.3/mclust/R/weights.R | 10
mclust-4.3/mclust/R/zzz.R | 1
mclust-4.3/mclust/build |only
mclust-4.3/mclust/data/Baudry_etal_2010_JCGS_examples.rda |binary
mclust-4.3/mclust/data/GvHD.rda |binary
mclust-4.3/mclust/data/chevron.rda |binary
mclust-4.3/mclust/data/cross.rda |binary
mclust-4.3/mclust/data/diabetes.rda |binary
mclust-4.3/mclust/data/wreath.rda |binary
mclust-4.3/mclust/inst/NEWS | 263
mclust-4.3/mclust/man/Mclust.Rd | 51
mclust-4.3/mclust/man/MclustDA.Rd | 6
mclust-4.3/mclust/man/MclustDR.Rd | 4
mclust-4.3/mclust/man/hc.Rd | 25
mclust-4.3/mclust/man/mclust-package.Rd |only
mclust-4.3/mclust/man/mclust.options.Rd | 30
mclust-4.3/mclust/man/mclust2Dplot.Rd | 14
mclust-4.3/mclust/man/mclustModelNames.Rd | 18
mclust-4.3/mclust/man/plot.Mclust.Rd | 6
mclust-4.3/mclust/man/predict.densityMclust.Rd | 6
mclust-4.3/mclust/man/surfacePlot.Rd | 29
30 files changed, 5784 insertions(+), 5612 deletions(-)
Title: Hawkes process simulation and calibration toolkit
Diff between hawkes versions 0.0-1 dated 2014-01-09 and 0.0-3 dated 2014-03-31
Description: The package allows to simulate Hawkes process both in univariate and multivariate settings. It gives functions to compute different moments of the number of jumps of the process on a given interval, such as mean, variance or autocorrelation of process jumps on time intervals separated by a lag.
Author: Riadh Zaatour
Maintainer: Riadh Zaatour
DESCRIPTION | 18 ++--
MD5 | 13 +--
NAMESPACE | 6 +
R/RcppExports.R | 4
man/likelihoodHawkes.Rd |only
man/simulateHawkes.Rd | 12 +-
src/RcppExports.cpp | 18 ++++
src/hawkes.cpp | 202 +++++++++++++++++++++++++++++++++++++++++-------
8 files changed, 224 insertions(+), 49 deletions(-)
Title: Bayesian Analysis in Extreme Value Theory
Diff between evdbayes versions 1.1-0 dated 2012-09-10 and 1.1-1 dated 2014-03-31
Description: Provides functions for the bayesian analysis of extreme
value models, using MCMC methods.
Author: Alec Stephenson and Mathieu Ribatet.
Maintainer: Mathieu Ribatet
evdbayes-1.1-0/evdbayes/R/zzz.R |only
evdbayes-1.1-1/evdbayes/DESCRIPTION | 11 +++----
evdbayes-1.1-1/evdbayes/MD5 | 5 +--
evdbayes-1.1-1/evdbayes/src/evdbayesTest.c | 44 +++++++++++++++++++++++++----
4 files changed, 46 insertions(+), 14 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.1.17 dated 2014-02-21 and 0.1.23 dated 2014-03-31
Description: R tools for combining and cleaning data sets, including filling in
missing observations with data from another data frame and creating
lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 12 +-
MD5 | 28 ++---
NAMESPACE | 6 +
NEWS | 76 ++++++++++---
R/DropNA.R | 49 ++++++++-
R/FillIn.R | 11 +-
R/slide.R | 288 ++++++++++++++++++++++++++++++++++++++++++++++++++---
R/utils.R | 14 ++
README.md | 18 ++-
man/FillIn.Rd | 3
man/FindReplace.Rd | 3
man/NaVar.Rd |only
man/SpreadDummy.Rd |only
man/StartEnd.Rd |only
man/shift.Rd | 6 -
man/slide.Rd | 2
man/slideMA.Rd |only
17 files changed, 448 insertions(+), 68 deletions(-)
Title: Spatially explicit capture-recapture
Diff between secr versions 2.7.0 dated 2013-10-30 and 2.8.0 dated 2014-03-31
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 10
MD5 | 166 ++++----
NAMESPACE | 31 +
NEWS | 102 ++++
R/CV.R |only
R/D.designdata.R | 2
R/Dsurface.R | 15
R/PG.R |only
R/Rsurface.R |only
R/addCovariates.R | 4
R/autoini.R | 6
R/clone.R |only
R/derivedMS.R | 64 +--
R/ellipse.secr.R | 25 +
R/esa.R | 30 +
R/fxi.R | 8
R/make.mask.R | 17
R/mask.check.R | 2
R/methods.R | 566 ++++++++-------------------
R/par.secr.fit.R |only
R/pdot.R | 121 +++--
R/plot.capthist.r |only
R/plot.secr.R | 5
R/rbind.capthist.R | 23 +
R/read.traps.R | 3
R/reduce.R | 5
R/regionN.R | 55 +-
R/score.test.R | 8
R/secr.design.MS.R | 73 ++-
R/secr.fit.R | 206 +++++----
R/secrloglik.R | 742 +++++++++++++++++++++---------------
R/sim.capthist.R | 8
R/sim.popn.R | 37 +
R/sim.secr.R | 2
R/suggest.buffer.R | 110 +++--
R/telemetry.R | 274 +++++++++----
R/utility.R | 114 +++++
R/verify.R | 32 -
data/deermouse.RData |binary
data/housemouse.RData |binary
data/ovenbird.RData |binary
data/ovensong.RData |binary
data/possum.RData |binary
data/secrdemo.RData |binary
data/stoatDNA.RData |binary
inst/doc/index.html | 42 +-
inst/doc/secr-manual.pdf |binary
inst/doc/secr-overview.pdf |binary
inst/doc/secr-parameterisations.pdf |only
man/AIC.secr.Rd | 10
man/CV.Rd |only
man/PG.Rd |only
man/Parallel.Rd | 11
man/Rsurface.Rd |only
man/addTelemetry.Rd | 39 +
man/capthist.Rd | 6
man/capthistfn.Rd | 7
man/circular.Rd | 16
man/clone.Rd |only
man/contour.Rd | 17
man/covariates.Rd | 21 -
man/derivedMS.Rd | 12
man/details.Rd | 65 ++-
man/ellipse.secr.Rd | 54 ++
man/hcov.Rd | 18
man/par.secr.fit.Rd |only
man/plot.capthist.Rd | 39 +
man/plot.mask.Rd | 38 +
man/polyarea.Rd | 6
man/predict.secr.Rd | 4
man/rbind.capthist.Rd | 4
man/rbind.traps.Rd | 25 -
man/read.telemetry.Rd | 5
man/region.N.Rd | 16
man/score.test.Rd | 13
man/secr-package.Rd | 10
man/secr.design.MS.Rd | 4
man/secr.fit.Rd | 10
man/secrdemo.Rd | 2
man/sim.capthist.Rd | 6
man/sim.popn.Rd | 20
man/sim.secr.Rd | 6
man/speed.Rd | 4
man/stoatDNA.Rd | 8
man/trim.Rd | 2
man/troubleshooting.Rd | 10
src/detectfn.c | 42 +-
src/secr.c | 732 +++++++++++++++++++++--------------
src/secr.h | 2
src/trapping.c | 6
90 files changed, 2561 insertions(+), 1637 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 1.1-2-2 dated 2014-03-04 and 1.1-3 dated 2014-03-31
Description: Classes and methods for dense and sparse matrices and
operations on them using LAPACK and SuiteSparse.
Author: Douglas Bates
Maintainer: Martin Maechler
ChangeLog | 4
DESCRIPTION | 8
MD5 | 73 +
NAMESPACE | 17
R/Csparse.R | 5
R/Matrix.R | 18
R/Ops.R | 9
R/Tsparse.R | 12
R/dgTMatrix.R | 4
R/diagMatrix.R | 6
inst/doc/Comparisons.pdf |binary
inst/doc/Design-issues.pdf |binary
inst/doc/Intro2Matrix.pdf |binary
inst/doc/Introduction.pdf |binary
inst/doc/sparseModels.pdf |binary
inst/po/de/LC_MESSAGES/Matrix.mo |binary
inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary
inst/po/fr |only
inst/po/pl/LC_MESSAGES/Matrix.mo |binary
inst/po/pl/LC_MESSAGES/R-Matrix.mo |binary
inst/test-tools-1.R | 12
man/CHMfactor-class.Rd | 7
man/is.na-methods.Rd | 7
man/sparseMatrix.Rd | 19
po/Matrix.pot | 134 +--
po/R-Matrix.pot | 15
po/R-de.po | 190 ++---
po/R-fr.po |only
po/R-pl.po | 1200 ++++++++++++++------------------
po/de.po | 196 ++---
po/fr.po |only
po/pl.po | 1192 ++++++++++++++++---------------
src/dgCMatrix.c | 2
src/dtrMatrix.c | 2
src/t_gCMatrix_colSums.c | 12
tests/Simple.R | 7
tests/matprod.R | 4
39 files changed, 1538 insertions(+), 1617 deletions(-)
Title: Functions for wind resource assessment
Diff between bReeze versions 0.3-0 dated 2014-01-13 and 0.3-1 dated 2014-03-31
Description: A collection of functions to analyse, visualize and interpret wind data
and to calculate the potential energy production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul
DESCRIPTION | 9 +--
MD5 | 92 +++++++++++++++----------------
NAMESPACE | 2
R/aep.R | 20 +++++-
R/availability.R | 53 ++++++++++++------
R/clean.R | 12 ++--
R/createMast.R | 10 +--
R/energy.R | 23 ++++++-
R/frequency.R | 59 +++++++++++++-------
R/monthStats.R | 45 +++++++++++----
R/plotDay.R | 147 ++++++++++++++++++++++++++++++++++++++++++--------
R/plotEnergy.R | 2
R/plotFrequency.R | 2
R/plotMap.R | 12 ++--
R/plotMonthStats.R | 2
R/plotPC.R | 10 +--
R/plotPolar.R | 33 +++++++++--
R/plotProfile.R | 26 ++++++--
R/plotTimeSeries.R | 20 +++---
R/plotTurbIEC.R | 31 ++++++++--
R/plotTurbulence.R | 2
R/plotWbDir.R | 18 +++++-
R/plotWeibull.R | 23 ++++++-
R/printObject.R | 71 +++++++++++++-----------
R/profile.R | 86 +++++++++++++++++++----------
R/readPC.R | 2
R/turbulence.R | 73 ++++++++++++++++--------
R/weibull.R | 43 +++++++++++---
R/zzz.R | 48 ++++++++--------
data/winddata.RData |binary
inst/NEWS | 14 ++++
man/availability.Rd | 15 ++++-
man/bReeze-package.Rd | 8 +-
man/clean.Rd | 10 +--
man/formatTS.Rd | 4 -
man/frequency.Rd | 15 ++++-
man/monthStats.Rd | 17 ++++-
man/plotDay.Rd | 22 ++++++-
man/plotPC.Rd | 2
man/plotPolar.Rd | 17 ++++-
man/plotTimeSeries.Rd | 15 ++---
man/plotTurbIEC.Rd | 13 +++-
man/printObject.Rd | 3 -
man/profile.Rd | 18 ++++--
man/turbulence.Rd | 9 ++-
man/uncertainty.Rd | 2
man/weibull.Rd | 15 ++++-
47 files changed, 817 insertions(+), 358 deletions(-)
Title: Generation, reconstruction, simulation and analysis of
synchronous, asynchronous, and probabilistic Boolean networks
Diff between BoolNet versions 1.62 dated 2013-12-03 and 1.63 dated 2014-03-31
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler
DESCRIPTION | 8 +--
MD5 | 64 ++++++++++++-------------
R/attractorsToLaTeX.R | 14 ++---
R/edgeDetector.R | 6 +-
R/generateRandomNKNetwork.R | 6 +-
R/generateTimeSeries.R | 4 -
R/getAttractors.R | 6 +-
R/getPathToAttractor.R | 4 -
R/helpers.R | 12 ++--
R/loadBioTapestry.R | 4 -
R/loadNetwork.R | 2
R/perturbNetwork.R | 34 ++++++-------
R/plotAttractors.R | 18 +++----
R/plotNetworkWiring.R | 8 +--
R/plotSequence.R | 14 ++---
R/plotStateGraph.R | 4 -
R/print.AttractorInfo.R | 6 +-
R/print.MarkovSimulation.R | 2
R/print.TransitionTable.R | 2
R/reconstructNetwork.R | 12 ++--
R/scanStatistic.R | 10 +--
R/sequenceToLaTeX.R | 12 ++--
R/simplifyNetwork.R | 4 -
R/stateTransition.R | 4 -
R/testNetworkProperties.R | 14 ++---
R/toPajek.R | 2
R/zeta.R | 6 +-
inst/NEWS.Rd | 15 +++++
inst/doc/BoolNet_package_vignette.pdf |binary
man/BoolNet-package.Rd | 4 -
src/boolean_network.c | 86 ++++++++++++++++++++++++++++++----
src/probabilistic_boolean_network.c | 21 +++-----
src/reconstruct_network.c | 33 ++++++-------
33 files changed, 259 insertions(+), 182 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Diff between nlme versions 3.1-116 dated 2014-03-28 and 3.1-117 dated 2014-03-31
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
R-core [aut, cre]
Maintainer: R-core
ChangeLog | 12 +++++++++--
DESCRIPTION | 8 +++----
MD5 | 20 +++++++++----------
inst/po/de/LC_MESSAGES/R-nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/R-nlme.mo |binary
inst/po/en@quot/LC_MESSAGES/nlme.mo |binary
inst/po/fr/LC_MESSAGES/R-nlme.mo |binary
inst/po/pl/LC_MESSAGES/R-nlme.mo |binary
po/R-fr.po | 35 +++++++++++++++++++++++++---------
po/R-nlme.pot | 4 +--
po/nlme.pot | 4 +--
11 files changed, 54 insertions(+), 29 deletions(-)
Title: Cluster Analysis Extended Rousseeuw et al.
Diff between cluster versions 1.15.1 dated 2014-03-12 and 1.15.2 dated 2014-03-31
Description: Cluster Analysis Methods. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990)
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb]
Maintainer: Martin Maechler
ChangeLog | 5
DESCRIPTION | 8
MD5 | 50 -
R/0aaa.R | 9
R/agnes.q | 6
R/clara.q | 25
R/daisy.q | 22
R/diana.q | 6
R/ellipsoidhull.R | 4
R/fanny.q | 8
R/pam.q | 11
R/plotpart.q | 9
R/silhouette.R | 3
inst/po/de/LC_MESSAGES/R-cluster.mo |binary
inst/po/en@quot/LC_MESSAGES/R-cluster.mo |binary
inst/po/en@quot/LC_MESSAGES/cluster.mo |only
inst/po/fr |only
inst/po/pl/LC_MESSAGES/R-cluster.mo |binary
po/R-cluster.pot | 89 --
po/R-de.po | 205 +++--
po/R-fr.po |only
po/R-pl.po | 1129 ++++++++++++++++++++++---------
po/cluster.pot |only
src/clara.c | 13
src/pam.c | 2
src/twins.c | 2
tests/clara-NAs.Rout.save | 14
tests/ellipsoid-ex.Rout.save | 10
28 files changed, 1084 insertions(+), 546 deletions(-)
Title: Wright Map: IRT item-person map with ConQuest integration
Diff between WrightMap versions 1.0 dated 2014-03-03 and 1.1 dated 2014-03-31
Description: A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The WrightMap package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. eRm or IRToys in R, or Stata, Mplus, etc.), WrightMap features special integration with ConQuest to facilitate reading and plotting its output directly.The wrightMap function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The CQmodel function reads output files created using ConQuest software and creates a set of data frames for easy data manipulation, bundled in a CQmodel object. The wrightMap function can take a CQmodel object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Author: David Torres Irribarra & Rebecca Freund
Maintainer: David Torres Irribarra
DESCRIPTION | 11 +
MD5 | 40 +++++--
R/CQmodel.R | 236 +++++++++++++++++++++++++++++++++++-------
R/FitPlot.R |only
R/fitgraph.CQmodel.R |only
R/fitgraph.R |only
R/fitgraph.character.R |only
R/fitgraph.default.R |only
R/make.deltas.CQmodel.R |only
R/make.deltas.R |only
R/make.deltas.character.R |only
R/make.deltas.default.R |only
R/make.thresholds.CQmodel.R |only
R/make.thresholds.R |only
R/make.thresholds.character.R |only
R/make.thresholds.default.R |only
R/print.CQmodel.R | 5
R/wrightMap.CQmodel.R | 148 +++++++++++---------------
R/wrightMap.default.R | 67 ++++++++---
README.md | 8 -
inst/extdata/ex2a.eap |only
inst/extdata/ex2a.shw |only
inst/extdata/ex2b-2.shw |only
inst/extdata/ex2b.eap |only
inst/extdata/ex4a.mle |only
inst/extdata/ex4a.shw |only
man/CQmodel.Rd | 34 +++++-
man/WrightMap-package.Rd | 8 -
man/fitgraph.Rd |only
man/make.deltas.Rd |only
man/make.thresholds.Rd |only
man/wrightMap.Rd | 100 ++++++++++++++---
32 files changed, 473 insertions(+), 184 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation
Diff between mgcv versions 1.7-28 dated 2014-01-29 and 1.7-29 dated 2014-03-31
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML
or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
ChangeLog | 5 +++++
DESCRIPTION | 6 +++---
MD5 | 6 +++---
src/Makevars | 2 +-
4 files changed, 12 insertions(+), 7 deletions(-)
Title: Multi-objective parameter tuning for classifiers
Diff between TunePareto versions 2.3 dated 2013-08-09 and 2.4 dated 2014-03-31
Description: Generic methods for parameter tuning of classification algorithms using multiple scoring functions
Author: Christoph Müssel, Ludwig Lausser, Hans Kestler
Maintainer: Hans Kestler
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/classifiers.R | 12 ++++++++++--
inst/NEWS.Rd | 12 ++++++++++++
man/TunePareto-package.Rd | 4 ++--
5 files changed, 32 insertions(+), 12 deletions(-)
Title: Periodic Autoregressive Time Series Models
Diff between partsm versions 1.1 dated 2012-04-25 and 1.1-2 dated 2014-03-31
Description: This package performs basic functions to fit and predict periodic autoregressive time series models. These models are discussed in the book P.H. Franses (1996) "Periodicity and Stochastic Trends in Economic Time Series", Oxford University Press. Data set analyzed in that book is also provided. NOTE: the package was orphaned during several years. It is now only maintained, but no major enhancement are expected, and the maintainer cannot provide any support.
Author: Javier Lopez-de-Lacalle
Maintainer: Matthieu Stigler
DESCRIPTION | 22 ++++++++-------------
MD5 | 52 +++++++++++++++++++++++++++------------------------
NAMESPACE | 1
R/partsm.R | 19 +++++++++---------
build |only
data/canun.rda |binary
data/canunsa.rda |binary
data/gergnp.rda |binary
data/gergnpsa.rda |binary
data/swdipc.rda |binary
data/swndcpc.rda |binary
data/ukcons.rda |binary
data/ukexp.rda |binary
data/ukgdp.rda |binary
data/ukimp.rda |binary
data/ukinvest.rda |binary
data/ukndcons.rda |binary
data/ukpinvest.rda |binary
data/ukwf.rda |binary
data/usaipi.rda |binary
data/usaipisa.rda |binary
inst/ChangeLog | 5 ++++
inst/doc/partsm.R |only
inst/doc/partsm.Rnw | 2 -
inst/doc/partsm.pdf |binary
man/acf.ext1.Rd | 3 +-
tests |only
vignettes/partsm.Rnw | 2 -
28 files changed, 57 insertions(+), 49 deletions(-)
Title: Numeric routines for optically stimulated luminescence dating
Diff between numOSL versions 1.1 dated 2014-01-19 and 1.2 dated 2014-03-31
Description: Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation; decay curve decomposition and fast-component equivalent dose estimation; statistical age models analysis and radial plot drawing.
Author: Peng Jun
Maintainer: Peng Jun
DESCRIPTION | 8
MD5 | 45 +-
NEWS | 2
R/numOSL.R | 774 ++++++++++++++++++++++++++++++++++++++++++++-
man/Curvedata.Rd | 6
man/EDdata.Rd | 8
man/RadialPlotter.Rd | 93 +----
man/Signaldata.Rd | 14
man/calED.Rd | 70 +---
man/dbED.Rd | 43 --
man/decomp.Rd | 82 +---
man/decompc.Rd | 56 +--
man/fastED.Rd | 65 +--
man/mcFMM.Rd |only
man/mcMAM.Rd |only
man/numOSL-package.Rd | 29 -
man/print.RadialPlotter.Rd | 15
man/reportSAM.Rd |only
man/sgcED.Rd | 47 --
src/CAM.f90 | 6
src/FineED.f90 | 4
src/FineED1.f90 | 6
src/mcCAM.f90 |only
src/mcFMM2.f90 |only
src/mcFMM3.f90 |only
src/mcFMM4.f90 |only
src/mcMam3.f90 |only
src/mcMam4.f90 |only
28 files changed, 1011 insertions(+), 362 deletions(-)