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Title: R Client for the COLOURlovers API
Description: Provides access to the COLOURlovers <http://www.colourlovers.com/> API, which offers color inspiration and color palettes.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between colourlovers versions 0.1.4 dated 2014-12-20 and 0.2.0 dated 2015-12-22
colourlovers-0.1.4/colourlovers/R/clquery.r |only colourlovers-0.2.0/colourlovers/DESCRIPTION | 15 - colourlovers-0.2.0/colourlovers/MD5 | 24 - colourlovers-0.2.0/colourlovers/NAMESPACE | 11 colourlovers-0.2.0/colourlovers/NEWS | 9 colourlovers-0.2.0/colourlovers/R/clQuery.r |only colourlovers-0.2.0/colourlovers/R/clcolors.r | 6 colourlovers-0.2.0/colourlovers/R/cllovers.r | 4 colourlovers-0.2.0/colourlovers/R/clpalettes.r | 4 colourlovers-0.2.0/colourlovers/R/clpatterns.r | 4 colourlovers-0.2.0/colourlovers/R/clstats.r | 6 colourlovers-0.2.0/colourlovers/README.md | 369 ++++++++++++++++--------- colourlovers-0.2.0/colourlovers/man/swatch.Rd | 6 colourlovers-0.2.0/colourlovers/tests |only 14 files changed, 293 insertions(+), 165 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between plotROC versions 1.3.3 dated 2015-03-16 and 2.0.0 dated 2015-12-22
plotROC-1.3.3/plotROC/R/ggroc.R |only plotROC-1.3.3/plotROC/R/modCss.R |only plotROC-1.3.3/plotROC/R/modJs.R |only plotROC-1.3.3/plotROC/R/plot_journal_roc.R |only plotROC-1.3.3/plotROC/inst/shinyApp/shinyapps |only plotROC-1.3.3/plotROC/man/modCss.Rd |only plotROC-1.3.3/plotROC/man/modJs.Rd |only plotROC-1.3.3/plotROC/man/plotROC-package.Rd |only plotROC-2.0.0/plotROC/DESCRIPTION | 15 plotROC-2.0.0/plotROC/MD5 | 79 plotROC-2.0.0/plotROC/NAMESPACE | 37 plotROC-2.0.0/plotROC/NEWS | 11 plotROC-2.0.0/plotROC/R/calculate_roc.R | 146 + plotROC-2.0.0/plotROC/R/deprecated.R |only plotROC-2.0.0/plotROC/R/geom_roc.R |only plotROC-2.0.0/plotROC/R/geom_rocci.R |only plotROC-2.0.0/plotROC/R/getD3.R | 10 plotROC-2.0.0/plotROC/R/interactive_roc.R | 151 - plotROC-2.0.0/plotROC/R/plotROC-package.R |only plotROC-2.0.0/plotROC/R/style_roc.R |only plotROC-2.0.0/plotROC/README.md |only plotROC-2.0.0/plotROC/build/vignette.rds |binary plotROC-2.0.0/plotROC/inst/clickCis.js |only plotROC-2.0.0/plotROC/inst/d3.v3.min.js | 10 plotROC-2.0.0/plotROC/inst/doc/examples.R | 172 + plotROC-2.0.0/plotROC/inst/doc/examples.Rmd | 239 +- plotROC-2.0.0/plotROC/inst/doc/examples.html | 1806 ++++++++++---------- plotROC-2.0.0/plotROC/inst/hoverPoints.js |only plotROC-2.0.0/plotROC/inst/shinyApp/help.html | 18 plotROC-2.0.0/plotROC/inst/shinyApp/help.md | 2 plotROC-2.0.0/plotROC/inst/shinyApp/server.R | 82 plotROC-2.0.0/plotROC/inst/shinyApp/ui.R | 19 plotROC-2.0.0/plotROC/man/calc_auc.Rd |only plotROC-2.0.0/plotROC/man/calculate_multi_roc.Rd | 12 plotROC-2.0.0/plotROC/man/calculate_roc.Rd | 17 plotROC-2.0.0/plotROC/man/direct_label.Rd |only plotROC-2.0.0/plotROC/man/export_interactive_roc.Rd | 58 plotROC-2.0.0/plotROC/man/geom_roc.Rd |only plotROC-2.0.0/plotROC/man/geom_rocci.Rd |only plotROC-2.0.0/plotROC/man/getD3.Rd |only plotROC-2.0.0/plotROC/man/ggroc.Rd | 22 plotROC-2.0.0/plotROC/man/melt_roc.Rd |only plotROC-2.0.0/plotROC/man/multi_ggroc.Rd | 22 plotROC-2.0.0/plotROC/man/plotROC.Rd |only plotROC-2.0.0/plotROC/man/plot_interactive_roc.Rd | 2 plotROC-2.0.0/plotROC/man/plot_journal_roc.Rd | 24 plotROC-2.0.0/plotROC/man/shiny_plotROC.Rd | 2 plotROC-2.0.0/plotROC/man/stat_roc.Rd |only plotROC-2.0.0/plotROC/man/stat_rocci.Rd |only plotROC-2.0.0/plotROC/man/style_roc.Rd |only plotROC-2.0.0/plotROC/man/verify_d.Rd | 6 plotROC-2.0.0/plotROC/tests/testthat/Rplots.pdf |only plotROC-2.0.0/plotROC/tests/testthat/test-calc.R | 28 plotROC-2.0.0/plotROC/vignettes/examples.Rmd | 239 +- 54 files changed, 1864 insertions(+), 1365 deletions(-)
Title: Datasets for 'Statistics: Unlocking the Power of Data'
Description: Data sets and other utilities for
'Statistics: Unlocking the Power of Data'
by Lock, Lock, Lock, Lock and Lock
(ISBN : 978-0-470-60187-7, http://lock5stat.com/).
Author: Randall Pruim
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between Lock5withR versions 1.2.0 dated 2015-12-18 and 1.2.2 dated 2015-12-22
Lock5withR-1.2.0/Lock5withR/data/AllCountries.R |only Lock5withR-1.2.0/Lock5withR/data/AtmosphericCO2.R |only Lock5withR-1.2.0/Lock5withR/data/BikeCommute.R |only Lock5withR-1.2.0/Lock5withR/data/BodyTemp50.R |only Lock5withR-1.2.0/Lock5withR/data/CaffeineTaps.R |only Lock5withR-1.2.0/Lock5withR/data/EmployedACS.R |only Lock5withR-1.2.0/Lock5withR/data/Flight179.R |only Lock5withR-1.2.0/Lock5withR/data/GPAGender.R |only Lock5withR-1.2.0/Lock5withR/data/ICUAdmissions.R |only Lock5withR-1.2.0/Lock5withR/data/MiamiHeat.R |only Lock5withR-1.2.0/Lock5withR/data/MindsetMatters.R |only Lock5withR-1.2.0/Lock5withR/data/NFLScores2011.R |only Lock5withR-1.2.0/Lock5withR/data/NutritionStudy.R |only Lock5withR-1.2.0/Lock5withR/data/RestaurantTips.R |only Lock5withR-1.2.0/Lock5withR/data/RetailSales.R |only Lock5withR-1.2.0/Lock5withR/data/SalaryGender.R |only Lock5withR-1.2.0/Lock5withR/data/SampCountries.R |only Lock5withR-1.2.0/Lock5withR/data/SandP500.R |only Lock5withR-1.2.0/Lock5withR/data/SleepStudy.R |only Lock5withR-1.2.0/Lock5withR/data/SpeedDating.R |only Lock5withR-1.2.0/Lock5withR/data/StudentSurvey.R |only Lock5withR-1.2.0/Lock5withR/data/USStates.R |only Lock5withR-1.2.0/Lock5withR/data/WaterTaste.R |only Lock5withR-1.2.0/Lock5withR/data/Wetsuits.R |only Lock5withR-1.2.2/Lock5withR/DESCRIPTION | 16 Lock5withR-1.2.2/Lock5withR/MD5 | 218 +++++------- Lock5withR-1.2.2/Lock5withR/data/ACS.rda |binary Lock5withR-1.2.2/Lock5withR/data/APMultipleChoice.rda |binary Lock5withR-1.2.2/Lock5withR/data/AllCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/April14Temps.rda |binary Lock5withR-1.2.2/Lock5withR/data/AtmosphericCO2.rda |binary Lock5withR-1.2.2/Lock5withR/data/BaseballHits.rda |binary Lock5withR-1.2.2/Lock5withR/data/BaseballTimes.rda |binary Lock5withR-1.2.2/Lock5withR/data/Benford.rda |binary Lock5withR-1.2.2/Lock5withR/data/BikeCommute.rda |binary Lock5withR-1.2.2/Lock5withR/data/BodyFat.rda |binary Lock5withR-1.2.2/Lock5withR/data/BodyTemp50.rda |binary Lock5withR-1.2.2/Lock5withR/data/BootAtlantaCorr.rda |binary Lock5withR-1.2.2/Lock5withR/data/CAOSExam.rda |binary Lock5withR-1.2.2/Lock5withR/data/CaffeineTaps.rda |binary Lock5withR-1.2.2/Lock5withR/data/Cereal.rda |binary Lock5withR-1.2.2/Lock5withR/data/CocaineTreatment.rda |binary Lock5withR-1.2.2/Lock5withR/data/ColaCalcium.rda |binary Lock5withR-1.2.2/Lock5withR/data/CommuteAtlanta.rda |binary Lock5withR-1.2.2/Lock5withR/data/CommuteStLouis.rda |binary Lock5withR-1.2.2/Lock5withR/data/CompassionateRats.rda |binary Lock5withR-1.2.2/Lock5withR/data/CricketChirps.rda |binary Lock5withR-1.2.2/Lock5withR/data/Digits.rda |binary Lock5withR-1.2.2/Lock5withR/data/DogOwner.rda |binary Lock5withR-1.2.2/Lock5withR/data/ElectionMargin.rda |binary Lock5withR-1.2.2/Lock5withR/data/EmployedACS.rda |binary Lock5withR-1.2.2/Lock5withR/data/ExerciseHours.rda |binary Lock5withR-1.2.2/Lock5withR/data/FacebookFriends.rda |binary Lock5withR-1.2.2/Lock5withR/data/FatMice18.rda |binary Lock5withR-1.2.2/Lock5withR/data/FishGills12.rda |binary Lock5withR-1.2.2/Lock5withR/data/FishGills3.rda |binary Lock5withR-1.2.2/Lock5withR/data/Flight179.rda |binary Lock5withR-1.2.2/Lock5withR/data/FloridaLakes.rda |binary Lock5withR-1.2.2/Lock5withR/data/GPAGender.rda |binary Lock5withR-1.2.2/Lock5withR/data/GlobalInternet.rda |binary Lock5withR-1.2.2/Lock5withR/data/HappyPlanetIndex.rda |binary Lock5withR-1.2.2/Lock5withR/data/HockeyPenalties.rda |binary Lock5withR-1.2.2/Lock5withR/data/HollywoodMovies2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSale.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleCA.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleCanton.rda |binary Lock5withR-1.2.2/Lock5withR/data/HomesForSaleNY.rda |binary Lock5withR-1.2.2/Lock5withR/data/HoneybeeCircuits.rda |binary Lock5withR-1.2.2/Lock5withR/data/HoneybeeWaggle.rda |binary Lock5withR-1.2.2/Lock5withR/data/HotDogs.rda |binary Lock5withR-1.2.2/Lock5withR/data/ICUAdmissions.rda |binary Lock5withR-1.2.2/Lock5withR/data/ImmuneTea.rda |binary Lock5withR-1.2.2/Lock5withR/data/InkjetPrinters.rda |binary Lock5withR-1.2.2/Lock5withR/data/LifeExpectancyVehicles.rda |binary Lock5withR-1.2.2/Lock5withR/data/LightatNight.rda |binary Lock5withR-1.2.2/Lock5withR/data/MalevolentUniformsNFL.rda |binary Lock5withR-1.2.2/Lock5withR/data/MalevolentUniformsNHL.rda |binary Lock5withR-1.2.2/Lock5withR/data/MammalLongevity.rda |binary Lock5withR-1.2.2/Lock5withR/data/ManhattanApartments.rda |binary Lock5withR-1.2.2/Lock5withR/data/MarriageAges.rda |binary Lock5withR-1.2.2/Lock5withR/data/MastersGolf.rda |binary Lock5withR-1.2.2/Lock5withR/data/MentalMuscle.rda |binary Lock5withR-1.2.2/Lock5withR/data/MiamiHeat.rda |binary Lock5withR-1.2.2/Lock5withR/data/MindsetMatters.rda |binary Lock5withR-1.2.2/Lock5withR/data/MinistersRum.rda |binary Lock5withR-1.2.2/Lock5withR/data/MustangPrice.rda |binary Lock5withR-1.2.2/Lock5withR/data/NBAPlayers2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/NBAStandings.rda |binary Lock5withR-1.2.2/Lock5withR/data/NFLScores2011.rda |binary Lock5withR-1.2.2/Lock5withR/data/NutritionStudy.rda |binary Lock5withR-1.2.2/Lock5withR/data/OlympicMarathon.rda |binary Lock5withR-1.2.2/Lock5withR/data/OttawaSenators.rda |binary Lock5withR-1.2.2/Lock5withR/data/PizzaGirl.rda |binary Lock5withR-1.2.2/Lock5withR/data/QuizPulse10.rda |binary Lock5withR-1.2.2/Lock5withR/data/RandomP50N200.rda |binary Lock5withR-1.2.2/Lock5withR/data/RestaurantTips.rda |binary Lock5withR-1.2.2/Lock5withR/data/RetailSales.rda |binary Lock5withR-1.2.2/Lock5withR/data/RockandRoll.rda |binary Lock5withR-1.2.2/Lock5withR/data/SalaryGender.rda |binary Lock5withR-1.2.2/Lock5withR/data/SampCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandP500.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandwichAnts.rda |binary Lock5withR-1.2.2/Lock5withR/data/SandwichAnts2.rda |binary Lock5withR-1.2.2/Lock5withR/data/SkateboardPrices.rda |binary Lock5withR-1.2.2/Lock5withR/data/SleepCaffeine.rda |binary Lock5withR-1.2.2/Lock5withR/data/SleepStudy.rda |binary Lock5withR-1.2.2/Lock5withR/data/Smiles.rda |binary Lock5withR-1.2.2/Lock5withR/data/SpeedDating.rda |binary Lock5withR-1.2.2/Lock5withR/data/StatGrades.rda |binary Lock5withR-1.2.2/Lock5withR/data/StatisticsPhD.rda |binary Lock5withR-1.2.2/Lock5withR/data/StockChanges.rda |binary Lock5withR-1.2.2/Lock5withR/data/StorySpoilers.rda |binary Lock5withR-1.2.2/Lock5withR/data/StressedMice.rda |binary Lock5withR-1.2.2/Lock5withR/data/StudentSurvey.rda |binary Lock5withR-1.2.2/Lock5withR/data/TenCountries.rda |binary Lock5withR-1.2.2/Lock5withR/data/TextbookCosts.rda |binary Lock5withR-1.2.2/Lock5withR/data/ToenailArsenic.rda |binary Lock5withR-1.2.2/Lock5withR/data/TrafficFlow.rda |binary Lock5withR-1.2.2/Lock5withR/data/USStates.rda |binary Lock5withR-1.2.2/Lock5withR/data/WaterStriders.rda |binary Lock5withR-1.2.2/Lock5withR/data/WaterTaste.rda |binary Lock5withR-1.2.2/Lock5withR/data/Wetsuits.rda |binary 122 files changed, 106 insertions(+), 128 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove <sabanesd@roche.com>,
Wai Yin Yeung <w.yeung1@lancaster.ac.uk>,
Giuseppe Palermo <giuseppe.palermo@roche.com>,
Thomas Jaki <jaki.thomas@gmail.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between crmPack versions 0.1.5 dated 2015-11-12 and 0.1.6 dated 2015-12-22
crmPack-0.1.5/crmPack/man/StoppingGstarsamplesCIRatio-class.Rd |only crmPack-0.1.5/crmPack/man/StoppingGstarsamplesCIRatio.Rd |only crmPack-0.1.5/crmPack/man/StoppingTDsamplesCIRatio-class.Rd |only crmPack-0.1.5/crmPack/man/StoppingTDsamplesCIRatio.Rd |only crmPack-0.1.6/crmPack/DESCRIPTION | 6 crmPack-0.1.6/crmPack/MD5 | 78 ++-- crmPack-0.1.6/crmPack/NAMESPACE | 10 crmPack-0.1.6/crmPack/R/Data-class.R | 76 +++ crmPack-0.1.6/crmPack/R/Data-methods.R | 4 crmPack-0.1.6/crmPack/R/Design-methods.R | 10 crmPack-0.1.6/crmPack/R/Model-class.R | 193 ++++++++-- crmPack-0.1.6/crmPack/R/Rules-class.R | 121 +----- crmPack-0.1.6/crmPack/R/Rules-methods.R | 35 + crmPack-0.1.6/crmPack/R/Simulations-methods.R | 18 crmPack-0.1.6/crmPack/R/crmPack-package.R | 5 crmPack-0.1.6/crmPack/R/fromQuantiles.R | 11 crmPack-0.1.6/crmPack/R/mcmc.R | 14 crmPack-0.1.6/crmPack/inst/NEWS | 28 + crmPack-0.1.6/crmPack/inst/doc/example.R | 27 - crmPack-0.1.6/crmPack/inst/doc/example.Rnw | 54 +- crmPack-0.1.6/crmPack/inst/doc/example.pdf |binary crmPack-0.1.6/crmPack/man/AllModels-class.Rd | 4 crmPack-0.1.6/crmPack/man/DataMixture-class.Rd |only crmPack-0.1.6/crmPack/man/DataMixture.Rd |only crmPack-0.1.6/crmPack/man/LogisticLogNormalMixture-class.Rd |only crmPack-0.1.6/crmPack/man/LogisticLogNormalMixture.Rd |only crmPack-0.1.6/crmPack/man/MinimalInformative.Rd | 4 crmPack-0.1.6/crmPack/man/Quantiles2LogisticNormal.Rd | 8 crmPack-0.1.6/crmPack/man/Stopping-class.Rd | 3 crmPack-0.1.6/crmPack/man/StoppingHighestDose-class.Rd |only crmPack-0.1.6/crmPack/man/StoppingHighestDose.Rd |only crmPack-0.1.6/crmPack/man/examine.Rd | 2 crmPack-0.1.6/crmPack/man/mcmc.Rd | 6 crmPack-0.1.6/crmPack/man/plot-DualSimulations-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-DualSimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-GeneralSimulations-missing-method.Rd | 98 ----- crmPack-0.1.6/crmPack/man/plot-GeneralSimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/plot-PseudoDualFlexiSimulations-missing-method.Rd | 4 crmPack-0.1.6/crmPack/man/plot-PseudoDualSimulations-missing-method.Rd | 4 crmPack-0.1.6/crmPack/man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 72 +-- crmPack-0.1.6/crmPack/man/plot-PseudoSimulationsSummary-missing-method.Rd | 30 - crmPack-0.1.6/crmPack/man/plot-SimulationsSummary-missing-method.Rd | 2 crmPack-0.1.6/crmPack/man/show-DualSimulationsSummary-method.Rd | 2 crmPack-0.1.6/crmPack/man/stopTrial.Rd | 101 ++++- crmPack-0.1.6/crmPack/vignettes/example.Rnw | 54 +- 45 files changed, 651 insertions(+), 439 deletions(-)
Title: Time-Course Gene Set Analysis
Description: Implementation of TcGSA, a method for analyzing longitudinal
gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre],
Damien Chimits [aut]
Maintainer: Boris P. Hejblum <bhejblum@hsph.harvard.edu>
Diff between TcGSA versions 0.9.8 dated 2014-04-28 and 0.10.1 dated 2015-12-22
DESCRIPTION | 34 +- LICENSE | 495 +++++++++++++++++++++---------- MD5 | 82 ++--- NAMESPACE | 86 ++++- R/MYheatmap.2.R | 742 +++++++++++++++++++++++------------------------ R/STSdist.R | 5 R/TcGSA-internal.R | 6 R/TcGSA-package.R | 10 R/TcGSA.LR.R | 74 ++-- R/TcGSA.LR.parallel.R | 248 ++++++++------- R/TcGSA.dataLME.R | 16 - R/TcGSA.formula.R | 129 ++++---- R/clustTrend.R | 62 ++- R/multtest.TcGSA.R | 10 R/plot.TcGSA.R | 639 +++++++++++++++++++++------------------- R/plot1GS.R | 286 ++++++++++++------ R/plotFit.GS.R | 30 + R/plotPat.1GS.R | 47 +- R/plotPat.TcGSA.R | 34 +- R/plotSelect.GS.R | 40 +- R/pval_simu.R | 8 R/rmixchisq.R | 9 R/signifLRT.TcGSA.R | 13 R/summary.TcGSA.R | 13 README | 39 +- inst/CITATION | 30 + man/TcGSA-internal.Rd | 8 man/TcGSA-package.Rd | 33 +- man/TcGSA.LR.Rd | 268 +++++++--------- man/TcGSA.LR.parallel.Rd | 294 ++++++++---------- man/clustTrend.Rd | 373 ++++++++++------------- man/multtest.TcGSA.Rd | 77 ++-- man/plot.TcGSA.Rd | 624 +++++++++++++++++---------------------- man/plot1GS.Rd | 483 ++++++++++++++---------------- man/plotFit.GS.Rd | 141 +++----- man/plotPat.1GS.Rd | 424 +++++++++++--------------- man/plotPat.TcGSA.Rd | 592 ++++++++++++++++--------------------- man/plotSelect.GS.Rd | 437 ++++++++++++--------------- man/pval_simu.Rd | 20 - man/rmixchisq.Rd | 65 ++-- man/signifLRT.TcGSA.Rd | 118 +++---- man/summary.TcGSA.Rd | 36 +- 42 files changed, 3676 insertions(+), 3504 deletions(-)
Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between simsalapar versions 1.0-6 dated 2015-12-14 and 1.0-7 dated 2015-12-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/varlist.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Beta-Diversity of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of
why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between betalink versions 2.1.0 dated 2015-08-15 and 2.2.0 dated 2015-12-22
betalink-2.1.0/betalink/data/clownfishes.rdata |only betalink-2.1.0/betalink/man/clownfishes.Rd |only betalink-2.2.0/betalink/DESCRIPTION | 12 +- betalink-2.2.0/betalink/MD5 | 66 +++++++---- betalink-2.2.0/betalink/NAMESPACE | 20 +++ betalink-2.2.0/betalink/R/betalink.r | 15 ++ betalink-2.2.0/betalink/R/measures.r | 106 +++++++++++++++++-- betalink-2.2.0/betalink/R/network_betadiversity.R | 53 ++++----- betalink-2.2.0/betalink/R/prepare_networks.R | 3 betalink-2.2.0/betalink/README.md | 5 betalink-2.2.0/betalink/man/B01.Rd | 6 - betalink-2.2.0/betalink/man/B02.Rd | 6 - betalink-2.2.0/betalink/man/B03.Rd | 6 - betalink-2.2.0/betalink/man/B04.Rd | 6 - betalink-2.2.0/betalink/man/B05.Rd | 6 - betalink-2.2.0/betalink/man/B06.Rd | 6 - betalink-2.2.0/betalink/man/B07.Rd | 6 - betalink-2.2.0/betalink/man/B08.Rd |only betalink-2.2.0/betalink/man/B09.Rd |only betalink-2.2.0/betalink/man/B10.Rd |only betalink-2.2.0/betalink/man/B11.Rd |only betalink-2.2.0/betalink/man/B12.Rd |only betalink-2.2.0/betalink/man/B13.Rd |only betalink-2.2.0/betalink/man/B14.Rd |only betalink-2.2.0/betalink/man/B15.Rd |only betalink-2.2.0/betalink/man/B16.Rd |only betalink-2.2.0/betalink/man/B17.Rd |only betalink-2.2.0/betalink/man/B18.Rd |only betalink-2.2.0/betalink/man/B19.Rd |only betalink-2.2.0/betalink/man/B20.Rd |only betalink-2.2.0/betalink/man/B21.Rd |only betalink-2.2.0/betalink/man/B22.Rd |only betalink-2.2.0/betalink/man/B23.Rd |only betalink-2.2.0/betalink/man/B24.Rd |only betalink-2.2.0/betalink/man/anemonefish.Rd | 4 betalink-2.2.0/betalink/man/beta_os_prime.Rd | 2 betalink-2.2.0/betalink/man/betalink.Rd | 2 betalink-2.2.0/betalink/man/betapart.Rd | 2 betalink-2.2.0/betalink/man/df_from_A.Rd | 4 betalink-2.2.0/betalink/man/metaweb.Rd | 2 betalink-2.2.0/betalink/man/name_networks.Rd |only betalink-2.2.0/betalink/man/network_betadiversity.Rd | 2 betalink-2.2.0/betalink/man/network_betaplot.Rd | 2 betalink-2.2.0/betalink/man/prepare_networks.Rd | 2 44 files changed, 243 insertions(+), 101 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, DOI: 10.1007/s11104-009-0005-2), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) Root System Markup Language: toward a unified root architecture description language, Plant Physiology, DOI: 10.1104/pp.114.253625). More information can be found in Delory et al (2015) archiDART: an R package for the automated computation of plant root architectural traits, Plant and Soil, DOI: 10.1007/s11104-015-2673-4.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 1.1 dated 2015-06-08 and 1.2 dated 2015-12-22
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++-- man/archidraw.Rd | 10 ++++++---- man/archigrow.Rd | 8 +++++--- man/architect.Rd | 10 ++++++---- man/ch7lie.Rd | 2 +- man/ch7rac.Rd | 2 +- man/ch7tps.Rd | 2 +- man/latdist.Rd | 10 ++++++---- man/trajectory.Rd | 10 ++++++---- 11 files changed, 51 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-09 0.1.0
Title: Advanced Data Analysis of Immune Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor and
Immunoglobulin repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.2.1 dated 2015-11-07 and 2.2.1.7 dated 2015-12-22
tcR-2.2.1.7/tcR/DESCRIPTION | 17 +- tcR-2.2.1.7/tcR/MD5 | 200 ++++++++++++------------ tcR-2.2.1.7/tcR/NAMESPACE | 4 tcR-2.2.1.7/tcR/R/dataproc.R | 67 +++++++- tcR-2.2.1.7/tcR/R/datatools.R | 16 + tcR-2.2.1.7/tcR/R/docdata.R | 21 ++ tcR-2.2.1.7/tcR/R/infoanalysis.R | 10 - tcR-2.2.1.7/tcR/R/io.R | 2 tcR-2.2.1.7/tcR/R/parsing.R | 139 ++++++++++++++-- tcR-2.2.1.7/tcR/R/plots.R | 143 +++++++++++++++-- tcR-2.2.1.7/tcR/R/repoverlap.R | 11 - tcR-2.2.1.7/tcR/R/segments.R | 6 tcR-2.2.1.7/tcR/R/strtools.R | 4 tcR-2.2.1.7/tcR/README.md | 6 tcR-2.2.1.7/tcR/inst/doc/tcrvignette.Rmd | 4 tcR-2.2.1.7/tcR/inst/doc/tcrvignette.html | 57 ++---- tcR-2.2.1.7/tcR/man/AA_TABLE.Rd | 2 tcR-2.2.1.7/tcR/man/apply.symm.Rd | 2 tcR-2.2.1.7/tcR/man/assymetry.Rd | 2 tcR-2.2.1.7/tcR/man/barcodes.to.reads.Rd | 2 tcR-2.2.1.7/tcR/man/beta.prob.Rd | 4 tcR-2.2.1.7/tcR/man/bootstrap.tcr.Rd | 2 tcR-2.2.1.7/tcR/man/check.distribution.Rd | 2 tcR-2.2.1.7/tcR/man/clonal.space.homeostasis.Rd | 2 tcR-2.2.1.7/tcR/man/cloneset.stats.Rd | 6 tcR-2.2.1.7/tcR/man/codon.variants.Rd | 6 tcR-2.2.1.7/tcR/man/column.summary.Rd | 2 tcR-2.2.1.7/tcR/man/contamination.stats.Rd | 10 - tcR-2.2.1.7/tcR/man/convergence.index.Rd | 2 tcR-2.2.1.7/tcR/man/cosine.sharing.Rd | 2 tcR-2.2.1.7/tcR/man/cosine.similarity.Rd | 6 tcR-2.2.1.7/tcR/man/entropy.Rd | 6 tcR-2.2.1.7/tcR/man/entropy.seg.Rd | 6 tcR-2.2.1.7/tcR/man/find.clonotypes.Rd | 2 tcR-2.2.1.7/tcR/man/find.similar.sequences.Rd | 2 tcR-2.2.1.7/tcR/man/fix.alleles.Rd | 2 tcR-2.2.1.7/tcR/man/gc.content.Rd | 2 tcR-2.2.1.7/tcR/man/geneUsage.Rd | 8 tcR-2.2.1.7/tcR/man/generate.kmers.Rd | 2 tcR-2.2.1.7/tcR/man/generate.tcr.Rd | 6 tcR-2.2.1.7/tcR/man/get.all.substrings.Rd | 2 tcR-2.2.1.7/tcR/man/get.deletions.alpha.Rd | 6 tcR-2.2.1.7/tcR/man/get.inframes.Rd | 2 tcR-2.2.1.7/tcR/man/get.kmers.Rd | 2 tcR-2.2.1.7/tcR/man/gibbs.sampler.Rd | 2 tcR-2.2.1.7/tcR/man/group.clonotypes.Rd | 2 tcR-2.2.1.7/tcR/man/has.class.Rd | 2 tcR-2.2.1.7/tcR/man/intersectClonesets.Rd | 12 - tcR-2.2.1.7/tcR/man/inverse.simpson.Rd | 6 tcR-2.2.1.7/tcR/man/kmer.profile.Rd | 4 tcR-2.2.1.7/tcR/man/kmer.table.Rd | 2 tcR-2.2.1.7/tcR/man/loglikelihood.Rd | 2 tcR-2.2.1.7/tcR/man/matrixSubgroups.Rd | 2 tcR-2.2.1.7/tcR/man/matrixdiagcopy.Rd | 2 tcR-2.2.1.7/tcR/man/mutated.neighbours.Rd | 2 tcR-2.2.1.7/tcR/man/mutation.network.Rd | 2 tcR-2.2.1.7/tcR/man/ozScore.Rd | 2 tcR-2.2.1.7/tcR/man/parse.cloneset.Rd | 2 tcR-2.2.1.7/tcR/man/parse.folder.Rd | 21 +- tcR-2.2.1.7/tcR/man/pca.segments.Rd | 2 tcR-2.2.1.7/tcR/man/pca2euclid.Rd | 2 tcR-2.2.1.7/tcR/man/permutDistTest.Rd | 2 tcR-2.2.1.7/tcR/man/permutedf.Rd | 2 tcR-2.2.1.7/tcR/man/rarefaction.Rd | 2 tcR-2.2.1.7/tcR/man/repDiversity.Rd | 6 tcR-2.2.1.7/tcR/man/repLoad.Rd | 4 tcR-2.2.1.7/tcR/man/repOverlap.Rd | 10 - tcR-2.2.1.7/tcR/man/repSave.Rd | 2 tcR-2.2.1.7/tcR/man/resample.Rd |only tcR-2.2.1.7/tcR/man/revcomp.Rd | 2 tcR-2.2.1.7/tcR/man/reverse.string.Rd | 2 tcR-2.2.1.7/tcR/man/sample.clones.Rd | 2 tcR-2.2.1.7/tcR/man/sample2D.Rd | 2 tcR-2.2.1.7/tcR/man/segments.alphabets.Rd | 10 - tcR-2.2.1.7/tcR/man/segments.list.Rd | 2 tcR-2.2.1.7/tcR/man/set.group.vector.Rd | 2 tcR-2.2.1.7/tcR/man/set.pb.Rd | 2 tcR-2.2.1.7/tcR/man/set.people.vector.Rd | 2 tcR-2.2.1.7/tcR/man/set.rank.Rd | 2 tcR-2.2.1.7/tcR/man/shared.repertoire.Rd | 2 tcR-2.2.1.7/tcR/man/spectratyping.Rd | 4 tcR-2.2.1.7/tcR/man/startmitcr.Rd | 10 - tcR-2.2.1.7/tcR/man/tailbound.proportion.Rd | 2 tcR-2.2.1.7/tcR/man/top.cross.Rd | 6 tcR-2.2.1.7/tcR/man/top.fun.Rd | 2 tcR-2.2.1.7/tcR/man/twinsdata.Rd | 4 tcR-2.2.1.7/tcR/man/vis.clonal.dynamics.Rd | 2 tcR-2.2.1.7/tcR/man/vis.clonal.space.Rd | 4 tcR-2.2.1.7/tcR/man/vis.count.len.Rd | 2 tcR-2.2.1.7/tcR/man/vis.gene.usage.Rd | 2 tcR-2.2.1.7/tcR/man/vis.group.boxplot.Rd | 4 tcR-2.2.1.7/tcR/man/vis.heatmap.Rd | 11 + tcR-2.2.1.7/tcR/man/vis.kmer.histogram.Rd | 2 tcR-2.2.1.7/tcR/man/vis.logo.Rd | 4 tcR-2.2.1.7/tcR/man/vis.number.count.Rd | 2 tcR-2.2.1.7/tcR/man/vis.pca.Rd | 2 tcR-2.2.1.7/tcR/man/vis.radarlike.Rd | 2 tcR-2.2.1.7/tcR/man/vis.rarefaction.Rd | 2 tcR-2.2.1.7/tcR/man/vis.shared.clonotypes.Rd |only tcR-2.2.1.7/tcR/man/vis.top.proportions.Rd | 2 tcR-2.2.1.7/tcR/vignettes/tcrvignette.Rmd | 4 tcR-2.2.1/tcR/R/tmp.R |only tcR-2.2.1/tcR/man/get.n.barcodes.Rd |only 103 files changed, 658 insertions(+), 349 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.5-88 dated 2015-03-17 and 0.5-92 dated 2015-12-22
ChangeLog | 2236 +++++++++++++++++------------------------- DESCRIPTION | 19 MD5 | 78 - NAMESPACE | 22 R/EBI.R | 24 R/error.spsarlm.R | 3 R/geary.R | 4 R/impacts.R | 2 R/lag.spsarlm.R | 2 R/lm.morantest.R | 4 R/mcmcsamp.R | 2 R/moran.R | 4 R/moran.exact.R | 4 R/mtlocalmoran.R | 4 R/mtmoran.R | 2 R/nb2mat.R | 27 R/sacsarlm.R | 19 R/sarlm.R | 951 ++++++++++++----- R/summary.spsarlm.R | 6 build/vignette.rds |binary inst/ChangeLog | 2236 +++++++++++++++++------------------------- inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/nb_igraph.html | 27 inst/doc/sids.pdf |binary man/EBImoran.mc.Rd | 6 man/boston.Rd | 13 man/dnearneigh.Rd | 2 man/eire.Rd | 2 man/house.Rd | 2 man/invIrM.Rd | 4 man/knearneigh.Rd | 2 man/lm.morantest.exact.Rd | 4 man/lm.morantest.sad.Rd | 2 man/localmoran.Rd | 10 man/localmoran.exact.Rd | 2 man/localmoran.sad.Rd | 13 man/nb2blocknb.Rd | 2 man/predict.sarlm.Rd | 70 - 40 files changed, 2776 insertions(+), 3034 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means.
Author: Dennis Walvoort [aut, cre, cph],
Dick Brus [aut, cph],
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.3-5 dated 2013-05-02 and 0.3-6 dated 2015-12-22
spcosa-0.3-5/spcosa/inst/doc/spcosa.pdf |only spcosa-0.3-6/spcosa/DESCRIPTION | 22 ++++++++++----------- spcosa-0.3-6/spcosa/MD5 | 30 ++++++++++++++++++++--------- spcosa-0.3-6/spcosa/NAMESPACE | 22 ++++++--------------- spcosa-0.3-6/spcosa/R/methods_plot.R | 3 -- spcosa-0.3-6/spcosa/R/onAttach.R | 2 - spcosa-0.3-6/spcosa/build/spcosa.pdf |binary spcosa-0.3-6/spcosa/demo/sphere1.R | 4 +-- spcosa-0.3-6/spcosa/inst/NEWS.Rd | 8 +++++++ spcosa-0.3-6/spcosa/inst/doc/spcosa.html |only spcosa-0.3-6/spcosa/java |only spcosa-0.3-6/spcosa/tests/unitTesting.html | 22 ++++++++++----------- 12 files changed, 62 insertions(+), 51 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.13.0 dated 2015-12-15 and 0.13.1 dated 2015-12-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Rvcg-package.R | 4 ++-- inst/NEWS.Rd | 8 ++++++++ man/Rvcg-package.Rd | 4 ++-- src/vcglib/vcg/math/base.h | 8 ++++++-- 6 files changed, 27 insertions(+), 15 deletions(-)
Title: ProPublica API Client
Description: Client for accessing data journalism APIs from ProPublica <http://www.propublica.org/>.
Author: Thomas J. Leeper [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between RPublica versions 0.1.2 dated 2014-12-20 and 0.1.3 dated 2015-12-22
DESCRIPTION | 14 +- MD5 | 24 ++-- NAMESPACE | 4 NEWS | 8 - R/nonprofitexplorer.R | 12 +- README.md | 242 ++++++++++------------------------------------- man/committees.Rd | 2 man/filing.Rd | 2 man/forensics.Rd | 2 man/market.Rd | 2 man/nonprofitexplorer.Rd | 2 man/ppQuery.Rd | 2 man/station.Rd | 2 13 files changed, 92 insertions(+), 226 deletions(-)
Title: An Rcmdr Plug-in for Kaplan-Meier Plots and Other Plots by Using
the ggplot2 Package
Description: A GUI front-end for ggplot2 allows Kaplan-Meier plot, histogram,
Q-Q plot, box plot, errorbar plot, scatter plot, line chart, pie chart,
bar chart, contour plot, and distribution plot.
Author: Triad sou. and Kengo NAGASHIMA
Maintainer: Triad sou. <triadsou@gmail.com>
Diff between RcmdrPlugin.KMggplot2 versions 0.2-1 dated 2015-12-14 and 0.2-2 dated 2015-12-22
DESCRIPTION | 12 - MD5 | 36 ++- NEWS | 206 +++++++++++----------- NEWS.md |only R/guiparts-toolbox.R | 22 +- R/plot-aaa.R | 98 ++++++---- R/plot-factorise.R | 2 R/plot-gbox.R | 60 +----- R/plot-gkm.R | 53 +---- R/plot-gqq.R | 8 R/zzz.R | 9 README.md |only build |only inst/doc |only inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.KMggplot2.mo |binary inst/po/sl/LC_MESSAGES/R-RcmdrPlugin.KMggplot2.mo |binary po/R-RcmdrPlugin.KMggplot2-ja.po | 186 +++++++++---------- po/R-RcmdrPlugin.KMggplot2-sl.po | 186 +++++++++---------- vignettes |only 19 files changed, 443 insertions(+), 435 deletions(-)
More information about RcmdrPlugin.KMggplot2 at CRAN
Permanent link
Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Bjorn Andersson, Kenny Branberg and Marie Wiberg
Maintainer: Bjorn Andersson <bjoern.h.andersson@gmail.com>
Diff between kequate versions 1.4.0 dated 2014-06-04 and 1.5.0 dated 2015-12-22
DESCRIPTION | 14 MD5 | 20 NAMESPACE | 4 NEWS | 5 R/kernel.R | 2282 ++++++++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/irtguide.pdf |binary inst/doc/kequate.pdf |binary man/irtose.Rd | 27 man/kequate-package.Rd | 6 man/plot-methods.Rd | 52 - 11 files changed, 1692 insertions(+), 718 deletions(-)
Title: Client Package for the U.S. Federal Register API
Description: Access data from the Federal Register API <https://www.federalregister.gov/developers/api/v1>.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between federalregister versions 0.1.2 dated 2014-08-06 and 0.2.0 dated 2015-12-22
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 9 +++++---- NEWS | 6 ++++++ R/agencies.r | 11 ++++------- R/fr_get.r | 14 ++++++-------- R/fr_search.r | 30 +++++++++++++++--------------- R/pi_current.r | 11 ++++------- R/pi_get.r | 11 ++++------- R/pi_search.r | 15 ++++++--------- README.md | 36 ++++++++++++++---------------------- man/agencies.Rd | 3 ++- man/fr_get.Rd | 3 ++- man/fr_search.Rd | 6 +++++- man/pi_current.Rd | 3 ++- man/pi_get.Rd | 3 ++- man/pi_search.Rd | 3 ++- 17 files changed, 102 insertions(+), 108 deletions(-)
More information about federalregister at CRAN
Permanent link
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.3 dated 2015-11-26 and 0.3.4 dated 2015-12-22
DESCRIPTION | 8 +++--- MD5 | 27 +++++++++++----------- NAMESPACE | 1 NEWS | 6 ++++ R/genomic.R | 25 +++++++++++++++----- R/utils.R | 4 +-- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.pdf |binary man/col2value.rd | 1 man/colorRamp2.rd | 2 - man/smartAlign.rd |only 15 files changed, 48 insertions(+), 26 deletions(-)
Title: Measures of the Sturdiness of Regression Coefficients
Description: The sValues package implements the s-values proposed by Ed. Leamer.
It provides a context-minimal approach for sensitivity analysis using extreme
bounds to assess the sturdiness of regression coefficients.
Author: Carlos Cinelli
Maintainer: Carlos Cinelli <carloscinelli@hotmail.com>
Diff between sValues versions 0.1.2 dated 2015-10-25 and 0.1.4 dated 2015-12-22
DESCRIPTION | 9 +++-- MD5 | 34 +++++++++---------- NAMESPACE | 4 +- R/internal_functions.R | 10 +++-- R/sValues.R | 2 - build/vignette.rds |binary inst/doc/sValues.Rnw | 3 + inst/doc/sValues.pdf |binary man/coef.sValues.Rd | 16 +++++---- man/economic_growth.Rd | 73 +----------------------------------------- man/plot.sValues.Rd | 5 +- man/print.sValues.Rd | 19 ++++++---- man/sValues-package.Rd | 8 ++-- man/sValues.Rd | 39 +++++++++++----------- man/str.sValues.Rd | 4 +- man/summary.sValues.Rd | 2 - tests/testthat/test-sValues.R | 18 +++++++++- vignettes/sValues.Rnw | 3 + 18 files changed, 106 insertions(+), 143 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help organize Monte Carlo simulations in R. The package
controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.4.1 dated 2015-11-20 and 0.5 dated 2015-12-22
DESCRIPTION | 22 +-- MD5 | 52 +++---- NAMESPACE | 2 R/SimDesign.R | 17 +- R/SimDesign_functions.R | 103 +++++++++----- R/add_missing.R |only R/aggregate_simulations.R | 22 +-- R/analysis.R | 34 +++- R/functions.R | 103 ++++++++------ R/runSimulation.R | 313 +++++++++++++++++++++++++++---------------- R/summary_functions.R | 255 +++++++++++++++++++---------------- R/util.R | 22 ++- man/ECR.Rd | 18 +- man/EDR.Rd | 14 + man/MAE.Rd | 31 ++-- man/RE.Rd | 19 +- man/RMSE.Rd | 40 ++--- man/SimDesign.Rd | 15 -- man/SimDesign_functions.Rd | 16 +- man/add_missing.Rd |only man/aggregate_simulations.Rd | 10 - man/analyse.Rd | 33 ++-- man/bias.Rd | 32 ++-- man/check_error.Rd | 7 man/generate.Rd | 18 +- man/runSimulation.Rd | 222 +++++++++++++++++++----------- man/summarise.Rd | 23 +-- tests/tests/test-SimDesign.R | 88 ++++++++++-- 28 files changed, 954 insertions(+), 577 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.8.1 dated 2015-10-09 and 0.9 dated 2015-12-22
DESCRIPTION | 9 +- MD5 | 104 ++++++++++++++--------------- NAMESPACE | 2 R/beamer_presentation.R | 42 +++++++++-- R/html_document.R | 6 - R/html_document_base.R | 3 R/html_resources.R | 5 - R/md_document.R | 6 - R/output_format.R | 17 +++- R/pandoc.R | 22 +++--- R/params.R | 15 +++- R/pdf_document.R | 15 +++- R/render.R | 104 ++++++++++++++++++----------- R/slidy_presentation.R | 5 - R/tufte_handout.R | 2 R/util.R | 111 ++++++++++++++++++++++++++++++- inst/NEWS | 36 +++++++++- inst/rmd/slidy/Slidy2/scripts/slidy.js | 2 man/beamer_presentation.Rd | 25 +++--- man/default_output_format.Rd | 2 man/draft.Rd | 2 man/find_external_resources.Rd | 18 ++--- man/html_document.Rd | 11 +-- man/html_document_base.Rd | 6 - man/html_fragment.Rd | 12 +-- man/html_vignette.Rd | 6 + man/includes.Rd | 2 man/ioslides_presentation.Rd | 2 man/knit_params_ask.Rd | 2 man/knitr_options.Rd | 6 - man/knitr_options_html.Rd | 2 man/knitr_options_pdf.Rd | 2 man/md_document.Rd | 21 +++-- man/metadata.Rd | 7 - man/output_format.Rd | 7 + man/pandoc_args.Rd | 4 - man/pandoc_available.Rd | 14 +-- man/pandoc_convert.Rd | 7 + man/pandoc_options.Rd | 14 ++- man/pandoc_path_arg.Rd | 8 +- man/pandoc_self_contained_html.Rd | 2 man/pandoc_template.Rd | 2 man/pdf_document.Rd | 21 +++-- man/relative_to.Rd | 2 man/render_delayed.Rd | 3 man/render_supporting_files.Rd | 2 man/rmarkdown_format.Rd | 5 - man/run.Rd | 4 - man/slidy_presentation.Rd | 24 +++--- man/tufte_handout.Rd | 10 +- man/word_document.Rd | 9 +- tests/testthat/resources/file-exists.Rmd |only tests/testthat/resources/quotes.Rmd |only tests/testthat/test-resources.R | 30 ++++++++ 54 files changed, 546 insertions(+), 254 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.38 dated 2015-10-26 and 1.39 dated 2015-12-22
aSPU-1.38/aSPU/R/aSPUpathSingle.r |only aSPU-1.38/aSPU/man/aSPUpathSingle.Rd |only aSPU-1.39/aSPU/DESCRIPTION | 15 +++--- aSPU-1.39/aSPU/MD5 | 65 ++++++++++++++++------------ aSPU-1.39/aSPU/NAMESPACE | 11 +++- aSPU-1.39/aSPU/R/GATES2.R | 2 aSPU-1.39/aSPU/R/GEEaSPU.R | 12 +++-- aSPU-1.39/aSPU/R/GatesSimes.R | 2 aSPU-1.39/aSPU/R/Hyst.R | 2 aSPU-1.39/aSPU/R/MTaSPUs.R |only aSPU-1.39/aSPU/R/RcppExports.R |only aSPU-1.39/aSPU/R/aSPU.R | 13 +---- aSPU-1.39/aSPU/R/aSPUpath.r | 6 +- aSPU-1.39/aSPU/R/aSPUpermC2.R |only aSPU-1.39/aSPU/R/aSPUs.R | 22 +++------ aSPU-1.39/aSPU/R/aSPUsPath.r | 18 +++---- aSPU-1.39/aSPU/R/aSPUsimC2.R |only aSPU-1.39/aSPU/R/aSPUw.R | 2 aSPU-1.39/aSPU/R/estcov.R |only aSPU-1.39/aSPU/R/minP.R |only aSPU-1.39/aSPU/R/simPathAR1SNP.R | 2 aSPU-1.39/aSPU/README.md | 81 ++++++++++++++++++++++++++++++++++- aSPU-1.39/aSPU/man/GATES2.Rd | 9 ++- aSPU-1.39/aSPU/man/GEEaSPU.Rd | 18 ++++--- aSPU-1.39/aSPU/man/GatesSimes.Rd | 7 ++- aSPU-1.39/aSPU/man/Hyst.Rd | 6 +- aSPU-1.39/aSPU/man/MTaSPUs.Rd |only aSPU-1.39/aSPU/man/aSPU.Rd | 10 ++-- aSPU-1.39/aSPU/man/aSPUpath.Rd | 16 +++--- aSPU-1.39/aSPU/man/aSPUs.Rd | 28 +++++------- aSPU-1.39/aSPU/man/aSPUsPath.Rd | 18 +++---- aSPU-1.39/aSPU/man/aSPUw.Rd | 10 ++-- aSPU-1.39/aSPU/man/estcov.Rd |only aSPU-1.39/aSPU/man/getlogitp.Rd | 9 ++- aSPU-1.39/aSPU/man/kegg9.Rd | 14 +++++- aSPU-1.39/aSPU/man/minP.Rd |only aSPU-1.39/aSPU/man/simPathAR1Snp.Rd | 12 +++-- aSPU-1.39/aSPU/src/Makevars |only aSPU-1.39/aSPU/src/Makevars.win |only aSPU-1.39/aSPU/src/RcppExports.cpp |only aSPU-1.39/aSPU/src/aSPU.cpp |only 41 files changed, 265 insertions(+), 145 deletions(-)