Title: Dynamic Simulations of Autoregressive Relationships
Description: Dynamic simulations and graphical depictions of autoregressive relationships.
Author: Christopher Gandrud [aut, cre],
Laron K. Williams [aut],
Guy D. Whitten [aut]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between dynsim versions 1.0 dated 2014-08-13 and 1.2 dated 2015-07-24
dynsim-1.0/dynsim/data/grunfeld.tab.gz |only dynsim-1.2/dynsim/DESCRIPTION | 35 ++++++++----- dynsim-1.2/dynsim/MD5 | 30 +++++++---- dynsim-1.2/dynsim/NAMESPACE | 6 +- dynsim-1.2/dynsim/NEWS | 43 +++++++++++----- dynsim-1.2/dynsim/R/dynsim.R | 87 ++++++++++++++++++++++----------- dynsim-1.2/dynsim/R/dynsimGG.R | 58 +++++++++++++--------- dynsim-1.2/dynsim/R/utils.R | 46 +++++++---------- dynsim-1.2/dynsim/README.md | 8 +-- dynsim-1.2/dynsim/build |only dynsim-1.2/dynsim/data/grunfeld.tab |only dynsim-1.2/dynsim/demo |only dynsim-1.2/dynsim/inst |only dynsim-1.2/dynsim/man/dynsim.Rd | 22 ++++++-- dynsim-1.2/dynsim/man/dynsimGG.Rd | 21 +++++-- dynsim-1.2/dynsim/man/grunfeld.Rd | 3 - dynsim-1.2/dynsim/vignettes |only 17 files changed, 226 insertions(+), 133 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.3 dated 2015-07-23 and 1.1.3.1 dated 2015-07-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/depth.potential.r | 4 ++-- man/ddalpha-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, ctb],
Wouter Thielen [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4-4 dated 2015-03-08 and 0.4-5 dated 2015-07-24
DESCRIPTION | 13 ++++---- MD5 | 30 +++++++++---------- NAMESPACE | 77 +++++++++++++++++++++++++++++++++++++++++-------- R/Defaults.R | 19 ++++++------ R/addTA.R | 12 +++---- R/getDividends.R | 2 - R/getFinancials.R | 2 + R/getOptionChain.R | 14 +++++++- R/getQuote.R | 2 - R/getSplits.R | 2 - R/getSymbols.R | 64 +++++++++++++++++++++------------------- R/loadSymbols.R | 5 ++- R/tools.R | 34 +++++++++++++++++++++ man/Delt.Rd | 12 +++---- man/getSymbols.FRED.Rd | 12 +++++++ man/getSymbols.csv.Rd | 2 + 16 files changed, 210 insertions(+), 92 deletions(-)
Title: Example Datasets from Archaeological Research
Description: The archdata package provides several types of data that are typically used in archaeological research.
Author: David L. Carlson
Maintainer: David L. Carlson <dcarlson@tamu.edu>
Diff between archdata versions 0.1 dated 2014-07-15 and 1.0 dated 2015-07-24
archdata-0.1/archdata/R |only archdata-1.0/archdata/DESCRIPTION | 10 +-- archdata-1.0/archdata/MD5 | 63 ++++++++++++++++-------- archdata-1.0/archdata/data/Acheulean.rda |binary archdata-1.0/archdata/data/BACups.rda |only archdata-1.0/archdata/data/BarmoseI.grid.rda |binary archdata-1.0/archdata/data/BarmoseI.pp.rda |binary archdata-1.0/archdata/data/Bornholm.rda |only archdata-1.0/archdata/data/DartPoints.rda |binary archdata-1.0/archdata/data/EIAGraves.rda |only archdata-1.0/archdata/data/ESASites.rda |only archdata-1.0/archdata/data/EWBurials.rda |binary archdata-1.0/archdata/data/EndScrapers.rda |binary archdata-1.0/archdata/data/EngrBone.rda |only archdata-1.0/archdata/data/Fibulae.rda |only archdata-1.0/archdata/data/Handaxes.rda |binary archdata-1.0/archdata/data/MaskSite.rda |only archdata-1.0/archdata/data/Mesolithic.rda |only archdata-1.0/archdata/data/Nelson.rda |binary archdata-1.0/archdata/data/Olorgesailie.maj.rda |binary archdata-1.0/archdata/data/Olorgesailie.sub.rda |binary archdata-1.0/archdata/data/PitHouses.rda |only archdata-1.0/archdata/data/RBGlass1.rda |only archdata-1.0/archdata/data/RBGlass2.rda |only archdata-1.0/archdata/data/RBPottery.rda |only archdata-1.0/archdata/data/Snodgrass.rda |binary archdata-1.0/archdata/data/TRBPottery.rda |only archdata-1.0/archdata/man/BACups.Rd |only archdata-1.0/archdata/man/BarmoseI.grid.Rd | 4 - archdata-1.0/archdata/man/Bornholm.Rd |only archdata-1.0/archdata/man/EIAGraves.Rd |only archdata-1.0/archdata/man/ESASites.Rd |only archdata-1.0/archdata/man/EWBurials.Rd | 11 ++-- archdata-1.0/archdata/man/EngrBone.Rd |only archdata-1.0/archdata/man/Fibulae.Rd |only archdata-1.0/archdata/man/MaskSite.Rd |only archdata-1.0/archdata/man/Mesolithic.Rd |only archdata-1.0/archdata/man/Nelson.Rd | 6 +- archdata-1.0/archdata/man/Olorgesailie.sub.Rd | 8 +-- archdata-1.0/archdata/man/PitHouses.Rd |only archdata-1.0/archdata/man/RBGlass1.Rd |only archdata-1.0/archdata/man/RBGlass2.Rd |only archdata-1.0/archdata/man/RBPottery.Rd |only archdata-1.0/archdata/man/Snodgrass.Rd | 4 - archdata-1.0/archdata/man/TRBPottery.Rd |only archdata-1.0/archdata/man/archdata-package.Rd | 22 ++++++-- 46 files changed, 85 insertions(+), 43 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Christoph Berreth [ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.0.62 dated 2015-02-03 and 3.1.0 dated 2015-07-24
RandomFields-3.0.62/RandomFields/man/Baysian.Rd |only RandomFields-3.0.62/RandomFields/man/Print.Rd |only RandomFields-3.0.62/RandomFields/src/kriging.cc |only RandomFields-3.1.0/RandomFields/DESCRIPTION | 21 RandomFields-3.1.0/RandomFields/MD5 | 492 RandomFields-3.1.0/RandomFields/NAMESPACE | 16 RandomFields-3.1.0/RandomFields/R/Class.R | 61 RandomFields-3.1.0/RandomFields/R/Crossvalidation.R | 118 RandomFields-3.1.0/RandomFields/R/D.H.R | 44 RandomFields-3.1.0/RandomFields/R/Likelihoodratio.R | 53 RandomFields-3.1.0/RandomFields/R/Methods-RFsp.R | 65 RandomFields-3.1.0/RandomFields/R/Methods-aux.R | 124 RandomFields-3.1.0/RandomFields/R/RC_GLOBALS.R | 33 RandomFields-3.1.0/RandomFields/R/RCauto.R | 156 RandomFields-3.1.0/RandomFields/R/RFempvario-Methods-plots.R | 632 - RandomFields-3.1.0/RandomFields/R/RFempvario.R | 396 RandomFields-3.1.0/RandomFields/R/RFfit.R | 584 RandomFields-3.1.0/RandomFields/R/RFgui.R | 54 RandomFields-3.1.0/RandomFields/R/RMmodels-Methods-plots.R | 63 RandomFields-3.1.0/RandomFields/R/RMmodels.R | 6224 ++-------- RandomFields-3.1.0/RandomFields/R/RMmodelsConvenience.R | 126 RandomFields-3.1.0/RandomFields/R/RMmodelsSpecial.R | 60 RandomFields-3.1.0/RandomFields/R/basic.fctns.R | 423 RandomFields-3.1.0/RandomFields/R/bigdata.R |only RandomFields-3.1.0/RandomFields/R/convert.R | 696 - RandomFields-3.1.0/RandomFields/R/convert_new.R | 253 RandomFields-3.1.0/RandomFields/R/fitbernoulli.R | 22 RandomFields-3.1.0/RandomFields/R/fitbr.R | 23 RandomFields-3.1.0/RandomFields/R/fitgauss.R | 4142 ++---- RandomFields-3.1.0/RandomFields/R/fitmaxstable.R | 24 RandomFields-3.1.0/RandomFields/R/fitpoisson.R | 23 RandomFields-3.1.0/RandomFields/R/generatemodels.R | 157 RandomFields-3.1.0/RandomFields/R/getNset.R | 126 RandomFields-3.1.0/RandomFields/R/internal_use.R | 124 RandomFields-3.1.0/RandomFields/R/kriging.R | 1312 -- RandomFields-3.1.0/RandomFields/R/nicht.nachladbar.R | 24 RandomFields-3.1.0/RandomFields/R/obsolete.R | 107 RandomFields-3.1.0/RandomFields/R/rf-plots.R | 298 RandomFields-3.1.0/RandomFields/R/rf.R | 528 RandomFields-3.1.0/RandomFields/R/zzz.R | 33 RandomFields-3.1.0/RandomFields/inst/CITATION | 5 RandomFields-3.1.0/RandomFields/man/BRspecific.Rd | 15 RandomFields-3.1.0/RandomFields/man/Bayesian.Rd |only RandomFields-3.1.0/RandomFields/man/CoordinateSystems.Rd | 36 RandomFields-3.1.0/RandomFields/man/MajorRevisions.Rd | 16 RandomFields-3.1.0/RandomFields/man/QMath.Rd | 58 RandomFields-3.1.0/RandomFields/man/RC.Rd | 27 RandomFields-3.1.0/RandomFields/man/RF.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFboxcox.Rd |only RandomFields-3.1.0/RandomFields/man/RFcrossvalidate.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFempVariog-class.Rd | 65 RandomFields-3.1.0/RandomFields/man/RFempiricalvariogram.Rd | 18 RandomFields-3.1.0/RandomFields/man/RFfit-class.Rd | 82 RandomFields-3.1.0/RandomFields/man/RFfit.Rd | 69 RandomFields-3.1.0/RandomFields/man/RFfitOptimiser.Rd |only RandomFields-3.1.0/RandomFields/man/RFformula.Rd | 27 RandomFields-3.1.0/RandomFields/man/RFfractaldim.Rd | 7 RandomFields-3.1.0/RandomFields/man/RFgetModelInfo.Rd | 47 RandomFields-3.1.0/RandomFields/man/RFgridDataFrame-class.Rd | 4 RandomFields-3.1.0/RandomFields/man/RFhurst.Rd | 9 RandomFields-3.1.0/RandomFields/man/RFinterpolate.Rd | 42 RandomFields-3.1.0/RandomFields/man/RFlinearpart.Rd |only RandomFields-3.1.0/RandomFields/man/RFloglikelihood.Rd |only RandomFields-3.1.0/RandomFields/man/RFoptions.Rd | 485 RandomFields-3.1.0/RandomFields/man/RFoptionsAdvanced.Rd | 28 RandomFields-3.1.0/RandomFields/man/RFpar.Rd | 2 RandomFields-3.1.0/RandomFields/man/RFratiotest.Rd | 4 RandomFields-3.1.0/RandomFields/man/RFsimulate.Rd | 9 RandomFields-3.1.0/RandomFields/man/RFsimulate.sophisticated.examples.Rd | 9 RandomFields-3.1.0/RandomFields/man/RFsimulateAdvanced.Rd | 15 RandomFields-3.1.0/RandomFields/man/RFspatialGridDataFrame-class.Rd | 6 RandomFields-3.1.0/RandomFields/man/RM.Rd |only RandomFields-3.1.0/RandomFields/man/RMS.Rd | 14 RandomFields-3.1.0/RandomFields/man/RMangle.Rd | 17 RandomFields-3.1.0/RandomFields/man/RMaskey.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMball.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbcw.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbernoulli.Rd | 13 RandomFields-3.1.0/RandomFields/man/RMbessel.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbigneiting.Rd | 37 RandomFields-3.1.0/RandomFields/man/RMbiwm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMbr2.Rd | 8 RandomFields-3.1.0/RandomFields/man/RMbr2bg.Rd | 7 RandomFields-3.1.0/RandomFields/man/RMbrownresnick.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcauchy.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcauchytbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMchoquet.Rd |only RandomFields-3.1.0/RandomFields/man/RMcircular.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMcovariate.Rd | 58 RandomFields-3.1.0/RandomFields/man/RMcoxisham.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcubic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcurlfree.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMcutoff.Rd | 9 RandomFields-3.1.0/RandomFields/man/RMdagum.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdampedcos.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdewijsian.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMdivfree.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMepscauchy.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfix.Rd | 78 RandomFields-3.1.0/RandomFields/man/RMfractdiff.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMfractgauss.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgauss.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgencauchy.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMgenfbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgengneiting.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMgneiting.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMgneitingdiff.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMhyperbolic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMiaco.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMintern.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMintexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMintrinsic.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMkolmogorov.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMlgd.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMma.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmastein.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmatern.Rd | 14 RandomFields-3.1.0/RandomFields/man/RMmodel-class.Rd | 59 RandomFields-3.1.0/RandomFields/man/RMmodel.Rd | 21 RandomFields-3.1.0/RandomFields/man/RMmodelsAdvanced.Rd | 175 RandomFields-3.1.0/RandomFields/man/RMmodelsAuxiliary.Rd | 7 RandomFields-3.1.0/RandomFields/man/RMmodelsMultivariate.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsNonstatationary.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsSpaceTime.Rd |only RandomFields-3.1.0/RandomFields/man/RMmodelsSphere.Rd | 26 RandomFields-3.1.0/RandomFields/man/RMmodelsTailcorrelation.Rd | 13 RandomFields-3.1.0/RandomFields/man/RMmodelsTrend.Rd |only RandomFields-3.1.0/RandomFields/man/RMmppplus.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMmqam.Rd | 5 RandomFields-3.1.0/RandomFields/man/RMmult.Rd | 2 RandomFields-3.1.0/RandomFields/man/RMmultiquad.Rd |only RandomFields-3.1.0/RandomFields/man/RMnatsc.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMnonstwm.Rd | 41 RandomFields-3.1.0/RandomFields/man/RMnsst.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMnugget.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMoesting.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMparswm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpenta.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpoissonpoly.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMpolynome.Rd |only RandomFields-3.1.0/RandomFields/man/RMpower.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMprod.Rd | 9 RandomFields-3.1.0/RandomFields/man/RMqam.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMqexp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMschlather.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMschur.Rd | 6 RandomFields-3.1.0/RandomFields/man/RMsign.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMsinepower.Rd |only RandomFields-3.1.0/RandomFields/man/RMspheric.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstable.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstein.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstp.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMstrokorb.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMtbm.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMtrend.Rd | 141 RandomFields-3.1.0/RandomFields/man/RMtruncsupport.Rd | 3 RandomFields-3.1.0/RandomFields/man/RMuser.Rd | 28 RandomFields-3.1.0/RandomFields/man/RMvector.Rd | 4 RandomFields-3.1.0/RandomFields/man/RMwave.Rd | 3 RandomFields-3.1.0/RandomFields/man/RPbernoulli.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPbrownresnick.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPchi2.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPcirculant.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPcoin.Rd | 16 RandomFields-3.1.0/RandomFields/man/RPgauss.Rd | 9 RandomFields-3.1.0/RandomFields/man/RPhyperplane.Rd | 16 RandomFields-3.1.0/RandomFields/man/RPmaxstable.Rd | 24 RandomFields-3.1.0/RandomFields/man/RPmaxstableAdvanced.Rd | 22 RandomFields-3.1.0/RandomFields/man/RPnugget.Rd | 8 RandomFields-3.1.0/RandomFields/man/RPopitz.Rd | 4 RandomFields-3.1.0/RandomFields/man/RPpoisson.Rd | 6 RandomFields-3.1.0/RandomFields/man/RPschlather.Rd | 7 RandomFields-3.1.0/RandomFields/man/RPsequential.Rd | 32 RandomFields-3.1.0/RandomFields/man/RPsmith.Rd | 8 RandomFields-3.1.0/RandomFields/man/RPspecific.Rd | 17 RandomFields-3.1.0/RandomFields/man/RPspectral.Rd | 9 RandomFields-3.1.0/RandomFields/man/RPt.Rd | 10 RandomFields-3.1.0/RandomFields/man/RPtbm.Rd | 10 RandomFields-3.1.0/RandomFields/man/RR.Rd | 6 RandomFields-3.1.0/RandomFields/man/RRdistr.Rd | 15 RandomFields-3.1.0/RandomFields/man/RRmcmc.Rd | 4 RandomFields-3.1.0/RandomFields/man/RRrectangular.Rd | 7 RandomFields-3.1.0/RandomFields/man/RandomFields.Rd | 125 RandomFields-3.1.0/RandomFields/man/fitgauss.Rd | 2 RandomFields-3.1.0/RandomFields/man/internal.Rd | 9 RandomFields-3.1.0/RandomFields/man/obsolete.Rd | 7 RandomFields-3.1.0/RandomFields/man/papers.GSPSJ06.Rd | 21 RandomFields-3.1.0/RandomFields/man/papers.S02.Rd | 7 RandomFields-3.1.0/RandomFields/man/papers.S10.Rd | 97 RandomFields-3.1.0/RandomFields/man/papers.SBS14.Rd | 9 RandomFields-3.1.0/RandomFields/man/papers.SS11.Rd | 11 RandomFields-3.1.0/RandomFields/man/papers.jss14.Rd | 20 RandomFields-3.1.0/RandomFields/man/plot-method.Rd | 181 RandomFields-3.1.0/RandomFields/man/soil.Rd | 55 RandomFields-3.1.0/RandomFields/man/sp2RF.Rd | 2 RandomFields-3.1.0/RandomFields/src/AutoRandomFields.cc | 39 RandomFields-3.1.0/RandomFields/src/AutoRandomFields.h | 102 RandomFields-3.1.0/RandomFields/src/Brown.cc | 95 RandomFields-3.1.0/RandomFields/src/Coordinate_systems.cc | 494 RandomFields-3.1.0/RandomFields/src/Coordinate_systems.h | 42 RandomFields-3.1.0/RandomFields/src/D.H.cc | 2 RandomFields-3.1.0/RandomFields/src/Families.h | 26 RandomFields-3.1.0/RandomFields/src/Gneiting.cc | 206 RandomFields-3.1.0/RandomFields/src/Huetchen.cc | 21 RandomFields-3.1.0/RandomFields/src/InternalCov.cc | 502 RandomFields-3.1.0/RandomFields/src/KeyInfo.cc | 1060 - RandomFields-3.1.0/RandomFields/src/MLE.cc | 1316 +- RandomFields-3.1.0/RandomFields/src/Operator.h | 57 RandomFields-3.1.0/RandomFields/src/PoissonPolygon.h | 25 RandomFields-3.1.0/RandomFields/src/Primitive.cc | 1259 +- RandomFields-3.1.0/RandomFields/src/RF.h | 1286 +- RandomFields-3.1.0/RandomFields/src/RandomFields.h | 117 RandomFields-3.1.0/RandomFields/src/Specific.cc | 38 RandomFields-3.1.0/RandomFields/src/SpherModels.cc | 175 RandomFields-3.1.0/RandomFields/src/SpherModels.h | 14 RandomFields-3.1.0/RandomFields/src/SpherModelsInitNerror.cc |only RandomFields-3.1.0/RandomFields/src/SpherModelsInitNerror.h |only RandomFields-3.1.0/RandomFields/src/Userinterfaces.h |only RandomFields-3.1.0/RandomFields/src/Xempvario.cc | 4 RandomFields-3.1.0/RandomFields/src/auxiliary.cc | 638 - RandomFields-3.1.0/RandomFields/src/auxiliary.h | 35 RandomFields-3.1.0/RandomFields/src/basic.h | 102 RandomFields-3.1.0/RandomFields/src/circulant.cc | 123 RandomFields-3.1.0/RandomFields/src/convhull2D.h | 29 RandomFields-3.1.0/RandomFields/src/cubicsolver.cc |only RandomFields-3.1.0/RandomFields/src/cubicsolver.h |only RandomFields-3.1.0/RandomFields/src/direct.cc | 77 RandomFields-3.1.0/RandomFields/src/empvario.cc | 105 RandomFields-3.1.0/RandomFields/src/error.h | 59 RandomFields-3.1.0/RandomFields/src/extremes.cc | 229 RandomFields-3.1.0/RandomFields/src/families.cc | 103 RandomFields-3.1.0/RandomFields/src/fftVario.cc | 12 RandomFields-3.1.0/RandomFields/src/gauss.cc | 406 RandomFields-3.1.0/RandomFields/src/gausslikeli.cc |only RandomFields-3.1.0/RandomFields/src/getNset.cc | 1413 +- RandomFields-3.1.0/RandomFields/src/hilfsdateien.cc | 4 RandomFields-3.1.0/RandomFields/src/hyperplan.cc | 111 RandomFields-3.1.0/RandomFields/src/initNerror.cc | 942 - RandomFields-3.1.0/RandomFields/src/initNerrorSpherModels.cc |only RandomFields-3.1.0/RandomFields/src/matrix_mult.cc |only RandomFields-3.1.0/RandomFields/src/metropolis.cc | 2 RandomFields-3.1.0/RandomFields/src/nugget.cc | 50 RandomFields-3.1.0/RandomFields/src/operator.cc | 491 RandomFields-3.1.0/RandomFields/src/plusmalS.cc | 940 - RandomFields-3.1.0/RandomFields/src/primitive.h | 64 RandomFields-3.1.0/RandomFields/src/rf_interfaces.cc | 1165 + RandomFields-3.1.0/RandomFields/src/sequential.cc | 45 RandomFields-3.1.0/RandomFields/src/shape_processes.h | 56 RandomFields-3.1.0/RandomFields/src/spectral.cc | 36 RandomFields-3.1.0/RandomFields/src/startGetNset.cc | 190 RandomFields-3.1.0/RandomFields/src/tbm.cc | 307 RandomFields-3.1.0/RandomFields/src/trend.cc | 371 RandomFields-3.1.0/RandomFields/src/userinterfaces.cc | 611 RandomFields-3.1.0/RandomFields/src/variogramAndCo.cc | 404 RandomFields-3.1.0/RandomFields/src/variogramAndCo.h | 163 RandomFields-3.1.0/RandomFields/src/win_linux_aux.cc | 2 RandomFields-3.1.0/RandomFields/src/win_linux_aux.h | 25 RandomFields-3.1.0/RandomFields/src/xport.cc |only RandomFields-3.1.0/RandomFields/src/xport.h |only 261 files changed, 17532 insertions(+), 19196 deletions(-)
Title: Dual-Agent Dose Escalation for Phase I Trials using the PIPE
Design
Description: Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ. Statistics in Medicine 2015. doi: 10.1002/sim.6434.
Author: Michael Sweeting
Maintainer: Michael Sweeting <mjs212@medschl.cam.ac.uk>
Diff between pipe.design versions 0.2 dated 2015-05-12 and 0.3 dated 2015-07-24
pipe.design-0.2/pipe.design/R/pipe.design_0.2.R |only pipe.design-0.3/pipe.design/DESCRIPTION | 8 ++++---- pipe.design-0.3/pipe.design/MD5 | 10 +++++----- pipe.design-0.3/pipe.design/NAMESPACE | 3 +++ pipe.design-0.3/pipe.design/NEWS | 6 ++++++ pipe.design-0.3/pipe.design/R/pipe.design_0.3.R |only pipe.design-0.3/pipe.design/man/pipe.design.Rd | 6 +++--- 7 files changed, 21 insertions(+), 12 deletions(-)
Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.6.8 dated 2014-03-20 and 0.8.0 dated 2015-07-24
phylobase-0.6.8/phylobase/NEWS |only phylobase-0.6.8/phylobase/R/class-multiphylo4.R |only phylobase-0.6.8/phylobase/R/class-oldclasses.R |only phylobase-0.6.8/phylobase/R/class-phylo4.R |only phylobase-0.6.8/phylobase/R/class-phylo4d.R |only phylobase-0.6.8/phylobase/R/class-phylomats.R |only phylobase-0.6.8/phylobase/R/methods-multiphylo4.R |only phylobase-0.6.8/phylobase/R/methods-oldclasses.R |only phylobase-0.6.8/phylobase/R/methods-phylo4.R |only phylobase-0.6.8/phylobase/R/methods-phylo4d.R |only phylobase-0.6.8/phylobase/R/phylo4.R |only phylobase-0.6.8/phylobase/R/prune.R |only phylobase-0.6.8/phylobase/R/setAs-Methods.R |only phylobase-0.6.8/phylobase/R/subset.R |only phylobase-0.6.8/phylobase/R/treewalk.R |only phylobase-0.6.8/phylobase/inst/doc/developer.Rnw |only phylobase-0.6.8/phylobase/inst/doc/developer.pdf |only phylobase-0.6.8/phylobase/inst/doc/phylobase-plotvcvphylo.pdf |only phylobase-0.6.8/phylobase/inst/nexusfiles/badnex.nex |only phylobase-0.6.8/phylobase/inst/nexusfiles/multiLines.Rdata |only phylobase-0.6.8/phylobase/inst/unitTests |only phylobase-0.6.8/phylobase/man/addData.Rd |only phylobase-0.6.8/phylobase/man/as-methods.Rd |only phylobase-0.6.8/phylobase/man/check.phylo4.Rd |only phylobase-0.6.8/phylobase/man/extract.tree.Rd |only phylobase-0.6.8/phylobase/man/getNode.Rd |only phylobase-0.6.8/phylobase/man/hasSingles.Rd |only phylobase-0.6.8/phylobase/man/phylo4-accessors.Rd |only phylobase-0.6.8/phylobase/man/phylo4-display.Rd |only phylobase-0.6.8/phylobase/man/phylo4-labels.Rd |only phylobase-0.6.8/phylobase/man/phylo4.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-display.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-hasData.Rd |only phylobase-0.6.8/phylobase/man/phylo4d-nData.Rd |only phylobase-0.6.8/phylobase/man/phylo4d.Rd |only phylobase-0.6.8/phylobase/man/phylog.Rd |only phylobase-0.6.8/phylobase/man/printphylo4.Rd |only phylobase-0.6.8/phylobase/man/readNCL.Rd |only phylobase-0.6.8/phylobase/man/tdata.Rd |only phylobase-0.6.8/phylobase/man/treewalk.Rd |only phylobase-0.6.8/phylobase/src/GetNCL.cpp |only phylobase-0.6.8/phylobase/src/ncl |only phylobase-0.6.8/phylobase/src/nxsassumptionsblock.cpp |only phylobase-0.6.8/phylobase/src/nxsblock.cpp |only phylobase-0.6.8/phylobase/src/nxscharactersblock.cpp |only phylobase-0.6.8/phylobase/src/nxscxxdiscretematrix.cpp |only phylobase-0.6.8/phylobase/src/nxsdatablock.cpp |only phylobase-0.6.8/phylobase/src/nxsdistancedatum.cpp |only phylobase-0.6.8/phylobase/src/nxsdistancesblock.cpp |only phylobase-0.6.8/phylobase/src/nxsemptyblock.cpp |only phylobase-0.6.8/phylobase/src/nxsexception.cpp |only phylobase-0.6.8/phylobase/src/nxsmultiformat.cpp |only phylobase-0.6.8/phylobase/src/nxspublicblocks.cpp |only phylobase-0.6.8/phylobase/src/nxsreader.cpp |only phylobase-0.6.8/phylobase/src/nxssetreader.cpp |only phylobase-0.6.8/phylobase/src/nxsstring.cpp |only phylobase-0.6.8/phylobase/src/nxstaxablock.cpp |only phylobase-0.6.8/phylobase/src/nxstoken.cpp |only phylobase-0.6.8/phylobase/src/nxstreesblock.cpp |only phylobase-0.6.8/phylobase/src/nxsunalignedblock.cpp |only phylobase-0.6.8/phylobase/tests/doRUnit.R |only phylobase-0.6.8/phylobase/tests/misctests.Rout.save |only phylobase-0.6.8/phylobase/tests/phylo4dtests.Rout.save |only phylobase-0.6.8/phylobase/tests/phylosubtest.Rout.save |only phylobase-0.6.8/phylobase/tests/phylotorture.Rout.save |only phylobase-0.6.8/phylobase/tests/plottest.Rout.save |only phylobase-0.6.8/phylobase/tests/roundtrip.Rout.save |only phylobase-0.6.8/phylobase/tests/testprune.Rout.save |only phylobase-0.6.8/phylobase/vignettes/developer.Rnw |only phylobase-0.8.0/phylobase/DESCRIPTION | 41 phylobase-0.8.0/phylobase/MD5 | 261 +-- phylobase-0.8.0/phylobase/NAMESPACE | 210 +- phylobase-0.8.0/phylobase/NEWS.md |only phylobase-0.8.0/phylobase/R/MRCA-methods.R |only phylobase-0.8.0/phylobase/R/RcppExports.R | 8 phylobase-0.8.0/phylobase/R/addData-methods.R |only phylobase-0.8.0/phylobase/R/ancestors.R |only phylobase-0.8.0/phylobase/R/checkdata.R | 428 +++-- phylobase-0.8.0/phylobase/R/edgeLength-methods.R |only phylobase-0.8.0/phylobase/R/extractTree.R |only phylobase-0.8.0/phylobase/R/formatData.R | 120 - phylobase-0.8.0/phylobase/R/getNode-methods.R |only phylobase-0.8.0/phylobase/R/internal-constructors.R |only phylobase-0.8.0/phylobase/R/labels-methods.R |only phylobase-0.8.0/phylobase/R/multiphylo4-class.R |only phylobase-0.8.0/phylobase/R/nodeId-methods.R |only phylobase-0.8.0/phylobase/R/oldclasses-class.R |only phylobase-0.8.0/phylobase/R/pdata.R | 126 - phylobase-0.8.0/phylobase/R/phylo4-accessors.R |only phylobase-0.8.0/phylobase/R/phylo4-class.R |only phylobase-0.8.0/phylobase/R/phylo4-methods.R |only phylobase-0.8.0/phylobase/R/phylo4d-accessors.R |only phylobase-0.8.0/phylobase/R/phylo4d-class.R |only phylobase-0.8.0/phylobase/R/phylo4d-methods.R |only phylobase-0.8.0/phylobase/R/phylobase-package.R | 185 +- phylobase-0.8.0/phylobase/R/phylobase.options.R | 53 phylobase-0.8.0/phylobase/R/phylomats-class.R |only phylobase-0.8.0/phylobase/R/print-methods.R |only phylobase-0.8.0/phylobase/R/readNCL.R | 735 +++++----- phylobase-0.8.0/phylobase/R/reorder-methods.R |only phylobase-0.8.0/phylobase/R/root-methods.R |only phylobase-0.8.0/phylobase/R/setAs-methods.R |only phylobase-0.8.0/phylobase/R/shortestPath-methods.R |only phylobase-0.8.0/phylobase/R/subset-methods.R |only phylobase-0.8.0/phylobase/R/summary-methods.R |only phylobase-0.8.0/phylobase/R/tbind.R | 183 -- phylobase-0.8.0/phylobase/R/tdata-methods.R |only phylobase-0.8.0/phylobase/R/treePlot.R | 591 ++++---- phylobase-0.8.0/phylobase/R/treestruc.R | 174 +- phylobase-0.8.0/phylobase/R/zzz.R | 2 phylobase-0.8.0/phylobase/build/vignette.rds |binary phylobase-0.8.0/phylobase/inst/doc/phylobase.Rnw | 580 +++++-- phylobase-0.8.0/phylobase/inst/doc/phylobase.pdf |binary phylobase-0.8.0/phylobase/inst/nexmlfiles |only phylobase-0.8.0/phylobase/inst/nexusfiles/testSubsetTaxa.nex |only phylobase-0.8.0/phylobase/inst/nexusfiles/test_min.nex |only phylobase-0.8.0/phylobase/man/MRCA.Rd |only phylobase-0.8.0/phylobase/man/addData-methods.Rd |only phylobase-0.8.0/phylobase/man/ancestors.Rd |only phylobase-0.8.0/phylobase/man/checkPhylo4.Rd |only phylobase-0.8.0/phylobase/man/edgeLength-methods.Rd |only phylobase-0.8.0/phylobase/man/edges-accessors.Rd |only phylobase-0.8.0/phylobase/man/extractTree.Rd |only phylobase-0.8.0/phylobase/man/formatData.Rd | 149 +- phylobase-0.8.0/phylobase/man/geospiza.Rd | 33 phylobase-0.8.0/phylobase/man/getNode-methods.Rd |only phylobase-0.8.0/phylobase/man/labels-methods.Rd |only phylobase-0.8.0/phylobase/man/multiPhylo-class.Rd | 68 phylobase-0.8.0/phylobase/man/nTips-methods.Rd |only phylobase-0.8.0/phylobase/man/nodeId-methods.Rd |only phylobase-0.8.0/phylobase/man/owls4.Rd | 22 phylobase-0.8.0/phylobase/man/pdata-class.Rd | 58 phylobase-0.8.0/phylobase/man/pdata.Rd | 39 phylobase-0.8.0/phylobase/man/phylo4-class.Rd | 51 phylobase-0.8.0/phylobase/man/phylo4-methods.Rd |only phylobase-0.8.0/phylobase/man/phylo4d-accessors.Rd |only phylobase-0.8.0/phylobase/man/phylo4d-class.Rd | 60 phylobase-0.8.0/phylobase/man/phylo4d-methods.Rd |only phylobase-0.8.0/phylobase/man/phyloXXYY.Rd | 53 phylobase-0.8.0/phylobase/man/phylobase-package.Rd | 83 - phylobase-0.8.0/phylobase/man/phylobase.options.Rd | 66 phylobase-0.8.0/phylobase/man/phylobubbles.Rd | 74 - phylobase-0.8.0/phylobase/man/phylomat-class.Rd | 64 phylobase-0.8.0/phylobase/man/plotOneTree.Rd | 67 phylobase-0.8.0/phylobase/man/print-methods.Rd |only phylobase-0.8.0/phylobase/man/readNexus.Rd |only phylobase-0.8.0/phylobase/man/reorder-methods.Rd | 89 - phylobase-0.8.0/phylobase/man/root-methods.Rd |only phylobase-0.8.0/phylobase/man/setAs-methods.Rd |only phylobase-0.8.0/phylobase/man/shortestPath-methods.Rd |only phylobase-0.8.0/phylobase/man/subset-methods.Rd | 241 +-- phylobase-0.8.0/phylobase/man/summary-methods.Rd |only phylobase-0.8.0/phylobase/man/tdata-methods.Rd |only phylobase-0.8.0/phylobase/man/tip.data.plot.Rd | 56 phylobase-0.8.0/phylobase/man/treePlot-methods.Rd | 132 + phylobase-0.8.0/phylobase/man/treeStructure-methods.Rd |only phylobase-0.8.0/phylobase/src/RcppExports.cpp | 299 +--- phylobase-0.8.0/phylobase/src/checkPhylo4.cpp | 45 phylobase-0.8.0/phylobase/tests/misctests.R | 4 phylobase-0.8.0/phylobase/tests/plottest.R | 6 phylobase-0.8.0/phylobase/tests/testthat/test.checkdata.R |only phylobase-0.8.0/phylobase/tests/testthat/test.class-phylo4.R |only phylobase-0.8.0/phylobase/tests/testthat/test.class-phylo4d.R |only phylobase-0.8.0/phylobase/tests/testthat/test.formatData.R |only phylobase-0.8.0/phylobase/tests/testthat/test.methods-oldclasses.R |only phylobase-0.8.0/phylobase/tests/testthat/test.methods-phylo4.R | 113 + phylobase-0.8.0/phylobase/tests/testthat/test.pdata.R |only phylobase-0.8.0/phylobase/tests/testthat/test.phylo4.R |only phylobase-0.8.0/phylobase/tests/testthat/test.phylobase.options.R |only phylobase-0.8.0/phylobase/tests/testthat/test.prune.R |only phylobase-0.8.0/phylobase/tests/testthat/test.readNCL.R |only phylobase-0.8.0/phylobase/tests/testthat/test.setAs-Methods.R |only phylobase-0.8.0/phylobase/tests/testthat/test.subset.R |only phylobase-0.8.0/phylobase/tests/testthat/test.tbind.R |only phylobase-0.8.0/phylobase/tests/testthat/test.treePlot.R |only phylobase-0.8.0/phylobase/tests/testthat/test.treestruc.R |only phylobase-0.8.0/phylobase/tests/testthat/test.treewalk.R | 42 phylobase-0.8.0/phylobase/vignettes/auto |only phylobase-0.8.0/phylobase/vignettes/phylobase.Rnw | 580 +++++-- 179 files changed, 3356 insertions(+), 2835 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.5.9 dated 2014-11-11 and 1.6.0 dated 2015-07-24
mombf-1.5.9/mombf/R/zbfknown.R |only mombf-1.5.9/mombf/R/zbfunknown.R |only mombf-1.5.9/mombf/R/zellnerbf.R |only mombf-1.5.9/mombf/R/zellnerbf.knownsig.R |only mombf-1.5.9/mombf/R/zellnerbf.lm.R |only mombf-1.5.9/mombf/R/zellnerbf.unknownsig.R |only mombf-1.6.0/mombf/ChangeLog | 4 mombf-1.6.0/mombf/DESCRIPTION | 27 mombf-1.6.0/mombf/MD5 | 63 - mombf-1.6.0/mombf/NAMESPACE | 11 mombf-1.6.0/mombf/R/AllGenerics.R | 2 mombf-1.6.0/mombf/R/cox.R | 48 + mombf-1.6.0/mombf/R/derivatives_nlps.R |only mombf-1.6.0/mombf/R/margpimom.R | 4 mombf-1.6.0/mombf/R/margpmom.R | 6 mombf-1.6.0/mombf/R/modelSelection.R | 129 ++- mombf-1.6.0/mombf/R/msPriorSpec.R | 7 mombf-1.6.0/mombf/R/postMode.R | 18 mombf-1.6.0/mombf/R/pplProbit.R | 5 mombf-1.6.0/mombf/R/rmom.R | 85 +- mombf-1.6.0/mombf/R/zellnerLM.R | 224 ++++++ mombf-1.6.0/mombf/build/vignette.rds |binary mombf-1.6.0/mombf/data/hald.rda |binary mombf-1.6.0/mombf/inst/doc/mombf.R | 4 mombf-1.6.0/mombf/inst/doc/mombf.Rnw | 26 mombf-1.6.0/mombf/inst/doc/mombf.pdf |binary mombf-1.6.0/mombf/man/modelSelection.Rd | 27 mombf-1.6.0/mombf/man/msPriorSpec-class.Rd | 7 mombf-1.6.0/mombf/man/nlpMarginals.Rd | 5 mombf-1.6.0/mombf/man/rnlp.Rd | 9 mombf-1.6.0/mombf/src/cstat.cpp | 608 +++++++++++++---- mombf-1.6.0/mombf/src/cstat.h | 51 + mombf-1.6.0/mombf/src/do_mombf.h | 9 mombf-1.6.0/mombf/src/modelSel.cpp | 989 ++++++++++++++++++++++++++--- mombf-1.6.0/mombf/src/modelSel.h | 66 + mombf-1.6.0/mombf/vignettes/mombf.Rnw | 26 36 files changed, 2018 insertions(+), 442 deletions(-)
Title: Community Structure Detection via Modularity Maximization
Description: The algorithms implemented here are used to detect the community structure of a network.
These algorithms follow different approaches, but are all based on the concept of modularity maximization.
Author: Maria Schelling, Cang Hui
Maintainer: Maria Schelling <schelling.rmaintainer@vodafone.de>
Diff between modMax versions 1.0 dated 2015-02-18 and 1.1 dated 2015-07-24
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 4 R/generalFunctions.R | 78 ++++++++++---- R/greedy.R | 235 ++++++++++++++++++++++++++++---------------- R/saMovements.R | 155 +++++++++++++++++++++++------ R/simulatedAnnealing.R | 15 ++ R/spectralOptimization.R | 59 +++++++---- man/geneticAlgorithm.Rd | 10 - man/spectralOptimization.Rd | 4 10 files changed, 404 insertions(+), 182 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson <christina@stat.umn.edu>
Diff between glmm versions 1.0.3 dated 2015-04-28 and 1.0.4 dated 2015-07-24
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>
Diff between MicSim versions 1.0.8 dated 2015-03-05 and 1.0.9 dated 2015-07-24
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 2 R/auxFctMicSim.r | 26 +-- R/convertToLong.r | 100 ++++++------- R/convertToWide.r | 14 - R/micSim.r | 367 ++++++++++++++++++++++++++------------------------ inst/NEWS.Rd | 6 man/MicSim-package.Rd | 4 9 files changed, 284 insertions(+), 259 deletions(-)
Title: Active Set and Generalized PAVA for Isotone Optimization
Description: Contains two main functions: one for
solving general isotone regression problems using the
pool-adjacent-violators algorithm (PAVA); another one provides
a framework for active set methods for isotone optimization
problems with arbitrary order restrictions. Various types of
loss functions are prespecified.
Author: Patrick Mair [aut, cre], Jan De Leeuw [aut], Kurt Hornik [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between isotone versions 1.0-2 dated 2014-09-10 and 1.1-0 dated 2015-07-24
isotone-1.0-2/isotone/COPYING |only isotone-1.0-2/isotone/inst/doc/vignettes |only isotone-1.1-0/isotone/DESCRIPTION | 22 ++++++++++++---------- isotone-1.1-0/isotone/MD5 | 28 +++++++++++++++------------- isotone-1.1-0/isotone/NAMESPACE | 5 ++++- isotone-1.1-0/isotone/R/mregnn.R |only isotone-1.1-0/isotone/build |only isotone-1.1-0/isotone/inst/doc/isotone.R |only isotone-1.1-0/isotone/inst/doc/isotone.Rnw |only isotone-1.1-0/isotone/inst/doc/isotone.pdf |only isotone-1.1-0/isotone/man/mregnn.Rd |only isotone-1.1-0/isotone/man/posturo.Rd | 4 ++-- isotone-1.1-0/isotone/vignettes |only 13 files changed, 33 insertions(+), 26 deletions(-)
Title: A General Framework for Multivariate Analysis with Optimal
Scaling
Description: Contains various functions for optimal scaling. One function performs optimal scaling by maximizing an aspect (i.e. a target function such as the sum of eigenvalues, sum of squared correlations, squared multiple correlations, etc.) of the corresponding correlation matrix. Another function performs implements the LINEALS approach for optimal scaling by minimization of an aspect based on pairwise correlations and correlation ratios. The resulting correlation matrix and category scores can be used for further multivariate methods such as structural equation models.
Author: Patrick Mair [cre, aut],
Jan De Leeuw [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between aspect versions 1.0-3 dated 2014-11-26 and 1.0-4 dated 2015-07-24
DESCRIPTION | 15 ++++++++------- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Tools for Making, Displaying and Spoiling Sudoku Games
Description: Tools for making, retrieving, displaying and solving sudoku games.
This package is an alternative to the earlier sudoku-solver package,
'sudoku'. The present package uses a slightly different algorithm, has a
simpler coding and presents a few more sugar tools, such as plot and print
methods. Solved sudoku games are of some interest in Experimental Design
as examples of Latin Square designs with additional balance constraints.
Author: Bill Venables <Bill.Venables@gmail.com>
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between sudokuAlt versions 0.1-4 dated 2014-11-13 and 0.1-5 dated 2015-07-24
DESCRIPTION | 10 +++---- MD5 | 31 ++++++++++++------------ NAMESPACE | 4 ++- R/sudokuAlt.R | 62 ++++++++++++++++++++++++++++++++++++++++-------- man/as.sudoku.Rd | 3 +- man/as.sudoku.matrix.Rd | 3 +- man/as.sudoku.sudoku.Rd | 3 +- man/daysAgo.Rd | 3 +- man/fetchAUGame.Rd |only man/fetchUKGame.Rd | 5 ++- man/makeGame.Rd | 3 +- man/originalGame.Rd | 3 +- man/plot.sudoku.Rd | 3 +- man/print.sudoku.Rd | 3 +- man/seedGame.Rd | 3 +- man/solve.sudoku.Rd | 3 +- man/solveGame.Rd | 3 +- 17 files changed, 101 insertions(+), 44 deletions(-)
Title: Analytical Tools for Zooarchaeological Data
Description: The analysis and inference of faunal remains recovered from archaeological sites concerns the field of zooarchaeology. The zooaRch package provides analytical tools to make inferences on zooarchaeological data. Functions in this package allow users to read, manipulate, visualize, and analyze zooarchaeological data.
Author: Erik Otarola-Castillo, Jesse Wolfhagen, Max D. Price
Maintainer: Erik Otarola-Castillo <eotarolacastillo@fas.harvard.edu>
Diff between zooaRch versions 1.0 dated 2015-04-05 and 1.1 dated 2015-07-24
zooaRch-1.0/zooaRch/data/marjRab_fuse.RData |only zooaRch-1.1/zooaRch/DESCRIPTION | 8 zooaRch-1.1/zooaRch/MD5 | 31 +- zooaRch-1.1/zooaRch/NAMESPACE | 5 zooaRch-1.1/zooaRch/R/zooaRch.r | 223 +++++++++++++++++++-- zooaRch-1.1/zooaRch/data/marjRab.fuse.RData |only zooaRch-1.1/zooaRch/data/winslow.fuse.RData |only zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.R | 55 ++++- zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.html | 55 ++++- zooaRch-1.1/zooaRch/inst/doc/zooaRch-vignette.rmd | 62 +++++ zooaRch-1.1/zooaRch/man/fuse.func.Rd | 2 zooaRch-1.1/zooaRch/man/marjRab.Rd | 2 zooaRch-1.1/zooaRch/man/marjRab.fuse.Rd | 2 zooaRch-1.1/zooaRch/man/mort.func.Rd |only zooaRch-1.1/zooaRch/man/speth83.Rd | 2 zooaRch-1.1/zooaRch/man/surv.func.Rd | 3 zooaRch-1.1/zooaRch/man/winslow.fuse.Rd |only zooaRch-1.1/zooaRch/man/zooaRch-package.Rd | 6 zooaRch-1.1/zooaRch/vignettes/zooaRch-vignette.rmd | 62 +++++ 19 files changed, 441 insertions(+), 77 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.1.0 dated 2015-05-09 and 0.1.1 dated 2015-07-24
DESCRIPTION | 9 ++-- MD5 | 16 +++---- NAMESPACE | 1 R/GuanTestUnif.R | 102 +++++++++++++++++++++++++++----------------------- R/GuanTestUnif_help.R | 66 ++++++++++++++++++++------------ R/MaityTest.R | 75 ++++++++++++++++++------------------ R/MaityTest_help.R | 13 +----- man/GuanTestUnif.Rd | 30 +++++++------- man/MaityTest.Rd | 34 +++++++++------- 9 files changed, 189 insertions(+), 157 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.0.6 dated 2015-02-03 and 3.0.8 dated 2015-07-24
ChangeLog | 9 ++ DESCRIPTION | 10 +- MD5 | 12 +- NAMESPACE | 3 R/buffesm.R | 258 +++++++++++++++++++++++++++++++++-------------------------- R/carb.R | 2 R/carbb.R |only man/carbb.Rd |only 8 files changed, 170 insertions(+), 124 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.8.6 dated 2015-07-03 and 0.8.8 dated 2015-07-24
DESCRIPTION | 6 +-- MD5 | 25 ++++++++------ R/gbif_names.R | 23 +++++++----- R/gbif_photos.r | 36 +++++++++++--------- R/occ_search.r | 6 +-- README.md | 2 - man/gbif_names.Rd | 1 man/occ_search.Rd | 6 +-- tests/testthat/test-datasets.r | 22 +++++++----- tests/testthat/test-elevation.R |only tests/testthat/test-gbif_names.R |only tests/testthat/test-gbif_photos.R |only tests/testthat/test-name_lookup.r | 16 +++++--- tests/testthat/test-networks.r | 57 ++++++++++++++++---------------- tests/testthat/test-occ_issues.R |only tests/testthat/test-occ_issues_lookup.R |only 16 files changed, 110 insertions(+), 90 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-10 dated 2015-07-02 and 1.0-11 dated 2015-07-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 11 ++++++----- inst/NEWS | 2 +- inst/doc/rEMM.pdf |binary 5 files changed, 16 insertions(+), 15 deletions(-)
Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to test and develop
recommender algorithms.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between recommenderlab versions 0.1-6 dated 2015-07-02 and 0.1-7 dated 2015-07-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 6 +++--- build/vignette.rds |binary data/Jester5k.rda |binary data/MSWeb.rda |binary data/MovieLense.rda |binary inst/NEWS | 2 +- inst/doc/recommenderlab.pdf |binary 9 files changed, 16 insertions(+), 16 deletions(-)
More information about recommenderlab at CRAN
Permanent link
Title: Function for Generating Random Names and a Dataset
Description: Function for generating random gender and ethnicity correct first and/or last names. Names are chosen proportionally based upon their probability of appearing in a large scale data base of real names.
Author: Damian W. Betebenner <dbetebenner@nciea.org>
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between randomNames versions 0.0-8 dated 2015-02-07 and 0.1-0 dated 2015-07-24
DESCRIPTION | 15 +++++++++------ MD5 | 9 +++++---- NAMESPACE | 2 ++ R/zzz.R |only inst/CITATION | 14 +++++++------- man/randomNames-package.Rd | 10 +++++----- 6 files changed, 28 insertions(+), 22 deletions(-)
Title: Power and Sample Size Calculation for Survival Analysis of
Epidemiological Studies
Description: Functions to calculate power and
sample size for testing main effect or interaction effect in
the survival analysis of epidemiological studies
(non-randomized studies), taking into account the
correlation between the covariate of the
interest and other covariates. Some calculations also take
into account the competing risks and stratified analysis.
This package also includes
a set of functions to calculate power and sample size
for testing main effect in the survival analysis of
randomized clinical trials.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>, Jorge Chavarro <JCHAVARR@hsph.harvard.edu>, Ross Lazarus <ross.lazarus@channing.harvard.edu>, Bernard Rosner <stbar@channing.harvard.edu>, Jing Ma <jing.ma@channing.harvard.edu>.
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerSurvEpi versions 0.0.6 dated 2012-03-31 and 0.0.9 dated 2015-07-24
powerSurvEpi-0.0.6/powerSurvEpi/log.txt |only powerSurvEpi-0.0.9/powerSurvEpi/DESCRIPTION | 41 +++++----- powerSurvEpi-0.0.9/powerSurvEpi/MD5 | 48 ++++++------ powerSurvEpi-0.0.9/powerSurvEpi/NAMESPACE | 13 +-- powerSurvEpi-0.0.9/powerSurvEpi/NEWS |only powerSurvEpi-0.0.9/powerSurvEpi/R/power.stratify.R | 2 powerSurvEpi-0.0.9/powerSurvEpi/data/Oph.rda |binary powerSurvEpi-0.0.9/powerSurvEpi/man/numDEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/numDEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/power.stratify.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiCont.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiCont.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt.default0.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt.default1.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/powerEpiInt2.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssize.stratify.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpi.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpi.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiCont.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiCont.default.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.default0.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt.default1.Rd | 2 powerSurvEpi-0.0.9/powerSurvEpi/man/ssizeEpiInt2.Rd | 2 26 files changed, 71 insertions(+), 71 deletions(-)
Title: Some Nonparametric Tests for Change-Point Detection in Possibly
Multivariate Observations
Description: Provides nonparametric tests for assessing whether possibly serially dependent univariate or multivariate observations have the same c.d.f. or not. In addition to tests focusing directly on the c.d.f., the package contains tests designed to be particularly sensitive to changes in the underlying copula, Spearman's rho or certain quantities that can be estimated using one-sample U-statistics of order two such as the variance, Gini's mean difference or Kendall's tau. The latest addition is a nonparametric test for detecting changes in the distribution of independent block maxima.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between npcp versions 0.1-1 dated 2014-12-20 and 0.1-6 dated 2015-07-24
DESCRIPTION | 15 +++--- MD5 | 27 ++++++----- NAMESPACE | 2 R/ci.R | 5 +- R/tests.R | 123 ++++++++++++++++++++++++++++++++++++++++++++++++++++- man/bOptEmpProc.Rd | 6 +- man/cpTestBM.Rd |only man/cpTestCn.Rd | 8 +-- man/cpTestFn.Rd | 6 +- man/cpTestRho.Rd | 7 +-- man/cpTestU.Rd | 6 +- src/bmtest.c |only src/ci.c | 75 ++++++++++++++++++++------------ src/utilities.c | 4 - src/utilities.h | 1 src/zeroin.c |only 16 files changed, 217 insertions(+), 68 deletions(-)
Title: Mazama Science Spatial Data Download and Utility Functions
Description: A suite of conversion scripts to create internally standardized
spatial polygons dataframes. Utility scripts use these datasets to return
values such as country, state, timezone, watershed, etc. associated with a
set of longitude/latitude pairs. (They also make cool maps.)
Author: Jonathan Callahan [aut, cre],
Will Leahy [aut],
Henry Nguyen [aut],
Robin Winstanley [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaSpatialUtils versions 0.3.1 dated 2015-07-10 and 0.3.2 dated 2015-07-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/MazamaSpatialUtils.R | 7 ++++++- R/getSpatialData.R | 34 ++++++++++++++++++++++++++-------- man/MazamaSpatialUtils.Rd | 7 ++++++- man/getSpatialData.Rd | 9 ++++++--- 6 files changed, 52 insertions(+), 21 deletions(-)
More information about MazamaSpatialUtils at CRAN
Permanent link
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is also available as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with RStudio and knitr including generation of knitr instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.3.1 dated 2015-04-28 and 3.3.3 dated 2015-07-24
lessR-3.3.1/lessR/R/cor_resid.R |only lessR-3.3.1/lessR/R/tAnd.R |only lessR-3.3.1/lessR/R/tNum.R |only lessR-3.3.1/lessR/R/tP.R |only lessR-3.3.1/lessR/R/tRow.R |only lessR-3.3.1/lessR/man/tAnd.Rd |only lessR-3.3.1/lessR/man/tNum.Rd |only lessR-3.3.1/lessR/man/tP.Rd |only lessR-3.3.1/lessR/man/tRow.Rd |only lessR-3.3.3/lessR/DESCRIPTION | 11 lessR-3.3.3/lessR/MD5 | 117 ++--- lessR-3.3.3/lessR/NAMESPACE | 15 lessR-3.3.3/lessR/NEWS | 55 ++ lessR-3.3.3/lessR/R/Correlation.R | 4 lessR-3.3.3/lessR/R/Logit.R | 13 lessR-3.3.3/lessR/R/Read.R | 111 +++-- lessR-3.3.3/lessR/R/Regression.R | 94 +++- lessR-3.3.3/lessR/R/Write.R | 2 lessR-3.3.3/lessR/R/cfa.R | 2 lessR-3.3.3/lessR/R/corCFA.R | 581 +++++++++++++++++----------- lessR-3.3.3/lessR/R/corEFA.R | 95 +--- lessR-3.3.3/lessR/R/corFA.zknitr.R | 243 +++++++++-- lessR-3.3.3/lessR/R/cor_mimm.R | 6 lessR-3.3.3/lessR/R/cr.data.frame.R | 5 lessR-3.3.3/lessR/R/details.R | 47 +- lessR-3.3.3/lessR/R/dist.zknitr.R | 33 + lessR-3.3.3/lessR/R/label.R | 12 lessR-3.3.3/lessR/R/logit.z4Pred.R | 2 lessR-3.3.3/lessR/R/reg.z1anvBasic.R | 6 lessR-3.3.3/lessR/R/reg.z1bckBasic.R | 7 lessR-3.3.3/lessR/R/reg.z1fitBasic.R | 2 lessR-3.3.3/lessR/R/reg.z1modelBasic.R | 4 lessR-3.3.3/lessR/R/reg.z2Relations.R | 10 lessR-3.3.3/lessR/R/reg.z3dnResidual.R | 4 lessR-3.3.3/lessR/R/reg.z3resfitResidual.R | 4 lessR-3.3.3/lessR/R/reg.z3txtResidual.R | 8 lessR-3.3.3/lessR/R/reg.z4Pred.R | 8 lessR-3.3.3/lessR/R/reg.z5Plot.R | 10 lessR-3.3.3/lessR/R/reg.zknitr.R | 595 +++++++++++++++++++---------- lessR-3.3.3/lessR/R/scales.R | 3 lessR-3.3.3/lessR/R/xAnd.R |only lessR-3.3.3/lessR/R/xNum.R |only lessR-3.3.3/lessR/R/xP.R |only lessR-3.3.3/lessR/R/xRow.R |only lessR-3.3.3/lessR/R/xU.R |only lessR-3.3.3/lessR/R/xW.R |only lessR-3.3.3/lessR/R/zzz.R | 238 +++++++++-- lessR-3.3.3/lessR/inst/CITATION | 2 lessR-3.3.3/lessR/man/BarChart.Rd | 9 lessR-3.3.3/lessR/man/BoxPlot.Rd | 2 lessR-3.3.3/lessR/man/Density.Rd | 2 lessR-3.3.3/lessR/man/Histogram.Rd | 2 lessR-3.3.3/lessR/man/LineChart.Rd | 2 lessR-3.3.3/lessR/man/Logit.Rd | 4 lessR-3.3.3/lessR/man/Read.Rd | 30 - lessR-3.3.3/lessR/man/Regression.Rd | 100 ++-- lessR-3.3.3/lessR/man/ScatterPlot.Rd | 10 lessR-3.3.3/lessR/man/Subset.Rd | 2 lessR-3.3.3/lessR/man/SummaryStats.Rd | 2 lessR-3.3.3/lessR/man/Write.Rd | 4 lessR-3.3.3/lessR/man/corCFA.Rd | 153 +++++-- lessR-3.3.3/lessR/man/corRead.Rd | 4 lessR-3.3.3/lessR/man/label.Rd | 4 lessR-3.3.3/lessR/man/ttest.Rd | 28 - lessR-3.3.3/lessR/man/xAnd.Rd |only lessR-3.3.3/lessR/man/xNum.Rd |only lessR-3.3.3/lessR/man/xP.Rd |only lessR-3.3.3/lessR/man/xRow.Rd |only lessR-3.3.3/lessR/man/xU.Rd |only lessR-3.3.3/lessR/man/xW.Rd |only 70 files changed, 1778 insertions(+), 929 deletions(-)
Title: Deconvolution of Tumour Profiles
Description: Deconvolution of mixed tumour profiles into normal and cancer for each patient, using
the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires
mixed tumour profiles and a set of unmatched "basis" normal profiles.
Author: Gerald Quon [aut], Catalina V Anghel [aut, trl], Syed Haider [aut], Francis Nguyen [aut], Amit G Deshwar [aut], Quaid D
Morris [aut], Paul C Boutros [aut, cre]
Maintainer: Paul C Boutros <Paul.Boutros@oicr.on.ca>
Diff between ISOpureR versions 1.0.8 dated 2015-01-08 and 1.0.18 dated 2015-07-24
ISOpureR-1.0.18/ISOpureR/DESCRIPTION | 10 ISOpureR-1.0.18/ISOpureR/MD5 | 64 ISOpureR-1.0.18/ISOpureR/NAMESPACE | 6 ISOpureR-1.0.18/ISOpureR/NEWS | 86 ISOpureR-1.0.18/ISOpureR/R/ISOpure.step1.CPE.R |only ISOpureR-1.0.18/ISOpureR/R/ISOpure.step2.PPE.R |only ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.new_model.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_core.optmodel.R | 23 ISOpureR-1.0.18/ISOpureR/R/ISOpureS1.model_optimize.opt_kappa.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_core.optmodel.R | 23 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.opt_kappa.R | 2 ISOpureR-1.0.18/ISOpureR/R/ISOpureS2.model_optimize.theta.theta_loglikelihood.R | 2 ISOpureR-1.0.18/ISOpureR/build/vignette.rds |binary ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.Rnw | 871 ++++++++-- ISOpureR-1.0.18/ISOpureR/inst/doc/ISOpureRGuide.pdf |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/alphapurities_full_dataset.txt |only ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.ISOpureS1model.1000.transcripts.30.patients.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.1000.transcripts.30.patients.rounded.RData |only ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.normaldata.1000.transcripts.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/beer.tumordata.1000.transcripts.30.patients.RData |binary ISOpureR-1.0.18/ISOpureR/inst/extdata/Beer/probeset_names.txt |only ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step1_beer.R | 3 ISOpureR-1.0.18/ISOpureR/inst/tests/test_ISOpure_step2_beer.R | 3 ISOpureR-1.0.18/ISOpureR/man/ISOpure.step1.CPE.Rd |only ISOpureR-1.0.18/ISOpureR/man/ISOpure.step2.PPE.Rd |only ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_core.new_model.Rd | 2 ISOpureR-1.0.18/ISOpureR/man/ISOpureS1.model_optimize.opt_kappa.Rd | 2 ISOpureR-1.0.18/ISOpureR/man/ISOpureS2.model_optimize.opt_kappa.Rd | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.cc_functions.R | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.kappa_vv_functions.R | 2 ISOpureR-1.0.18/ISOpureR/tests/test.ISOpureS2.model_optimize.theta_functions.R | 2 ISOpureR-1.0.18/ISOpureR/vignettes/Figures |only ISOpureR-1.0.18/ISOpureR/vignettes/ISOpureRGuide.Rnw | 871 ++++++++-- ISOpureR-1.0.8/ISOpureR/R/ISOpureS1.model_core.learnmodel.R |only ISOpureR-1.0.8/ISOpureR/R/ISOpureS2.model_core.learnmodel.R |only ISOpureR-1.0.8/ISOpureR/inst/extdata/Beer/beer.ISOpureS2model.1000.transcripts.30.patients.RData |only ISOpureR-1.0.8/ISOpureR/man/ISOpureS1.model_core.learnmodel.Rd |only ISOpureR-1.0.8/ISOpureR/man/ISOpureS2.model_core.learnmodel.Rd |only 38 files changed, 1734 insertions(+), 246 deletions(-)
Title: Tools for Detecting Influential Data in Mixed Effects Models
Description: Provides a collection of tools for
detecting influential cases in generalized mixed effects
models. It analyses models that were estimated using lme4. The
basic rationale behind identifying influential data is that
when iteratively single units are omitted from the data, models
based on these data should not produce substantially different
estimates. To standardize the assessment of how influential a
(single group of) observation(s) is, several measures of
influence are common practice, such as DFBETAS and Cook's Distance.
In addition, we provide a measure of percentage change of the fixed point
estimates and a simple procedure to detect changing levels of significance.
Author: Rense Nieuwenhuis, Ben Pelzer, Manfred te Grotenhuis
Maintainer: Rense Nieuwenhuis <rense.nieuwenhuis@sofi.su.se>
Diff between influence.ME versions 0.9-5 dated 2014-12-17 and 0.9-6 dated 2015-07-24
DESCRIPTION | 10 MD5 | 26 +- NAMESPACE | 44 ++-- R/cooks.distance.extex.r | 2 R/exclude.influence.R | 21 + R/influence.R | 483 ++++++++++++++++++++++---------------------- man/cooks.distance.estex.Rd | 6 man/dfbetas.estex.Rd | 6 man/exclude.influence.Rd | 6 man/grouping.levels.Rd | 2 man/influence.ME-package.Rd | 2 man/influence.mer.Rd | 17 - man/pchange.Rd | 4 man/plot.estex.Rd | 2 14 files changed, 327 insertions(+), 304 deletions(-)
Title: Into the extRemes Package
Description: Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between in2extRemes versions 1.0-1 dated 2014-01-28 and 1.0-2 dated 2015-07-24
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 13 insertions(+), 8 deletions(-)
Title: Method Functions for Confidence Intervals and to Distill
Information from an Object
Description: Some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between distillery versions 1.0-1 dated 2013-06-26 and 1.0-2 dated 2015-07-24
DESCRIPTION | 13 +++++-------- MD5 | 4 ++-- NAMESPACE | 10 ++++++++++ 3 files changed, 17 insertions(+), 10 deletions(-)
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 1.0.3 dated 2014-12-26 and 2.0.0 dated 2015-07-24
DESCRIPTION | 14 MD5 | 20 NAMESPACE | 8 R/cjoint.R | 2868 +++++++++++++++++++++++++++++++++----------------- demo/cjointdemo.R | 36 man/amce.Rd | 70 - man/cjoint-package.Rd | 8 man/makeDesign.Rd | 313 ++--- man/plot.amce.Rd | 117 +- man/summary.amce.Rd | 91 - tests |only 11 files changed, 2301 insertions(+), 1244 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.0.6 dated 2015-06-19 and 4.1.15 dated 2015-07-24
ChemoSpec-4.0.6/ChemoSpec/R/getMaxCovByFreq.R |only ChemoSpec-4.0.6/ChemoSpec/man/getMaxCovByFreq.Rd |only ChemoSpec-4.1.15/ChemoSpec/DESCRIPTION | 10 +- ChemoSpec-4.1.15/ChemoSpec/MD5 | 73 ++++++++++---------- ChemoSpec-4.1.15/ChemoSpec/NAMESPACE | 20 ++++- ChemoSpec-4.1.15/ChemoSpec/NEWS | 16 ++++ ChemoSpec-4.1.15/ChemoSpec/R/baselineSpectra.R | 6 + ChemoSpec-4.1.15/ChemoSpec/R/check4Gaps.R | 4 - ChemoSpec-4.1.15/ChemoSpec/R/cleanSTOCSYpeaks.R |only ChemoSpec-4.1.15/ChemoSpec/R/collapseRowsOrCols.R |only ChemoSpec-4.1.15/ChemoSpec/R/corSpectra.R | 42 +++++------ ChemoSpec-4.1.15/ChemoSpec/R/covSpectra.R | 14 +-- ChemoSpec-4.1.15/ChemoSpec/R/covSpectraJS.R | 14 +-- ChemoSpec-4.1.15/ChemoSpec/R/hcaScores.R | 5 - ChemoSpec-4.1.15/ChemoSpec/R/hcaSpectra.R | 5 - ChemoSpec-4.1.15/ChemoSpec/R/hmapSpectra.R | 7 + ChemoSpec-4.1.15/ChemoSpec/R/labelExtremes.R | 2 ChemoSpec-4.1.15/ChemoSpec/R/plot2Loadings.R | 5 + ChemoSpec-4.1.15/ChemoSpec/R/plotHCA.R | 8 +- ChemoSpec-4.1.15/ChemoSpec/R/sPlotSpectra.R | 4 - ChemoSpec-4.1.15/ChemoSpec/R/sortCrossPeaks.R |only ChemoSpec-4.1.15/ChemoSpec/R/sumSpectra.R | 14 +++ ChemoSpec-4.1.15/ChemoSpec/R/surveySpectra2.R | 18 +++- ChemoSpec-4.1.15/ChemoSpec/build/vignette.rds |binary ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.R | 14 +++ ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.Rnw | 18 +++- ChemoSpec-4.1.15/ChemoSpec/inst/doc/ChemoSpec.pdf |binary ChemoSpec-4.1.15/ChemoSpec/man/ChemoSpec-package.Rd | 10 -- ChemoSpec-4.1.15/ChemoSpec/man/check4Gaps.Rd | 3 ChemoSpec-4.1.15/ChemoSpec/man/cleanSTOCSYpeaks.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/corSpectra.Rd | 15 +--- ChemoSpec-4.1.15/ChemoSpec/man/hcaScores.Rd | 6 + ChemoSpec-4.1.15/ChemoSpec/man/hcaSpectra.Rd | 6 + ChemoSpec-4.1.15/ChemoSpec/man/hmapSpectra.Rd | 14 +-- ChemoSpec-4.1.15/ChemoSpec/man/plot2Loadings.Rd | 4 - ChemoSpec-4.1.15/ChemoSpec/man/plotHCA.Rd | 5 + ChemoSpec-4.1.15/ChemoSpec/man/plotSpectraJS.Rd | 2 ChemoSpec-4.1.15/ChemoSpec/man/sPlotSpectra.Rd | 4 - ChemoSpec-4.1.15/ChemoSpec/man/sortCrossPeaks.Rd |only ChemoSpec-4.1.15/ChemoSpec/man/surveySpectra.Rd | 2 ChemoSpec-4.1.15/ChemoSpec/vignettes/ChemoSpec.Rnw | 18 +++- 41 files changed, 239 insertions(+), 149 deletions(-)
Title: Function for Converting Cardinal to Ordinal Numbers by Adding a
Language Specific Ordinal Indicator to the Number
Description: Function for converting cardinal to ordinal numbers by adding a language specific ordinal indicator (http://en.wikipedia.org/wiki/Ordinal_indicator) to the number.
Author: Damian W. Betebenner [aut, cre],
Andrew Martin [ctb],
Jeff Erickson [ctb]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between toOrdinal versions 0.0-1 dated 2015-03-12 and 0.0-4 dated 2015-07-24
DESCRIPTION | 21 +++++-- MD5 | 17 +++--- NAMESPACE | 1 R/toOrdinal.R | 124 +++++++++++++++++++++++++++++++++-------------- inst/CITATION | 4 - inst/NEWS | 13 ++++ man/toOrdinal-package.Rd | 4 - man/toOrdinal.Rd | 12 +++- tests |only 9 files changed, 139 insertions(+), 57 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.2.0 dated 2015-07-07 and 1.2.1 dated 2015-07-24
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++--------------- NEWS | 15 ++++++++++++++ R/EpiModel-package.r | 4 +-- R/control.R | 12 ++++++----- R/icm.R | 3 -- R/net.utils.R | 18 ++++++++-------- R/netest.R | 7 ++---- R/plot.R | 48 +++++++++++++++++++++++++++------------------ R/verbose.R | 2 - inst/doc/Intro.html | 2 - inst/shiny/epiicm/server.R | 10 ++++----- man/EpiModel-package.Rd | 4 +-- man/comp_plot.Rd | 2 - man/control.icm.Rd | 5 ---- man/control.net.Rd | 2 + man/icm.Rd | 3 -- 17 files changed, 98 insertions(+), 79 deletions(-)