Title: Vector Generalized Linear and Additive Models
Diff between VGAM versions 0.9-4 dated 2014-05-28 and 0.9-5 dated 2014-11-05
Description: This package fits many (150+) models and
distributions by maximum likelihood estimation (MLE)
or penalized MLE, using Fisher scoring. This is done
via the vector generalized linear and additive model
(VGLM/VGAM) classes and associated models (reduced-rank
VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, row-column
interaction models). These are abbreviated RR-VGLMs,
QRR-VGLMs, RR-VGAMs and RCIMs. These include constrained
and unconstrained quadratic ordination (CQO/UQO) models
in ecology as well as constrained additive ordination
(CAO). Note that these functions are subject to change,
especially before version 1.0.0 is released; see the NEWS
file for latest changes.
Author: Thomas W. Yee
Maintainer: Thomas Yee
VGAM-0.9-4/VGAM/data/mmt.rda |only
VGAM-0.9-4/VGAM/man/AB.Ab.aB.ab2.Rd |only
VGAM-0.9-4/VGAM/man/G1G2G3.Rd |only
VGAM-0.9-4/VGAM/man/Pareto.Rd |only
VGAM-0.9-4/VGAM/man/SUR.Rd |only
VGAM-0.9-4/VGAM/man/amh.Rd |only
VGAM-0.9-4/VGAM/man/amhUC.Rd |only
VGAM-0.9-4/VGAM/man/beta.ab.Rd |only
VGAM-0.9-4/VGAM/man/betabinomial.ab.Rd |only
VGAM-0.9-4/VGAM/man/bigumbelI.Rd |only
VGAM-0.9-4/VGAM/man/bilogis4UC.Rd |only
VGAM-0.9-4/VGAM/man/bilogistic4.Rd |only
VGAM-0.9-4/VGAM/man/bivgamma.mckay.Rd |only
VGAM-0.9-4/VGAM/man/cennormal.Rd |only
VGAM-0.9-4/VGAM/man/cenpoisson.Rd |only
VGAM-0.9-4/VGAM/man/cgumbel.Rd |only
VGAM-0.9-4/VGAM/man/double.cennormal.Rd |only
VGAM-0.9-4/VGAM/man/expexp.Rd |only
VGAM-0.9-4/VGAM/man/expexp1.Rd |only
VGAM-0.9-4/VGAM/man/fgm.Rd |only
VGAM-0.9-4/VGAM/man/fgmUC.Rd |only
VGAM-0.9-4/VGAM/man/gamma2.ab.Rd |only
VGAM-0.9-4/VGAM/man/gammahyp.Rd |only
VGAM-0.9-4/VGAM/man/invbinomial.Rd |only
VGAM-0.9-4/VGAM/man/invlomax.Rd |only
VGAM-0.9-4/VGAM/man/invlomaxUC.Rd |only
VGAM-0.9-4/VGAM/man/invparalogistic.Rd |only
VGAM-0.9-4/VGAM/man/invparalogisticUC.Rd |only
VGAM-0.9-4/VGAM/man/koenker.Rd |only
VGAM-0.9-4/VGAM/man/koenkerUC.Rd |only
VGAM-0.9-4/VGAM/man/matched.binomial.Rd |only
VGAM-0.9-4/VGAM/man/mlogit.Rd |only
VGAM-0.9-4/VGAM/man/mmt.Rd |only
VGAM-0.9-4/VGAM/man/morgenstern.Rd |only
VGAM-0.9-4/VGAM/man/plackUC.Rd |only
VGAM-0.9-4/VGAM/man/plackett.Rd |only
VGAM-0.9-4/VGAM/man/recexp1.Rd |only
VGAM-0.9-4/VGAM/man/recnormal.Rd |only
VGAM-0.9-4/VGAM/man/weibull.Rd |only
VGAM-0.9-5/VGAM/DESCRIPTION | 15
VGAM-0.9-5/VGAM/MD5 | 600 +++---
VGAM-0.9-5/VGAM/NAMESPACE | 155 -
VGAM-0.9-5/VGAM/NEWS | 163 +
VGAM-0.9-5/VGAM/R/aamethods.q | 45
VGAM-0.9-5/VGAM/R/bAIC.q | 10
VGAM-0.9-5/VGAM/R/calibrate.q | 12
VGAM-0.9-5/VGAM/R/cao.R | 2
VGAM-0.9-5/VGAM/R/cao.fit.q | 159 -
VGAM-0.9-5/VGAM/R/cqo.fit.q | 8
VGAM-0.9-5/VGAM/R/deviance.vlm.q | 32
VGAM-0.9-5/VGAM/R/family.actuary.R | 516 ++---
VGAM-0.9-5/VGAM/R/family.aunivariate.R | 350 +--
VGAM-0.9-5/VGAM/R/family.basics.R | 178 +
VGAM-0.9-5/VGAM/R/family.binomial.R | 182 +
VGAM-0.9-5/VGAM/R/family.bivariate.R | 661 +++---
VGAM-0.9-5/VGAM/R/family.categorical.R | 134 -
VGAM-0.9-5/VGAM/R/family.censored.R | 143 -
VGAM-0.9-5/VGAM/R/family.circular.R | 10
VGAM-0.9-5/VGAM/R/family.exp.R | 22
VGAM-0.9-5/VGAM/R/family.extremes.R | 526 +++--
VGAM-0.9-5/VGAM/R/family.functions.R | 32
VGAM-0.9-5/VGAM/R/family.genetic.R | 457 +++-
VGAM-0.9-5/VGAM/R/family.glmgam.R | 116 -
VGAM-0.9-5/VGAM/R/family.loglin.R | 8
VGAM-0.9-5/VGAM/R/family.math.R | 33
VGAM-0.9-5/VGAM/R/family.mixture.R | 19
VGAM-0.9-5/VGAM/R/family.nonlinear.R | 4
VGAM-0.9-5/VGAM/R/family.normal.R | 274 +-
VGAM-0.9-5/VGAM/R/family.others.R | 378 ++--
VGAM-0.9-5/VGAM/R/family.positive.R | 44
VGAM-0.9-5/VGAM/R/family.qreg.R | 703 +++----
VGAM-0.9-5/VGAM/R/family.quantal.R | 8
VGAM-0.9-5/VGAM/R/family.rcim.R | 75
VGAM-0.9-5/VGAM/R/family.rcqo.R | 110 -
VGAM-0.9-5/VGAM/R/family.robust.R | 32
VGAM-0.9-5/VGAM/R/family.rrr.R | 293 +--
VGAM-0.9-5/VGAM/R/family.sur.R | 18
VGAM-0.9-5/VGAM/R/family.survival.R | 76
VGAM-0.9-5/VGAM/R/family.ts.R | 2
VGAM-0.9-5/VGAM/R/family.univariate.R | 2172 +++++++++++++++--------
VGAM-0.9-5/VGAM/R/family.zeroinf.R | 181 -
VGAM-0.9-5/VGAM/R/fittedvlm.R | 16
VGAM-0.9-5/VGAM/R/links.q | 27
VGAM-0.9-5/VGAM/R/logLik.vlm.q | 19
VGAM-0.9-5/VGAM/R/model.matrix.vglm.q | 74
VGAM-0.9-5/VGAM/R/nobs.R | 8
VGAM-0.9-5/VGAM/R/plot.vglm.q | 77
VGAM-0.9-5/VGAM/R/predict.vglm.q | 82
VGAM-0.9-5/VGAM/R/qrrvglm.control.q | 2
VGAM-0.9-5/VGAM/R/qtplot.q | 35
VGAM-0.9-5/VGAM/R/rrvglm.control.q | 10
VGAM-0.9-5/VGAM/R/rrvglm.fit.q | 2
VGAM-0.9-5/VGAM/R/smart.R | 646 +++---
VGAM-0.9-5/VGAM/R/summary.vglm.q | 65
VGAM-0.9-5/VGAM/R/summary.vlm.q | 20
VGAM-0.9-5/VGAM/R/vgam.control.q | 4
VGAM-0.9-5/VGAM/R/vglm.control.q | 20
VGAM-0.9-5/VGAM/R/vglm.fit.q | 3
VGAM-0.9-5/VGAM/R/vsmooth.spline.q | 2
VGAM-0.9-5/VGAM/build |only
VGAM-0.9-5/VGAM/data/Huggins89.t1.rda |binary
VGAM-0.9-5/VGAM/data/Huggins89table1.rda |binary
VGAM-0.9-5/VGAM/data/alclevels.rda |binary
VGAM-0.9-5/VGAM/data/alcoff.rda |binary
VGAM-0.9-5/VGAM/data/auuc.rda |binary
VGAM-0.9-5/VGAM/data/backPain.rda |binary
VGAM-0.9-5/VGAM/data/beggs.rda |binary
VGAM-0.9-5/VGAM/data/car.all.rda |binary
VGAM-0.9-5/VGAM/data/cfibrosis.rda |binary
VGAM-0.9-5/VGAM/data/corbet.rda |binary
VGAM-0.9-5/VGAM/data/crashbc.rda |binary
VGAM-0.9-5/VGAM/data/crashf.rda |binary
VGAM-0.9-5/VGAM/data/crashi.rda |binary
VGAM-0.9-5/VGAM/data/crashmc.rda |binary
VGAM-0.9-5/VGAM/data/crashp.rda |binary
VGAM-0.9-5/VGAM/data/crashtr.rda |binary
VGAM-0.9-5/VGAM/data/deermice.rda |binary
VGAM-0.9-5/VGAM/data/finney44.rda |binary
VGAM-0.9-5/VGAM/data/flourbeetle.rda |only
VGAM-0.9-5/VGAM/data/hspider.rda |binary
VGAM-0.9-5/VGAM/data/lakeO.rda |binary
VGAM-0.9-5/VGAM/data/leukemia.rda |binary
VGAM-0.9-5/VGAM/data/marital.nz.rda |binary
VGAM-0.9-5/VGAM/data/melbmaxtemp.rda |only
VGAM-0.9-5/VGAM/data/pneumo.rda |binary
VGAM-0.9-5/VGAM/data/prinia.rda |binary
VGAM-0.9-5/VGAM/data/ruge.rda |binary
VGAM-0.9-5/VGAM/data/toxop.rda |binary
VGAM-0.9-5/VGAM/data/venice.rda |binary
VGAM-0.9-5/VGAM/data/venice90.rda |binary
VGAM-0.9-5/VGAM/data/wine.rda |binary
VGAM-0.9-5/VGAM/inst/doc |only
VGAM-0.9-5/VGAM/man/A1A2A3.Rd |only
VGAM-0.9-5/VGAM/man/AA.Aa.aa.Rd | 69
VGAM-0.9-5/VGAM/man/AB.Ab.aB.ab.Rd | 9
VGAM-0.9-5/VGAM/man/ABO.Rd | 7
VGAM-0.9-5/VGAM/man/AICvlm.Rd | 4
VGAM-0.9-5/VGAM/man/Coef.Rd | 4
VGAM-0.9-5/VGAM/man/Coef.qrrvglm-class.Rd | 4
VGAM-0.9-5/VGAM/man/Coef.qrrvglm.Rd | 19
VGAM-0.9-5/VGAM/man/CommonVGAMffArguments.Rd | 29
VGAM-0.9-5/VGAM/man/Links.Rd | 6
VGAM-0.9-5/VGAM/man/MNSs.Rd | 6
VGAM-0.9-5/VGAM/man/Max.Rd | 8
VGAM-0.9-5/VGAM/man/Opt.Rd | 10
VGAM-0.9-5/VGAM/man/ParetoUC.Rd |only
VGAM-0.9-5/VGAM/man/QvarUC.Rd | 41
VGAM-0.9-5/VGAM/man/SURff.Rd |only
VGAM-0.9-5/VGAM/man/Select.Rd | 12
VGAM-0.9-5/VGAM/man/SurvS4.Rd | 4
VGAM-0.9-5/VGAM/man/VGAM-package.Rd | 2
VGAM-0.9-5/VGAM/man/alaplace3.Rd | 170 +
VGAM-0.9-5/VGAM/man/amlnormal.Rd | 24
VGAM-0.9-5/VGAM/man/benini.Rd | 34
VGAM-0.9-5/VGAM/man/beniniUC.Rd | 20
VGAM-0.9-5/VGAM/man/betaII.Rd | 4
VGAM-0.9-5/VGAM/man/betaR.Rd |only
VGAM-0.9-5/VGAM/man/betabinomUC.Rd | 4
VGAM-0.9-5/VGAM/man/betabinomial.Rd | 21
VGAM-0.9-5/VGAM/man/betabinomialff.Rd |only
VGAM-0.9-5/VGAM/man/betaff.Rd | 6
VGAM-0.9-5/VGAM/man/betageometric.Rd | 4
VGAM-0.9-5/VGAM/man/biamhcop.Rd |only
VGAM-0.9-5/VGAM/man/biamhcopUC.Rd |only
VGAM-0.9-5/VGAM/man/biclaytoncop.Rd | 15
VGAM-0.9-5/VGAM/man/biclaytoncopUC.Rd | 14
VGAM-0.9-5/VGAM/man/bifgmcop.Rd |only
VGAM-0.9-5/VGAM/man/bifgmcopUC.Rd |only
VGAM-0.9-5/VGAM/man/bifgmexp.Rd |only
VGAM-0.9-5/VGAM/man/bifrankcop.Rd | 4
VGAM-0.9-5/VGAM/man/bifrankcopUC.Rd | 20
VGAM-0.9-5/VGAM/man/bigamma.mckay.Rd |only
VGAM-0.9-5/VGAM/man/bigumbelIexp.Rd |only
VGAM-0.9-5/VGAM/man/bilogisUC.Rd |only
VGAM-0.9-5/VGAM/man/bilogistic.Rd |only
VGAM-0.9-5/VGAM/man/binom2.or.Rd | 7
VGAM-0.9-5/VGAM/man/binomialff.Rd | 16
VGAM-0.9-5/VGAM/man/binormal.Rd | 4
VGAM-0.9-5/VGAM/man/binormalUC.Rd | 4
VGAM-0.9-5/VGAM/man/biplackettcop.Rd |only
VGAM-0.9-5/VGAM/man/biplackettcopUC.Rd |only
VGAM-0.9-5/VGAM/man/bisa.Rd | 18
VGAM-0.9-5/VGAM/man/bisaUC.Rd | 14
VGAM-0.9-5/VGAM/man/bistudentt.Rd | 18
VGAM-0.9-5/VGAM/man/borel.tanner.Rd | 6
VGAM-0.9-5/VGAM/man/bortUC.Rd | 2
VGAM-0.9-5/VGAM/man/calibrate.qrrvglm.control.Rd | 2
VGAM-0.9-5/VGAM/man/cao.Rd | 4
VGAM-0.9-5/VGAM/man/cao.control.Rd | 2
VGAM-0.9-5/VGAM/man/cardioid.Rd | 2
VGAM-0.9-5/VGAM/man/cauchit.Rd | 6
VGAM-0.9-5/VGAM/man/cauchy.Rd | 10
VGAM-0.9-5/VGAM/man/cens.gumbel.Rd |only
VGAM-0.9-5/VGAM/man/cens.normal.Rd |only
VGAM-0.9-5/VGAM/man/cens.poisson.Rd |only
VGAM-0.9-5/VGAM/man/concoef-methods.Rd | 14
VGAM-0.9-5/VGAM/man/concoef.Rd | 11
VGAM-0.9-5/VGAM/man/cqo.Rd | 26
VGAM-0.9-5/VGAM/man/dagum.Rd | 4
VGAM-0.9-5/VGAM/man/dirichlet.Rd | 7
VGAM-0.9-5/VGAM/man/dirmul.old.Rd | 2
VGAM-0.9-5/VGAM/man/dirmultinomial.Rd | 11
VGAM-0.9-5/VGAM/man/double.cens.normal.Rd |only
VGAM-0.9-5/VGAM/man/double.expbinomial.Rd | 12
VGAM-0.9-5/VGAM/man/eexpUC.Rd | 14
VGAM-0.9-5/VGAM/man/enormUC.Rd | 14
VGAM-0.9-5/VGAM/man/erf.Rd | 15
VGAM-0.9-5/VGAM/man/erlang.Rd | 9
VGAM-0.9-5/VGAM/man/eunifUC.Rd | 16
VGAM-0.9-5/VGAM/man/expexpff.Rd |only
VGAM-0.9-5/VGAM/man/expexpff1.Rd |only
VGAM-0.9-5/VGAM/man/expgeometric.Rd | 4
VGAM-0.9-5/VGAM/man/explogff.Rd | 6
VGAM-0.9-5/VGAM/man/exponential.Rd | 31
VGAM-0.9-5/VGAM/man/exppoisson.Rd | 35
VGAM-0.9-5/VGAM/man/exppoissonUC.Rd | 31
VGAM-0.9-5/VGAM/man/fisk.Rd | 4
VGAM-0.9-5/VGAM/man/fittedvlm.Rd | 15
VGAM-0.9-5/VGAM/man/flourbeetle.Rd |only
VGAM-0.9-5/VGAM/man/foldnormal.Rd | 3
VGAM-0.9-5/VGAM/man/frechet.Rd | 14
VGAM-0.9-5/VGAM/man/frechetUC.Rd | 4
VGAM-0.9-5/VGAM/man/gamma1.Rd | 6
VGAM-0.9-5/VGAM/man/gamma2.Rd | 41
VGAM-0.9-5/VGAM/man/gammaR.Rd |only
VGAM-0.9-5/VGAM/man/gammahyperbola.Rd |only
VGAM-0.9-5/VGAM/man/gaussianff.Rd | 2
VGAM-0.9-5/VGAM/man/genbetaII.Rd | 4
VGAM-0.9-5/VGAM/man/gengamma.Rd | 37
VGAM-0.9-5/VGAM/man/gengammaUC.Rd | 38
VGAM-0.9-5/VGAM/man/genpoisson.Rd | 4
VGAM-0.9-5/VGAM/man/genrayleigh.Rd | 31
VGAM-0.9-5/VGAM/man/genrayleighUC.Rd | 24
VGAM-0.9-5/VGAM/man/get.smart.Rd | 12
VGAM-0.9-5/VGAM/man/gev.Rd | 34
VGAM-0.9-5/VGAM/man/gew.Rd | 5
VGAM-0.9-5/VGAM/man/gompertz.Rd | 13
VGAM-0.9-5/VGAM/man/gompertzUC.Rd | 27
VGAM-0.9-5/VGAM/man/gpd.Rd | 61
VGAM-0.9-5/VGAM/man/gpdUC.Rd | 3
VGAM-0.9-5/VGAM/man/grc.Rd | 12
VGAM-0.9-5/VGAM/man/gumbel.Rd | 2
VGAM-0.9-5/VGAM/man/gumbelII.Rd | 52
VGAM-0.9-5/VGAM/man/gumbelIIUC.Rd | 24
VGAM-0.9-5/VGAM/man/hormone.Rd | 8
VGAM-0.9-5/VGAM/man/huberUC.Rd | 4
VGAM-0.9-5/VGAM/man/hypersecant.Rd | 20
VGAM-0.9-5/VGAM/man/inv.binomial.Rd |only
VGAM-0.9-5/VGAM/man/inv.gaussianff.Rd | 4
VGAM-0.9-5/VGAM/man/inv.lomax.Rd |only
VGAM-0.9-5/VGAM/man/inv.lomaxUC.Rd |only
VGAM-0.9-5/VGAM/man/inv.paralogistic.Rd |only
VGAM-0.9-5/VGAM/man/inv.paralogisticUC.Rd |only
VGAM-0.9-5/VGAM/man/is.parallel.Rd | 4
VGAM-0.9-5/VGAM/man/is.smart.Rd | 18
VGAM-0.9-5/VGAM/man/levy.Rd | 96 -
VGAM-0.9-5/VGAM/man/lgammaUC.Rd | 30
VGAM-0.9-5/VGAM/man/lgammaff.Rd | 34
VGAM-0.9-5/VGAM/man/lindley.Rd | 2
VGAM-0.9-5/VGAM/man/lino.Rd | 21
VGAM-0.9-5/VGAM/man/lms.bcg.Rd | 4
VGAM-0.9-5/VGAM/man/lms.bcn.Rd | 24
VGAM-0.9-5/VGAM/man/lms.yjn.Rd | 6
VGAM-0.9-5/VGAM/man/logF.Rd | 2
VGAM-0.9-5/VGAM/man/logistic.Rd | 18
VGAM-0.9-5/VGAM/man/logit.Rd | 2
VGAM-0.9-5/VGAM/man/loglaplace.Rd | 14
VGAM-0.9-5/VGAM/man/lognormal.Rd | 110 -
VGAM-0.9-5/VGAM/man/lomax.Rd | 4
VGAM-0.9-5/VGAM/man/lqnorm.Rd | 4
VGAM-0.9-5/VGAM/man/lvplot.qrrvglm.Rd | 47
VGAM-0.9-5/VGAM/man/makeham.Rd | 12
VGAM-0.9-5/VGAM/man/makehamUC.Rd | 24
VGAM-0.9-5/VGAM/man/maxwell.Rd | 5
VGAM-0.9-5/VGAM/man/maxwellUC.Rd | 30
VGAM-0.9-5/VGAM/man/melbmaxtemp.Rd |only
VGAM-0.9-5/VGAM/man/mix2exp.Rd | 8
VGAM-0.9-5/VGAM/man/mix2poisson.Rd | 18
VGAM-0.9-5/VGAM/man/multilogit.Rd |only
VGAM-0.9-5/VGAM/man/multinomial.Rd | 2
VGAM-0.9-5/VGAM/man/nakagami.Rd | 26
VGAM-0.9-5/VGAM/man/nakagamiUC.Rd | 14
VGAM-0.9-5/VGAM/man/negbinomial.Rd | 39
VGAM-0.9-5/VGAM/man/negbinomial.size.Rd | 4
VGAM-0.9-5/VGAM/man/normal.vcm.Rd | 26
VGAM-0.9-5/VGAM/man/notdocumentedyet.Rd | 98 -
VGAM-0.9-5/VGAM/man/paralogistic.Rd | 4
VGAM-0.9-5/VGAM/man/paretoIV.Rd | 48
VGAM-0.9-5/VGAM/man/paretoff.Rd | 27
VGAM-0.9-5/VGAM/man/perks.Rd | 21
VGAM-0.9-5/VGAM/man/perksUC.Rd | 8
VGAM-0.9-5/VGAM/man/persp.qrrvglm.Rd | 14
VGAM-0.9-5/VGAM/man/plotrcim0.Rd | 16
VGAM-0.9-5/VGAM/man/plotvgam.Rd | 1
VGAM-0.9-5/VGAM/man/poissonff.Rd | 4
VGAM-0.9-5/VGAM/man/posbernoulli.t.Rd | 14
VGAM-0.9-5/VGAM/man/posbernoulli.tb.Rd | 15
VGAM-0.9-5/VGAM/man/posnegbinomial.Rd | 4
VGAM-0.9-5/VGAM/man/powerlink.Rd | 4
VGAM-0.9-5/VGAM/man/prats.Rd | 2
VGAM-0.9-5/VGAM/man/predictqrrvglm.Rd | 6
VGAM-0.9-5/VGAM/man/predictvglm.Rd | 6
VGAM-0.9-5/VGAM/man/prentice74.Rd | 10
VGAM-0.9-5/VGAM/man/put.smart.Rd | 12
VGAM-0.9-5/VGAM/man/qrrvglm.control.Rd | 6
VGAM-0.9-5/VGAM/man/quasipoissonff.Rd | 2
VGAM-0.9-5/VGAM/man/qvar.Rd | 10
VGAM-0.9-5/VGAM/man/rayleigh.Rd | 20
VGAM-0.9-5/VGAM/man/rcqo.Rd | 62
VGAM-0.9-5/VGAM/man/rec.exp1.Rd |only
VGAM-0.9-5/VGAM/man/rec.normal.Rd |only
VGAM-0.9-5/VGAM/man/riceUC.Rd | 70
VGAM-0.9-5/VGAM/man/riceff.Rd | 11
VGAM-0.9-5/VGAM/man/rlplot.egev.Rd | 9
VGAM-0.9-5/VGAM/man/rrvglm.Rd | 19
VGAM-0.9-5/VGAM/man/rrvglm.control.Rd | 16
VGAM-0.9-5/VGAM/man/rrvglm.optim.control.Rd | 25
VGAM-0.9-5/VGAM/man/sc.studentt2.Rd |only
VGAM-0.9-5/VGAM/man/sc.t2UC.Rd |only
VGAM-0.9-5/VGAM/man/simplex.Rd | 4
VGAM-0.9-5/VGAM/man/simulate.vlm.Rd | 90
VGAM-0.9-5/VGAM/man/sinmad.Rd | 4
VGAM-0.9-5/VGAM/man/skewnormal.Rd | 3
VGAM-0.9-5/VGAM/man/smart.expression.Rd | 11
VGAM-0.9-5/VGAM/man/smart.mode.is.Rd | 15
VGAM-0.9-5/VGAM/man/studentt.Rd | 13
VGAM-0.9-5/VGAM/man/tikuv.Rd | 3
VGAM-0.9-5/VGAM/man/tobit.Rd | 6
VGAM-0.9-5/VGAM/man/truncweibull.Rd | 14
VGAM-0.9-5/VGAM/man/undocumented-methods.Rd | 84
VGAM-0.9-5/VGAM/man/uninormal.Rd | 6
VGAM-0.9-5/VGAM/man/vgam.control.Rd | 8
VGAM-0.9-5/VGAM/man/vglm.control.Rd | 23
VGAM-0.9-5/VGAM/man/vonmises.Rd | 2
VGAM-0.9-5/VGAM/man/weibullR.Rd |only
VGAM-0.9-5/VGAM/man/weightsvglm.Rd | 6
VGAM-0.9-5/VGAM/man/zanegbinomial.Rd | 6
VGAM-0.9-5/VGAM/man/zinegbinomial.Rd | 10
VGAM-0.9-5/VGAM/man/zipoisson.Rd | 10
VGAM-0.9-5/VGAM/vignettes |only
340 files changed, 7571 insertions(+), 5488 deletions(-)
Title: High Dimensional Multiclass Classification Using Sparse Group
Lasso
Diff between msgl versions 2.0.125.0 dated 2014-03-26 and 2.0.125.1 dated 2014-11-05
Description: Sparse group lasso multiclass classification, suitable for
high dimensional problems with many classes. Fast algorithm for
solving the multinomial sparse group lasso convex optimization
problem. This package apply template metaprogramming
techniques, therefore -- when compiling the package from source
-- a high level of optimization is needed to gain full speed
(e.g. for the GCC compiler use -O3). Use of multiple processors
for cross validation and subsampling is supported through
OpenMP. The Armadillo C++ library is used as the primary linear
algebra engine.
Author: Martin Vincent
Maintainer: Martin Vincent
DESCRIPTION | 11 +++++------
MD5 | 4 ++--
src/rmsgl.cpp | 4 ++--
3 files changed, 9 insertions(+), 10 deletions(-)
Title: Linear Sparse Group Lasso
Diff between lsgl versions 1.0.123.0 dated 2014-03-25 and 1.0.123.1 dated 2014-11-05
Description: Linear multiple output using sparse group lasso
Author: Martin Vincent
Maintainer: Martin Vincent
DESCRIPTION | 9 ++++-----
MD5 | 14 +++++++-------
R/lsgl_cv.R | 4 ++--
R/lsgl_navigate.R | 8 ++++----
man/Err.lsgl.Rd | 2 +-
man/lsgl.cv.Rd | 2 +-
man/print.lsgl.Rd | 2 +-
src/lsgl.cpp | 4 ++--
8 files changed, 22 insertions(+), 23 deletions(-)
Title: Parsing Command-line Arguments and Variable Interpolation
Diff between GetoptLong versions 0.0.7 dated 2014-10-11 and 0.0.8 dated 2014-11-05
Description: Parsing command-line arguments by Perl module Getopt::Long.
It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 12 ++--
MD5 | 44 ++++++++---------
NAMESPACE | 20 +++----
NEWS | 14 +++--
R/global.R | 2
R/qq.R | 10 ++-
build/vignette.rds |binary
inst/doc/GetoptLong.R | 2
inst/doc/GetoptLong.Rnw | 20 +++----
inst/doc/GetoptLong.pdf |binary
inst/doc/variable_interpolation.R | 52 +++++++++-----------
inst/doc/variable_interpolation.Rnw | 56 ++++++++++-----------
inst/doc/variable_interpolation.pdf |binary
inst/tests/test_qq.R | 12 +++-
man/GetoptLong-package.rd | 36 +++++++-------
man/GetoptLong.options.rd | 62 ++++++++++++------------
man/GetoptLong.rd | 56 ++++++++++-----------
man/get_scriptname.rd | 40 +++++++--------
man/qq.options.rd | 62 ++++++++++++------------
man/qq.rd | 62 ++++++++++++------------
man/qqcat.rd | 90 +++++++++++++++++------------------
vignettes/GetoptLong.Rnw | 20 +++----
vignettes/variable_interpolation.Rnw | 56 ++++++++++-----------
23 files changed, 369 insertions(+), 359 deletions(-)
Title: elliptic functions
Diff between elliptic versions 1.3-3 dated 2013-12-05 and 1.3-5 dated 2014-11-05
Description:
A suite of elliptic and related functions including Weierstrass and
Jacobi forms. Also includes various tools for manipulating and
visualizing complex functions.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 6 +++---
MD5 | 18 +++++++++++-------
R/elliptic.R | 14 ++++++++++++++
build/vignette.rds |binary
inst/doc/ellipticpaper.pdf |binary
inst/doc/residuetheorem.R |only
inst/doc/residuetheorem.Rnw |only
inst/doc/residuetheorem.pdf |only
man/myintegrate.Rd | 41 ++++++++++++++++++++++++++++++++++++-----
man/newton_raphson.Rd | 6 +++---
man/view.Rd | 5 ++++-
vignettes/residuetheorem.Rnw |only
12 files changed, 71 insertions(+), 19 deletions(-)
Title: Stratigraphic Tree Analysis for Palaeontology
Diff between strap versions 1.3 dated 2014-08-08 and 1.4 dated 2014-11-05
Description: Functions for the stratigraphic analysis of phylogenetic trees.
Author: Mark A. Bell
Maintainer: Mark A. Bell
CHANGELOG |only
DESCRIPTION | 8 -
MD5 | 15 +--
R/DatePhylo.R | 8 -
R/StratPhyloCongruence.R | 47 ++++++++--
R/geoscalePhylo.R | 124 ++++++++++++++++++++--------
man/StratPhyloCongruence.Rd | 16 ++-
man/geoscalePhylo.Rd | 191 +++++++++++++++++++++++++++-----------------
man/strap-package.Rd | 5 -
9 files changed, 270 insertions(+), 144 deletions(-)
Title: Functions and Datasets to Accompany the Book "The R Software:
Fundamentals of Programming and Statistical Analysis"
Diff between TRSbook versions 1.0 dated 2014-11-03 and 1.0.1 dated 2014-11-05
Description: Functions and datasets for the reader of the book "The R Software: Fundamentals of Programming and Statistical Analysis".
Author: Lafaye de Micheaux Pierre, Drouilhet Remy, Liquet Benoit
Maintainer: P Lafaye de Micheaux
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/getaddr.c | 5 ++---
3 files changed, 8 insertions(+), 9 deletions(-)
Title: Multi-Patient Analysis of Genomic Markers
Diff between MPAgenomics versions 1.1.0 dated 2014-07-23 and 1.1.2 dated 2014-11-05
Description: Preprocess and analysis of genomic data. MPAgenomics
provides wrappers from commonly used packages to streamline their repeated
manipulation, offering an easy-to-use pipeline. The segmentation of
successive multiple profiles is performed with an automatic choice of
parameters involved in the wrapped packages. Considering multiple profiles
in the same time, MPAgenomics wraps efficient penalized regression methods
to select relevant markers associated with a given outcome.
Author: Quentin Grimonprez with contributions from Guillemette Marot and Samuel
Blanck. Some functions use code created by Sjoerd Vosse, Mark van de Wiel,
Pierre Neuvial, Henrik Bengtsson.
Maintainer: Samuel Blanck
MPAgenomics-1.1.0/MPAgenomics/vignettes/fig/dataFilesSingle2_old.png |only
MPAgenomics-1.1.0/MPAgenomics/vignettes/fig/dataFilesSingle2_sauv.png |only
MPAgenomics-1.1.2/MPAgenomics/DESCRIPTION | 29
MPAgenomics-1.1.2/MPAgenomics/MD5 | 108
MPAgenomics-1.1.2/MPAgenomics/NAMESPACE | 4
MPAgenomics-1.1.2/MPAgenomics/NEWS | 12
MPAgenomics-1.1.2/MPAgenomics/R/MPAgenomics-package.R | 6
MPAgenomics-1.1.2/MPAgenomics/R/SNPselection.R | 349
MPAgenomics-1.1.2/MPAgenomics/R/bivariateSignal.R | 1
MPAgenomics-1.1.2/MPAgenomics/R/cghcall.R | 10
MPAgenomics-1.1.2/MPAgenomics/R/cghcall_private.R | 8
MPAgenomics-1.1.2/MPAgenomics/R/cghseg.R | 45
MPAgenomics-1.1.2/MPAgenomics/R/createAromaArchitecture.R | 12
MPAgenomics-1.1.2/MPAgenomics/R/genotypeCalls.R | 118
MPAgenomics-1.1.2/MPAgenomics/R/getCNSignal.R | 80
MPAgenomics-1.1.2/MPAgenomics/R/getFracBSignal.R | 51
MPAgenomics-1.1.2/MPAgenomics/R/getGenotypeCalls.R | 32
MPAgenomics-1.1.2/MPAgenomics/R/getSymFracBsignal.R | 26
MPAgenomics-1.1.2/MPAgenomics/R/pelt.R | 41
MPAgenomics-1.1.2/MPAgenomics/R/segCalling.R | 32
MPAgenomics-1.1.2/MPAgenomics/R/segFracB.R | 34
MPAgenomics-1.1.2/MPAgenomics/R/signalPreprocess.R | 4
MPAgenomics-1.1.2/MPAgenomics/R/tumorboost.R | 82
MPAgenomics-1.1.2/MPAgenomics/build/vignette.rds |binary
MPAgenomics-1.1.2/MPAgenomics/inst/doc/MPAgenomics.R | 4
MPAgenomics-1.1.2/MPAgenomics/inst/doc/MPAgenomics.Rnw | 91
MPAgenomics-1.1.2/MPAgenomics/inst/doc/MPAgenomics.pdf | 4535 +++++-----
MPAgenomics-1.1.2/MPAgenomics/man/CNAobjectToCGHcallObject.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/HDlarsbivariate.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/MPAgenomics-package.Rd | 6
MPAgenomics-1.1.2/MPAgenomics/man/SignalNormalization.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/addChipType.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/addData.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/callingObject.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/callingProcess.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/cnSegCallingProcess.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/createArchitecture.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/createEmptyArchitecture.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/filterSeg.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/findPlateau.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/getCopyNumberSignal.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/getFracBSignal.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/getGenotypeCalls.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/getListOfFiles.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/getSymFracBSignal.Rd | 6
MPAgenomics-1.1.2/MPAgenomics/man/markerSelection.Rd | 19
MPAgenomics-1.1.2/MPAgenomics/man/segFracBSignal.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/segmentation.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/segmentationAroma.Rd | 8
MPAgenomics-1.1.2/MPAgenomics/man/segmentationObject.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/signalPreProcess.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/symmetrizeFracB.Rd | 2
MPAgenomics-1.1.2/MPAgenomics/man/variableSelection.Rd | 10
MPAgenomics-1.1.2/MPAgenomics/vignettes/MPAgenomics.Rnw | 91
MPAgenomics-1.1.2/MPAgenomics/vignettes/MPAgenomics.bib | 51
MPAgenomics-1.1.2/MPAgenomics/vignettes/fig/falsesel.png |only
MPAgenomics-1.1.2/MPAgenomics/vignettes/fig/truesel.png |only
57 files changed, 3197 insertions(+), 2750 deletions(-)
Title: Spatial Analysis of Animal Track Data
Diff between trip versions 1.1-18 dated 2014-09-23 and 1.1-19 dated 2014-11-05
Description: Functions for accessing and manipulating spatial data for
animal tracking. Filter for speed and create time spent plots
from animal track data.
Author: Michael D. Sumner [aut, cre],
Sebastian Luque [ctb]
Maintainer: Michael D. Sumner
ChangeLog | 44 ++++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NEWS | 8 +++++++-
R/trip.R | 7 +++----
README.md | 1 +
build/vignette.rds |binary
inst/doc/trip.pdf |binary
8 files changed, 66 insertions(+), 16 deletions(-)
Title: Functions for plotting graphical shapes, colors
Diff between shape versions 1.4.1 dated 2014-01-08 and 1.4.2 dated 2014-11-05
Description: Functions for plotting graphical shapes
such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert
Maintainer: Karline Soetaert
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/textflag.R | 6 ++++--
build/vignette.rds |binary
man/textflag.Rd | 8 +++++---
5 files changed, 18 insertions(+), 14 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.28-2 dated 2013-09-06 and 0.34-0 dated 2014-11-05
Description: Functions, examples and data from the book
'Numerical Methods and Optimization in Finance' by M.
Gilli, D. Maringer and E. Schumann. The package provides
implementations of several optimisation heuristics, such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting. There are also functions for the valuation of
financial instruments, such as bonds and options, and
functions that help with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann
DESCRIPTION | 26
MD5 | 100 +
NAMESPACE | 6
NEWS | 75 +
R/GAopt.R | 41
R/PSopt.R | 25
R/TAopt.R | 402 ++++----
R/bonds.R | 48
R/bracket.R | 28
R/callMerton.R |only
R/colSubset.R |only
R/drawdown.R |only
R/gridSearch.R | 26
R/integrate.R | 104 +-
R/internals.R | 2
R/mc.R | 5
R/randomp.R |only
R/restartOpt.R | 21
build |only
inst/CITATION | 6
inst/NMOFex/NMOFdist.R | 190 +--
inst/NMOFex/NMOFman.R | 2003 ++++++++++++++++++++++++----------------
inst/doc/An_overview.R |only
inst/doc/An_overview.Rnw |only
inst/doc/An_overview.pdf |only
inst/doc/DEnss.R | 33
inst/doc/DEnss.Rnw | 12
inst/doc/DEnss.pdf |binary
inst/doc/LSselect.R | 105 +-
inst/doc/LSselect.Rnw | 139 +-
inst/doc/LSselect.pdf |binary
inst/doc/PSlms.pdf |binary
inst/doc/TAportfolio.Rnw | 2
inst/doc/TAportfolio.pdf |binary
inst/doc/qTableEx.pdf |binary
inst/doc/repair.pdf |binary
inst/doc/vectorise.R | 30
inst/doc/vectorise.Rnw | 9
inst/doc/vectorise.pdf |binary
inst/unitTests/report.txt | 37
inst/unitTests/unitTestsBonds.R |only
inst/unitTests/unitTestsDEopt.R | 6
inst/unitTests/unitTestsPSopt.R | 24
man/NMOF-package.Rd | 80 +
man/PSopt.Rd | 14
man/TA.info.Rd |only
man/bonds.Rd | 65 +
man/callHestoncf.Rd | 2
man/callMerton.Rd |only
man/colSubset.Rd |only
man/drawdown.Rd |only
man/mc.Rd | 3
man/optionData.Rd | 88 -
vignettes/An_overview.Rnw |only
vignettes/DEnss.Rnw | 12
vignettes/LSselect.Rnw | 139 +-
vignettes/TAportfolio.Rnw | 2
vignettes/vectorise.Rnw | 9
58 files changed, 2298 insertions(+), 1621 deletions(-)
Title: Module Graphical Lasso
Diff between MGL versions 1.0 dated 2014-11-03 and 1.1 dated 2014-11-05
Description: An aggressive dimensionality reduction and network estimation
technique for a high-dimensional Gaussian graphical model (GGM). Please
refer to: Efficient Dimensionality Reduction for High-Dimensional Network
Estimation, Safiye Celik, Benjamin A. Logsdon, Su-In Lee, Proceedings of
The 31st International Conference on Machine Learning, 2014, p. 1953--1961.
Author: Safiye Celik
Maintainer: Safiye Celik
MGL-1.0/MGL/src/Makefile |only
MGL-1.1/MGL/DESCRIPTION | 6 +++---
MGL-1.1/MGL/MD5 | 5 ++---
MGL-1.1/MGL/src/MGL.c | 18 +++++++++---------
4 files changed, 14 insertions(+), 15 deletions(-)
Title: Multidimensional Adaptive Testing
Diff between MAT versions 2.0 dated 2014-09-26 and 2.2 dated 2014-11-05
Description: Simulate Multidimensional Adaptive Testing
Author: Seung W. Choi and David R. King
Maintainer: Seung W. Choi
DESCRIPTION | 6 ++---
MD5 | 8 +++---
R/MAT.R | 61 +++++++++++++++++++++++++++++++++--------------------
man/MAT-package.Rd | 5 +---
man/MAT.Rd | 12 +++++++---
5 files changed, 56 insertions(+), 36 deletions(-)
Title: Relabelling MCMC outputs of mixture models
Diff between label.switching versions 1.2 dated 2013-12-04 and 1.3 dated 2014-11-05
More information about label.switching at CRAN
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis
DESCRIPTION | 10
MD5 | 28 -
NAMESPACE | 2
R/relabelling_algorithms.R | 869 +++++++++++++++++++++++++++++++----------
man/aic.Rd |only
man/compare.clust.Rd | 1
man/dataBased.Rd |only
man/ecr.Rd | 12
man/ecr.iterative.1.Rd | 26 -
man/ecr.iterative.2.Rd | 26 -
man/label.switching-package.Rd | 24 -
man/label.switching.Rd | 75 ++-
man/permute.mcmc.Rd | 17
man/pra.Rd | 20
man/sjw.Rd | 32 -
man/stephens.Rd | 26 -
16 files changed, 809 insertions(+), 359 deletions(-)
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