Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).


Software and datasets to support 'Modern Applied Statistics with S', fourth edition, by W. N. Venables and B. D. Ripley. Springer, 2002, ISBN 0-387-95457-0.

This file documents software changes since the third edition.

  • eqscplot has new arguments ratio and uin.

  • stepAIC will not drop strata terms in coxph or survreg models.

  • profile.glm will report inadequate supplied glm fits, not just fail.

  • new method confint.lm.

  • fractions/rational allow missing values.

  • mvrnorm has an 'empirical' argument.

  • predict.lda and predict.qda try harder to avoid exponential underflow.

  • new function fitdistr for ML estimation of univariate distributions.

  • new function glmmPQL to use lme to fit GLMMs by PQL

  • truehist allows rule for nbins to be specified as a character string.

  • parcoord function.

  • new datasets bacteria, epil, nlschools, SP500

  • polr allows control argment for optim, reports lack of convergence.

  • stepAIC works again if formula has an offset (R had changed).

  • biplot.correspondence now shows the origin as a cross.

  • polr was not preserving contrasts to put in the fit object.

  • vcov methods for lme, gls, coxph and survReg.

  • Added 'tol' argument to isoMDS.

  • stepAIC now allow 'direction=both' starting from a full model.

  • glm.nb allows R-style 'start' argument.

  • truehist passes ... on to both plot.default() and rect().

  • isoMDS now uses the C interface to optim.

  • addterm, dropterm, stepAIC now work with lme and gls fits.

  • huber checks for MAD equal to zero.

  • glmmPQL now loads nlme if not already loaded.

  • glmmPQL handles list 'random' arguments (7.0-11).

  • The MASS datasets no longer require data(foo) to load them. (7.0-11)

  • mvrnorm uses eigen(EISPACK=TRUE) for back-compatibility (7.0-11, R 1.7.0)

  • print.summary.polr could lose dimnames for 1 coefficient.

  • remove heart as survival in R now has it.

  • confint.{lm,glm} didn't handle specifying parm in all cases.

  • confint and confint.lm have been migrated to base in R.

  • addterm.default, dropterm.default and stepAIC work better inside functions.

  • glm.nb now sets AIC in the object, and has a logLik() method.

  • truehist now accepts a 'ylab' argument.

  • negative.binomial and neg.bin no longer generate objects with package:MASS in their environment.

  • stepAIC now drops (if allowed) 0-df terms sequentially from the right.

  • lda(CV=TRUE) now works for rank-deficient fits.

  • predict methods for lda, polr now check newdata types.

  • model.frame.lda/polr now look for the environment of the original formula.

  • polr has a new `model' argument defaulting to TRUE.

  • fitdistr supports the trivial case of a Normal distribution.

  • sammon and isoMDS now allow missing values in the dissimilarity matrix, and isoMDS allows Minkowski distances in the configuration space.

  • cov.trob works better if wts are supplied, and may converge a little faster in any case.

  • The ch11.R script now uses mclust not mclust1998.

  • The default xlab for boxcox() is now greek lambda.

  • glmmPQL now handles offset terms.

  • add predict.rlm method to correct predict.lm in the case

  • weighted rlm fits are handled better, and default to "inv.var".

  • logtrans works without specifying 'data'.

  • predict() method for glmmPQL.

  • polr() has an option for probit or proportional hazard fits.

  • neg.bin() and negative.binomial() had an error in the aic() formula.

  • The ch05.R script now includes the code for Figure 5.8.

  • Datasets austres, fdeaths, lh, mdeaths, nottem and rock are now visible in the 'datasets' package of R 2.0.0 and so have been removed here.

  • Script ch07.R now gives details using the gam() function in package gam as well as that in package mgcv.

  • rlm's fitted component is now always unweighted.

  • theta.{md,ml,mm} now have one help file with examples.

  • polr() has a new method "cauchit" suggested by Roger Koenker. (Requires R >= 2.1.0)

  • polr() now works with transformed intercepts, and usually converges better (contributed by David Firth).

  • polr() handles a rank-deficient model matrix.

  • polr() now returns the method used, and uses it for predictions.

  • anova() method for polr (contributed by John Fox).

  • predict.glmmPQL was not using the na.action in the object as intended.

  • The default methods for addterm and dropterm and anova.polr now check for changes in the number of cases in use caused e.g. by na.action=na.omit.

  • Added vcov() method for rlm fits.

  • eqscplot() accepts reversed values for xlim and ylim.

  • Script ch10.R uses se.contrast to calculate se's missing from model.tables.

  • profile() and confint() methods for polr().

  • glm.convert() was not setting the `offset' component that R's glm objects have.

  • sammon() now checks for duplicates in the initial configuration.

  • isoMDS() and sammon() work around dropping of names.dist in 2.1.0

  • lda() now gives an explicit error message if all group means are the same.

  • fitdistr() now has a logLik() method, chooses the optim() method if not supplied, handles the log-normal by closed-form and no longer attempts to handle the uniform.

  • glm.nb() now accepts 'mustart'.

  • glm.nb() now supports weights: they used to be ignored when estimating theta.

  • fitdistr() now supports geometric and Poisson distributions, and uses closed-form results for the exponential.

  • lm.ridge, lqs and rlm allow offset() terms.

  • the 'prior' argument of predict.qda is now operational.

  • script ch12.R now has b1() adapted for R's contour().

  • anova.polr() quoted model dfs, not residual dfs.

  • stepAIC() applied to a polr fit now gets the correct rdf's in the anova table.

  • lm.gls() now returns fitted values and residuals on the original coordinates (not the uncorrelated ones).

  • parcoord() now allows missing values and has a new argument 'var.label' to label the variable axes. (Contributed by Fabian Scheipl.)

  • rlm() has a 'lqs.control' argument passed to lqs() where used for initialization.

  • rlm() could fail with some psi functions (e.g. psi.hampel) if 'init' was given as a numeric vector.

  • rlm() handles weighted fits slightly differently, in particular trying to give the same scale estimate if wt.method="case" as if replicating the cases.

  • confint.nls copes with plinear models in R (now profile.nls does).

  • The wrappers lmsreg() etc have been adapted to work in the MASS namespace.

  • qda() accepts formulae containing backquoted non-syntactic names.

  • polr() gives an explicit error message if 'start' is misspecified.

  • glmmPQL() evaluates the formulae for 'fixed' and 'random', which may help if they are given as variables and not values.

  • There are anova() and logLik() methods for class "glmmPQL" to stop misuse.

  • profile.polr() now works for a single-coefficient model.

  • The print and print.summary methods for polr and rlm make use of naprint() to print a message e.g. about deleted observations.

  • Class "ridgelm" now has a coef() method, and works for n < p.

  • lda() and qda() now check explicitly for non-finite 'x' values.

  • ch06.R has been updated for multcomp >= 0.991-1

  • profile.glm is more likely to find the model frame in complicated scopes.

  • message() is used for most messages.

  • truehist() checks more thoroughly for erroneous inputs.

  • polr(model=TRUE) works again.

  • add logLik() method for polr.

  • the summary() methods for classes "negbin" and "rlm" now default to correlation = FALSE.

  • there is a vcov() method for class "negbin": unlike the "glm" method this defaults to dispersion = 1.

  • coding for 'sex' in ?Melanoma has been corrected.

  • the example for gamma.shape has a better starting point and so converges

  • avoid abbreviation of survreg(dist=) in example(gehan)

  • profile() and confint() methods for "glm" objects now handle rank-deficient fits.

  • profile.glm() produced an output in a format plot.profile could not read for single-variable fits. Also for confint() on intercept-only fits.

  • The print() methods for fitdistr() and lm.ridge() now return invisibly.

  • vcov() and profile() methods for polr() used starting values in the external not internal parametrization, which could slow convergence.

  • glm.nb() called incorrect when weights were supplied whch did not sum to n.

  • removed unused argument 'nseg' to plot.profile.

  • 'alpha' in the "glm" and "polr" methods for profile() is now interpreted as two-tailed univariate for consistency with other profile methods.

  • 'mammals': corrected typos in names, some thanks to Arni Magnusson.

  • profile.glm() now works for binomial glm specified with a matrix response and a cmpletely zero row.

  • there is a "negbin" method for simulate()

  • the use of package mclust has been removed from the ch11.R script because of the change of licence conditions for that package.

  • change ch13.R script for change in package 'survival' 2.35-x.

  • glmmPQL looks up variables in its 'correlation' argument (if a formula) in the usual scope (wish of Ben Bolker: such arguments are unsupported).

  • added a simulate() method for unweighted polr() fits.

  • kde2d() allows a length-2 argument 'n'.

  • the default for truehist(col=) is now set to a colour, not a colour number.

  • the returned fitted values and (undocumented) linear predictor for polr() did not take any offset into account (reported by Ioannis Kosmides).

  • the vcov() method for polr() now returns on the zeta scale (suggested by Achim Zeileis).

  • fitdistr() gains a vcov() method (suggested by Achim Zeileis).

  • ch06.R has R alternatives to

  • ch11.R has R alternatives for ggobi and factor rotation.

  • hubers() copes in extreme cases when middle 50% of data is constant.

  • tests/ now includes dataset for polr.R, so checking depends only on base packages and lattice.

  • The "glm" method for profile() failed when given a binomial model with a two-column response.

  • fitdistr() works harder to rescale the problem when fitting a gamma.

  • cov.trob() handles zero weights without giving a warning (reported by John Fox).

  • boxcox() works better when 'y' is very badly scaled, e.g. around 1e-16 (patch by Martin Maechler).

  • mvrnorm() no longer defaults to the deprecated EISPACK=TRUE (and hence changes the results). It gains an argument 'EISPACK' for back-compatibility.

  • the "polr" method for profile() could lose dimensions in its return object (reported by Joris Meys)

  • kde2d() throws an error if given zero bandwidths or constant data.

  • ldahist(sep = TRUE) was missing a dev.flush().

  • addterm.glm() mis-calculated F statistics for df > 1.

  • anova.loglm() needed revision for changes in R.

  • the addterm() default method allows update() to fail.

  • polr(method = "cloglog") implemented what is more commonly called the log-log link. Now both are provided.

  • lqs() fits with intercepts and contrasts lost the latter from the return value.

  • addterm() and dropterm() now handle empty scopes, transparently.

  • glmmPQL uses requireNamespace('nlme'), not require().

  • mvnorm(EISPACK = TRUE) is now an error: it is unsupported by R >= 3.1.0.

  • the log-likelihood returned for fitdistr(, "geometric") was incorrect.

Reference manual

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7.3-54 by Brian Ripley, 7 months ago

Browse source code at

Authors: Brian Ripley [aut, cre, cph] , Bill Venables [ctb] , Douglas M. Bates [ctb] , Kurt Hornik [trl] (partial port ca 1998) , Albrecht Gebhardt [trl] (partial port ca 1998) , David Firth [ctb]

Documentation:   PDF Manual  

Task views: Probability Distributions, Econometrics, Analysis of Ecological and Environmental Data, Multivariate Statistics, Numerical Mathematics, Psychometric Models and Methods, Robust Statistical Methods, Statistics for the Social Sciences, Teaching Statistics

GPL-2 | GPL-3 license

Imports methods

Depends on grDevices, graphics, stats, utils

Suggests lattice, nlme, nnet, survival

Imported by ACEt, ACNE, ACSWR, AICcmodavg, AID, AROC, ARpLMEC, ActiveDriver, AdaSampling, AdaptiveSparsity, AppliedPredictiveModeling, BAT, BCEA, BDWreg, BEDASSLE, BFpack, BGGM, BGLR, BGVAR, BIGL, BLCOP, BMTAR, BNPMIXcluster, BOSO, BSBT, BSL, BSS, BaBooN, BaM, BasketballAnalyzeR, BayesCACE, BayesESS, BayesLN, BayesRGMM, BayesSampling, BayesianGLasso, BayesianTools, Bayesrel, Bchron, BigVAR, BinMat, Biocomb, BiplotGUI, BisRNA, BivRec, BoutrosLab.plotting.general, BrainCon, BreakPoints, C443, CADStat, CARlasso, CATkit, CCTpack, CDSeq, CEGO, CISE, CIplot, CKLRT, CLUSTShiny, CLVTools, COUNT, CPBayes, CSUV, CTP, CausalGPS, CausalMBSTS, CenBAR, ChainLadder, CluMP, ClusVis, CoTiMA, CollocInfer, Compack, Compind, Compositional, CondIndTests, ConformalSmallest, Corbi, Countr, CovSelHigh, Crossover, DA, DAMisc, DAP, DCEM, DCEtool, DCchoice, DESnowball, DFA.CANCOR, DLASSO, DOS, DOS2, DPtree, DR.SC, DTRreg, DeLorean, DescTools, DetR, DiSSMod, DistributionTest, DoE.base, DrBats, DySeq, EAinference, ECoL, EDNE.EQ, EFAutilities, EGRET, EHRtemporalVariability, EIX, EasyABC, Ecfun, EdSurvey, EnvStats, EnviroPRA, EnviroStat, Epi, EthSEQ, EvolutionaryGames, FABInference, FAOSTAT, FCGR, FDboost, FENmlm, FHtest, FIT, FKSUM, FMAdist, FME, FMradio, FPDclustering, FREEtree, FactoMineR, FamEvent, FastGP, FitUltD, FlexGAM, ForeCA, Frames2, GAS, GCPBayes, GDAtools, GDINA, GEInter, GFD, GFDsurv, GGMncv, GGMnonreg, GGRidge, GLIDE, GLMMadaptive, GLMaSPU, GLMpack, GMDH, GMDH2, GPSCDF, GPareto, GRPtests, GSMX, GUniFrac, GWEX, GWSDAT, GenAlgo, GenEst, GeneClusterNet, GeneralizedHyperbolic, GeodRegr, GlmSimulatoR, HCTR, HDBRR, HDtest, HIMA, HLMdiag, HLSM, HMP, Haplin, HeritSeq, HeteroGGM, Hmsc, HoRM, ICcalib, ICsurv, IDmeasurer, IMIX, IMTest, IPCAPS, IPEC, IQCC, IRCcheck, ISR, InspectChangepoint, Interatrix, IsoplotR, JMbayes, JOPS, JSmediation, JWileymisc, JointAI, JointNets, KOBT, KRMM, KScorrect, KnowGRRF, L0Learn, LAWBL, LCAvarsel, LCCR, LDPD, LINselect, LMMELSM, LMest, LMfilteR, LNIRT, LOST, 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oaColors, odds.n.ends, oddstream, odpc, omicwas, openCR, openair, optBiomarker, optiSel, optiSolve, opticut, ordinal, orthoDr, otinference, pCODE, packDAMipd, packMBPLSDA, pagoda2, pairwiseCI, palaeoSig, panelvar, partialAR, partialCI, partition, pbkrtest, pcgen, pdynmc, penPHcure, pencal, penfa, pensim, pguIMP, phase1PRMD, phytools, piecewiseSEM, pirate, pitchRx, pivmet, plink, plm, plsRbeta, plsRglm, plsVarSel, plsgenomics, pmclust, pmpp, pmwg, pop, porridge, powerbydesign, powerplus, ppclust, ppgam, predictionInterval, primePCA, profExtrema, projpred, provenance, pscl, pssm, pssmooth, pstest, purging, pwr2ppl, qcc, qgg, qif, qqconf, qqplotr, qrmix, qtl2pleio, qtlpoly, qualypsoss, quhomology, r2d2, r2glmm, rEMM, rKIN, rMVP, rSFA, rWishart,, radiant.multivariate, ragt2ridges, ramchoice,, randomUniformForest, rangeModelMetadata, rankFD, rareGE, ratematrix, rbmn, rcage, rdrobust, reReg, recapr, refitME, refund, reghelper, regmedint, replicationInterval, reproducer, restrictedMVN, restriktor, rewie, rfinterval, riskPredictClustData, rld, rlmDataDriven, rlme, rmda, rmgarch, rminer, rms, rmsb, robCompositions, robFitConGraph, robmixglm, robregcc, robust, robustHD, robustlm, rocTree, rockchalk, rpql, rr, rrpack, rrr, rsq, rsvddpd, rties, s2net, sNPLS, sads, saeME, saeRobust, saeSim, saeeb, sampling, samurais, sasfunclust, sate, sbw, scTenifoldKnk, scTenifoldNet, scoringRules, scpm, sctransform, sdPrior, sdcMicro, secr, secrlinear, secure, seeds, seer, sem, semiArtificial, semmcmc, semnova, sensR, senstrat, seqest, seriation, sfaR, sgd, shapeR, shapes, shazam, shrink, sigInt, sigQC, signal, sim2Dpredictr, simIReff, simPH, simPop, simTargetCov, simlandr, simmr, simputation, simukde, sinar, singcar, sizeMat, sjPlot, sjstats, skedastic, skewMLRM, slasso, slim, smacof, smartsizer, smcfcs, smd, smooth, smurf, smvgraph, soiltexture, sorocs, spBayesSurv, spaMM, spaceNet, sparseFLMM, sparseGAM, sparseLDA, spass, spathial, spatialEco, spatialreg, spdep, spduration, 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Enhanced by cornet, infutil, prediction, stargazer.

See at CRAN