1useDynLib(robustbase, .registration=TRUE) 2 3if(FALSE) {##MM 4 stopifnot(require(codetoolsBioC), require(robustbase)) 5 findExternalDeps("robustbase") 6} 7importFrom("grDevices", dev.interactive, extendrange) 8importFrom("graphics", 9 abline, axis, 10 box, legend, lines, matplot, mtext, 11 panel.smooth, par, plot, points, strheight, text, title) 12importFrom("stats", 13 aggregate, alias, as.formula, binomial, 14 coef, cor, cov, cov.wt, cov2cor, delete.response, deviance, dnorm, dpois, 15 family, fitted, fivenum, formula, 16 gaussian, glm, glm.fit, hatvalues, 17 integrate, is.empty.model, lm.fit, lm.wfit, 18 mad, mahalanobis, median, model.frame, model.matrix, model.matrix.lm, 19 model.offset, model.response, model.weights, 20 na.fail, na.omit, na.pass, napredict, naprint, naresid, 21 nlminb, nls, nls.control, nobs, 22 optim, optimize, pbinom, pchisq, pf, pgamma, pnorm, poisson, ppois, 23 predict, printCoefmat, pt, 24 qchisq, qnorm, qpois, qqline, qqnorm, qt, quantile, 25 resid, residuals, residuals.lm, setNames, splinefun, symnum, 26 terms, uniroot, var, vcov, weights, .checkMFClasses, .getXlevels, 27 28 ## S3 generics (*not* shown yet by findExternalDeps() above): 29 anova, case.names, confint, 30 dummy.coef, logLik, profile, variable.names 31 ) 32 33 34## ^^^^ MASS has a bit more; take it as example 35if(getRversion() >= "3.1.0") 36importFrom("stats", .lm.fit, confint.lm, dummy.coef.lm) 37if(getRversion() >= "3.3.0") { 38 importFrom("stats", sigma) 39} else { 40 export(sigma) 41 S3method(sigma, nls) 42} 43 44importFrom("utils", globalVariables, str) 45 46## MASS has many rlm S3 methods; should we use some of them - for rnls() ?! 47## we also currently use MASS::cov.rob(); but probably only temporarily 48importFrom("methods", is, new, setClass, setMethod, slot, "slot<-", 49 ## needed, e.g. for 'robustlmm' to work w/o warning: 50 as, "as<-", coerce, "coerce<-") 51 52importFrom("DEoptimR", JDEoptim) 53 54## Functions defined in this package 55export(Sn, Qn, Qn.old, 56 s_Sn, s_Qn, s_mad, s_IQR, 57 58 summarizeRobWeights, 59 wgt.himedian, 60 61 h.alpha.n, 62 covMcd, .MCDcons, .MCDcnp2, .MCDcnp2.rew, .MCDsingularityMsg, 63 robMD, mahalanobisD, # <- still "internal" 64 ltsReg, 65 tolEllipsePlot, 66 ## RENAME ?!? : 67 covPlot, ltsPlot, 68 ## NO! ddplot, distplot, chi2qqplot 69 rrcov.control,## << RENAME --- FIXME 70 huberM, 71 colMedians, rowMedians, 72 covOGK, covGK, hard.rejection, scaleTau2, 73 covComed, 74 ## comedian, COM, -- not yet 75 smoothWgt, .wgtFUN.covMcd, .wgtFUN.covComed, 76 psiFunc, huberPsi, hampelPsi, 77## Not yet: 78## tukeyPsi, # = biweight / bisquare 79 tukeyChi, tukeyPsi1, # TODO deprecate: see ./TODO 80 Mpsi, Mchi, Mwgt, MrhoInf, .Mpsi, .Mchi, .Mwgt, .MrhoInf, 81 .Mwgt.psi1, 82 .Mchi.tuning.default, .Mpsi.tuning.default, .regularize.Mpsi, 83 .Mchi.tuning.defaults, .Mpsi.tuning.defaults, 84 .psi2ipsi, .psi.const, .psi.ggw.findc, .psi.lqq.findc, 85 86 lmrob, lmrob.fit, 87 lmrob.fit.MM, lmrob..M..fit, lmrob..D..fit, 88 lmrob.S, lmrob.lar, lmrob.M.S, 89 lmrob.control, 90 .lmrob.hat, # was lmrob.leverages() 91 splitFrame, 92 outlierStats, 93 94 mc, # Mia Hubers's medcouple 95 adjbox, 96 adjboxStats, 97 adjOutlyingness, 98 fullRank, 99 glmrob, 100 nlrob, nlrob.control 101 , glmrobMqle.control, glmrobBY.control, glmrobMT.control 102 , BYlogreg ## R/BYlogreg.R FIXME: add to glmrob() and "deprecate" 103 ## , glmrobMT ## R/MTestimador2.R 104 , estimethod 105 ## related to detMCD() and to be used in rrcov etc: 106 , r6pack, doScale 107 , rankMM, classPC, .signflip 108 ) 109 110 111## S3 methods for ``our own'' S3 generics: 112S3method(ltsReg, default) 113S3method(ltsReg, formula) 114 115S3method(adjbox, default) 116S3method(adjbox, formula) 117 118 119## Register all the methods for S3 generics elsewhere 120## in case namespace is loaded but not currently attached. 121 122S3method(anova, lmrob) 123S3method(anova, glmrob) 124 125S3method(alias, lmrob) 126S3method(case.names, lmrob) 127S3method(confint, lmrob) 128S3method(confint, nlrob) 129S3method(dummy.coef, lmrob) 130S3method(estimethod, nlrob) 131S3method(family, lmrob) 132S3method(hatvalues, lmrob) 133S3method(kappa, lmrob) 134S3method(labels, lmrob) 135S3method(model.matrix, lmrob) 136S3method(nobs, lmrob) 137S3method(nobs, lmrob.S, nobs.lmrob)# use the same as "lmrob" 138S3method(nobs, mcd) 139S3method(residuals, lmrob) 140S3method(variable.names, lmrob) 141S3method(weights, glmrob) 142S3method(weights, lmrob) 143S3method(weights, lmrob.S, weights.lmrob)# use the same as "lmrob" 144S3method(weights, nlrob, weights.lmrob)# use the same as "lmrob" 145 146S3method(formula, nlrob) 147S3method(fitted, nlrob) 148S3method(plot, lts) 149S3method(plot, mcd) 150S3method(plot, lmrob) 151S3method(predict, lmrob) 152S3method(predict, glmrob) 153S3method(predict, nlrob) 154 155S3method(print, glmrob) 156S3method(print, lts) 157S3method(print, mcd) 158S3method(print, nlrob) 159S3method(print, lmrob) 160S3method(print, lmrob.S) 161S3method(print, summary.glmrob) 162S3method(print, summary.lmrob) 163S3method(print, summary.nlrob) 164S3method(print, summary.lts) 165 166S3method(qr, lmrob) 167## lmrob uses residuals.default 168S3method(residuals, nlrob) 169S3method(residuals, glmrob) 170 171S3method(summary, glmrob) 172S3method(summary, lmrob) 173S3method(summary, lts) 174S3method(summary, mcd) 175S3method(summary, nlrob) 176 177S3method(sigma, lmrob) 178S3method(sigma, nlrob) 179S3method(vcov, glmrob) 180S3method(vcov, lmrob) 181S3method(vcov, nlrob) 182S3method(print, summary.mcd) 183 184## S4 Generics {only those defined in this package}: 185export( 186 chgDefaults 187 ) 188 189exportClasses( 190 "functionX", # function(x, <tune_par>): VECTORIZED in 'x' 191 "functionXal", # a functional: function of tuning par.s only 192 "psi_func" # containing rho(), psi(), psi'(), ... 193 ) 194 195exportMethods( 196 chgDefaults, 197 plot 198 ) 199 200