R Under development (unstable) (2024-12-09 r87433 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > options(na.action=na.exclude) # preserve missings > options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type > library(survival) > > aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...) > > # fit1 and fit4 should follow identical iteration paths > fit1 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian, x=TRUE) > fit4 <- survreg(Surv(log(futime), fustat) ~age + ecog.ps, ovarian, + dist='extreme') > aeq(fit1$coef, fit4$coef) [1] TRUE > aeq(fit1$var, fit4$var) [1] TRUE > > resid(fit1, type='working') 1 2 3 4 5 6 -4.5081778 -0.5909810 -2.4878519 0.6032744 -5.8993431 0.6032744 7 8 9 10 11 12 -1.7462937 -0.8102883 0.6032744 -1.6593962 -0.8235265 0.6032744 13 14 15 16 17 18 0.6032744 0.6032744 0.6032744 0.6032744 0.6032744 0.6032744 19 20 21 22 23 24 0.6032744 0.6032744 0.6032744 0.2572623 -31.8006867 -0.7426277 25 26 -0.2857597 0.6032744 > resid(fit1, type='response') 1 2 3 4 5 6 -155.14523 -58.62744 -262.03173 -927.79842 -1377.84908 -658.86626 7 8 9 10 11 12 -589.74449 -318.93436 4.50671 -686.83338 -434.39281 -1105.68733 13 14 15 16 17 18 -42.43371 -173.09223 -4491.29974 -3170.49394 -5028.31053 -2050.91373 19 20 21 22 23 24 -150.65033 -2074.09345 412.32400 76.35826 -3309.40331 -219.81579 25 26 -96.19691 -457.76731 > resid(fit1, type='deviance') 1 2 3 4 5 6 7 -1.5842290 -0.6132746 -1.2876971 0.5387840 -1.7148539 0.6682580 -1.1102921 8 9 10 11 12 13 14 -0.7460191 1.4253843 -1.0849419 -0.7531720 0.6648130 1.3526380 1.1954382 15 16 17 18 19 20 21 0.2962391 0.3916044 0.3278067 0.5929057 1.2747643 0.6171130 1.9857606 22 23 24 25 26 0.6125492 -2.4504208 -0.7080652 -0.3642424 0.7317955 > resid(fit1, type='dfbeta') [,1] [,2] [,3] [,4] 1 0.43370970 -1.087867e-02 0.126322520 0.048379059 2 0.14426449 -5.144770e-03 0.088768478 -0.033939677 3 0.25768057 -3.066698e-03 -0.066578834 0.021817646 4 0.05772598 -5.068044e-04 -0.013121427 -0.007762466 5 -0.58773456 6.676156e-03 0.084189274 0.008064026 6 0.01499533 -7.881949e-04 0.026570173 -0.013513160 7 -0.17869321 4.126121e-03 -0.072760519 -0.015006956 8 -0.11851540 2.520303e-03 -0.045549628 -0.035686269 9 0.08327656 3.206404e-03 -0.141835350 0.024490806 10 -0.25083921 5.321702e-03 -0.073986269 -0.020648720 11 -0.21333934 4.155746e-03 -0.049832434 -0.040215681 12 0.13889770 -1.586136e-03 -0.019701151 -0.004686340 13 0.07892133 -2.706713e-03 0.085242459 0.007847879 14 0.29690157 -1.987141e-03 -0.085553120 0.017447343 15 0.04344618 -6.319243e-04 -0.001944285 -0.003533279 16 0.04866809 -1.068317e-03 0.012398602 -0.006340983 17 0.04368104 -9.248316e-04 0.009428718 -0.004869178 18 0.15684611 -2.081485e-03 -0.013068320 -0.003265399 19 0.48839511 -4.775829e-03 -0.093258090 0.032703354 20 0.17598922 -2.349254e-03 -0.014202966 -0.002486428 21 0.37869758 -8.442011e-03 0.163476417 0.100850775 22 -0.59761427 8.803638e-03 0.052784598 -0.053085234 23 -0.79017984 1.092304e-02 0.053690092 0.080780399 24 -0.02348526 8.331002e-04 -0.039028433 -0.032765737 25 -0.13948485 3.687927e-04 0.056781884 -0.055647859 26 0.05778937 3.766350e-06 -0.029232389 -0.008927920 > resid(fit1, type='dfbetas') [,1] [,2] [,3] [,4] 1 0.288846658 -0.4627232074 0.345395116 0.20574292 2 0.096078819 -0.2188323823 0.242713641 -0.14433617 3 0.171612884 -0.1304417700 -0.182041999 0.09278449 4 0.038444974 -0.0215568869 -0.035877029 -0.03301165 5 -0.391425795 0.2839697749 0.230193032 0.03429410 6 0.009986751 -0.0335258093 0.072649027 -0.05746778 7 -0.119008027 0.1755042532 -0.198944162 -0.06382048 8 -0.078930164 0.1072008799 -0.124543264 -0.15176395 9 0.055461420 0.1363841532 -0.387810796 0.10415271 10 -0.167056601 0.2263581990 -0.202295647 -0.08781336 11 -0.142082031 0.1767643342 -0.136253451 -0.17102630 12 0.092504589 -0.0674661531 -0.053867524 -0.01992972 13 0.052560878 -0.1151298322 0.233072686 0.03337488 14 0.197733705 -0.0845228882 -0.233922105 0.07419878 15 0.028934753 -0.0268788526 -0.005316126 -0.01502607 16 0.032412497 -0.0454407662 0.033900659 -0.02696647 17 0.029091172 -0.0393376416 0.025780305 -0.02070728 18 0.104458066 -0.0885357994 -0.035731824 -0.01388685 19 0.325266641 -0.2031395176 -0.254989284 0.13907843 20 0.117207199 -0.0999253459 -0.038834208 -0.01057410 21 0.252209096 -0.3590802699 0.446982501 0.42889079 22 -0.398005596 0.3744620571 0.144325354 -0.22575700 23 -0.526252483 0.4646108448 0.146801184 0.34353696 24 -0.015640965 0.0354358527 -0.106712804 -0.13934372 25 -0.092895624 0.0156865706 0.155254862 -0.23665514 26 0.038487186 0.0001602014 -0.079928144 -0.03796800 > resid(fit1, type='ldcase') 1 2 3 4 5 6 0.374432175 0.145690278 0.112678800 0.006399163 0.261176992 0.013280058 7 8 9 10 11 12 0.109842490 0.074103234 0.248285282 0.128482147 0.094038203 0.016111951 13 14 15 16 17 18 0.132812463 0.111857574 0.001698300 0.004730718 0.003131173 0.015840667 19 20 21 22 23 24 0.179925399 0.019071941 0.797119488 0.233096445 0.666613755 0.062959708 25 26 0.080117437 0.015922378 > resid(fit1, type='ldresp') 1 2 3 4 5 6 0.076910173 0.173810883 0.078356928 0.005310644 0.060742612 0.010002154 7 8 9 10 11 12 0.067356838 0.067065693 0.355103899 0.067043195 0.068142828 0.016740944 13 14 15 16 17 18 0.193444572 0.165021262 0.001494685 0.004083386 0.002767560 0.016400993 19 20 21 22 23 24 0.269571809 0.020129806 1.409736499 1.040266083 0.058637282 0.071819025 25 26 0.112702844 0.015105534 > resid(fit1, type='ldshape') 1 2 3 4 5 6 0.870628250 0.383362440 0.412503605 0.005534970 0.513991064 0.003310847 7 8 9 10 11 12 0.291860593 0.154910362 0.256160646 0.312329770 0.183191309 0.004184904 13 14 15 16 17 18 0.110215710 0.049299495 0.007678445 0.011633336 0.011588605 0.008641251 19 20 21 22 23 24 0.112967758 0.008271358 2.246729275 0.966929220 1.022043272 0.143857170 25 26 0.079754096 0.001606647 > resid(fit1, type='matrix') g dg ddg ds dds dsg 1 -1.74950763 -1.46198129 -0.32429540 0.88466493 -2.42358635 1.8800360 2 -0.68266980 -0.82027857 -1.38799493 -0.66206188 -0.57351872 1.3921043 3 -1.32369884 -1.33411374 -0.53625126 0.31503768 -1.83606321 1.8626973 4 -0.14514412 0.24059386 -0.39881329 -0.28013223 -0.26053084 0.2237590 5 -1.96497889 -1.50383619 -0.25491587 1.15700933 -2.68145423 1.8694717 6 -0.22328436 0.37012071 -0.61351964 -0.33477229 -0.16715487 0.1848047 7 -1.11099124 -1.23201028 -0.70550005 0.01052036 -1.48515401 1.8106760 8 -0.77288913 -0.95018808 -1.17265428 -0.51190170 -0.79753045 1.5525642 9 -1.01586016 1.68391053 -2.79128447 0.01598527 -0.01623681 -1.7104080 10 -1.08316634 -1.21566480 -0.73259465 -0.03052447 -1.43539383 1.7998987 11 -0.77825093 -0.95675178 -1.16177415 -0.50314979 -0.81016011 1.5600720 12 -0.22098818 0.36631452 -0.60721042 -0.33361394 -0.17002503 0.1866908 13 -0.91481479 1.51641567 -2.51364157 -0.08144930 0.07419757 -1.3814037 14 -0.71453621 1.18442981 -1.96333502 -0.24017106 0.15944438 -0.7863174 15 -0.04387880 0.07273440 -0.12056602 -0.13717935 -0.29168773 0.1546569 16 -0.07667699 0.12710134 -0.21068577 -0.19691828 -0.30879813 0.1993144 17 -0.05372862 0.08906165 -0.14763041 -0.15709224 -0.30221555 0.1713377 18 -0.17576861 0.29135764 -0.48296037 -0.30558900 -0.22570402 0.2151929 19 -0.81251205 1.34683655 -2.23254376 -0.16869744 0.13367171 -1.0672002 20 -0.19041424 0.31563454 -0.52320225 -0.31581218 -0.20797917 0.2078622 21 -1.97162252 3.26820173 -5.41743790 1.33844939 -2.24706488 -5.4868428 22 -0.68222519 1.23245193 -4.79064290 -0.58668577 -0.95209805 -2.8390386 23 -3.49689798 -1.62675999 -0.05115487 2.90949868 -4.20494743 1.7496975 24 -0.74529506 -0.91462436 -1.23160543 -0.55723389 -0.73139169 1.5108398 25 -0.56095318 -0.53280415 -1.86451840 -0.87536233 -0.22666819 0.9689667 26 -0.26776235 0.44384834 -0.73573207 -0.35281852 -0.11207472 0.1409908 > > aeq(resid(fit1, type='working'),resid(fit4, type='working')) [1] TRUE > #aeq(resid(fit1, type='response'), resid(fit4, type='response'))#should differ > aeq(resid(fit1, type='deviance'), resid(fit4, type='deviance')) [1] TRUE > aeq(resid(fit1, type='dfbeta'), resid(fit4, type='dfbeta')) [1] TRUE > aeq(resid(fit1, type='dfbetas'), resid(fit4, type='dfbetas')) [1] TRUE > aeq(resid(fit1, type='ldcase'), resid(fit4, type='ldcase')) [1] TRUE > aeq(resid(fit1, type='ldresp'), resid(fit4, type='ldresp')) [1] TRUE > aeq(resid(fit1, type='ldshape'), resid(fit4, type='ldshape')) [1] TRUE > aeq(resid(fit1, type='matrix'), resid(fit4, type='matrix')) [1] TRUE > > # Test suggested by Achim Zieleis: residuals should give a score vector > r1 <-residuals(fit1, type='matrix') > score <- c(as.vector(r1[,c("dg")]) %*% model.matrix(fit1), + "log(scale)" = sum(r1[,"ds"])) > all(abs(score) < 1e-6) [1] TRUE > > # repeat this with Gaussian (no transform = different code path) > tfit <- survreg(Surv(durable, durable>0, type='left') ~age + quant, + data=tobin, dist='gaussian') > r2 <- residuals(tfit, type='matrix') > score <- c(as.vector(r2[, "dg"]) %*% model.matrix(tfit), + "log(scale)" = sum(r2[,"ds"])) > all(score < 1e-6) [1] TRUE > > # > # Some tests of the quantile residuals > # > # These should agree exactly with Ripley and Venables' book > fit1 <- survreg(Surv(time, status) ~ temp, data= imotor) > summary(fit1) Call: survreg(formula = Surv(time, status) ~ temp, data = imotor) Value Std. Error z p (Intercept) 16.31852 0.62296 26.2 < 2e-16 temp -0.04531 0.00319 -14.2 < 2e-16 Log(scale) -1.09564 0.21480 -5.1 3.4e-07 Scale= 0.334 Weibull distribution Loglik(model)= -147.4 Loglik(intercept only)= -169.5 Chisq= 44.32 on 1 degrees of freedom, p= 2.8e-11 Number of Newton-Raphson Iterations: 8 n= 40 > > # > # The first prediction has the SE that I think is correct > # The third is the se found in an early draft of Ripley; fit1 ignoring > # the variation in scale estimate, except via it's impact on the > # upper left corner of the inverse information matrix. > # Numbers 1 and 3 differ little for this dataset > # > predict(fit1, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T) $fit [1] 10.306068 9.676248 $se.fit [1] 0.2135247 0.2202088 > > fit2 <- survreg(Surv(time, status) ~ temp, data=imotor, scale=fit1$scale) > predict(fit2, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T) $fit [1] 10.306068 9.676248 $se.fit 1 1 0.2057964 0.2057964 > > fit3 <- fit2 > fit3$var <- fit1$var[1:2,1:2] > predict(fit3, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T) $fit [1] 10.306068 9.676248 $se.fit 1 1 0.2219959 0.2219959 > > pp <- seq(.05, .7, length=40) > xx <- predict(fit1, data.frame(temp=130), type='uquantile', se=T, + p=pp) > #matplot(pp, cbind(xx$fit, xx$fit+2*xx$se, xx$fit - 2*xx$se), type='l') > > > # > # Now try out the various combinations of strata, #predicted, and > # number of quantiles desired > # > fit1 <- survreg(Surv(time, status) ~ inst + strata(inst) + age + sex, lung) > qq1 <- predict(fit1, type='quantile', p=.3, se=T) > qq2 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T) > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) > aeq(qq1$fit, qq2$fit[,2]) [1] TRUE > aeq(qq1$se.fit, qq2$se.fit[,2]) [1] TRUE > > qq3 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, + newdata= lung[1:5,]) > aeq(qq3$fit, qq2$fit[1:5,]) [1] TRUE > > qq4 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung[7,]) > aeq(qq4$fit, qq2$fit[7,]) [1] TRUE > > qq5 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung) > aeq(qq2$fit, qq5$fit) [1] TRUE > aeq(qq2$se.fit, qq5$se.fit) [1] TRUE > > proc.time() user system elapsed 0.84 0.07 0.92