98 lines
3.6 KiB
R
98 lines
3.6 KiB
R
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options(na.action=na.exclude) # preserve missings
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options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
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library(survival)
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aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
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# fit1 and fit4 should follow identical iteration paths
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fit1 <- survreg(Surv(futime, fustat) ~ age + ecog.ps, ovarian, x=TRUE)
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fit4 <- survreg(Surv(log(futime), fustat) ~age + ecog.ps, ovarian,
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dist='extreme')
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aeq(fit1$coef, fit4$coef)
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aeq(fit1$var, fit4$var)
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resid(fit1, type='working')
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resid(fit1, type='response')
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resid(fit1, type='deviance')
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resid(fit1, type='dfbeta')
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resid(fit1, type='dfbetas')
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resid(fit1, type='ldcase')
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resid(fit1, type='ldresp')
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resid(fit1, type='ldshape')
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resid(fit1, type='matrix')
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aeq(resid(fit1, type='working'),resid(fit4, type='working'))
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#aeq(resid(fit1, type='response'), resid(fit4, type='response'))#should differ
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aeq(resid(fit1, type='deviance'), resid(fit4, type='deviance'))
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aeq(resid(fit1, type='dfbeta'), resid(fit4, type='dfbeta'))
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aeq(resid(fit1, type='dfbetas'), resid(fit4, type='dfbetas'))
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aeq(resid(fit1, type='ldcase'), resid(fit4, type='ldcase'))
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aeq(resid(fit1, type='ldresp'), resid(fit4, type='ldresp'))
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aeq(resid(fit1, type='ldshape'), resid(fit4, type='ldshape'))
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aeq(resid(fit1, type='matrix'), resid(fit4, type='matrix'))
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# Test suggested by Achim Zieleis: residuals should give a score vector
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r1 <-residuals(fit1, type='matrix')
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score <- c(as.vector(r1[,c("dg")]) %*% model.matrix(fit1),
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"log(scale)" = sum(r1[,"ds"]))
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all(abs(score) < 1e-6)
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# repeat this with Gaussian (no transform = different code path)
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tfit <- survreg(Surv(durable, durable>0, type='left') ~age + quant,
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data=tobin, dist='gaussian')
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r2 <- residuals(tfit, type='matrix')
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score <- c(as.vector(r2[, "dg"]) %*% model.matrix(tfit),
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"log(scale)" = sum(r2[,"ds"]))
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all(score < 1e-6)
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#
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# Some tests of the quantile residuals
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#
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# These should agree exactly with Ripley and Venables' book
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fit1 <- survreg(Surv(time, status) ~ temp, data= imotor)
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summary(fit1)
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#
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# The first prediction has the SE that I think is correct
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# The third is the se found in an early draft of Ripley; fit1 ignoring
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# the variation in scale estimate, except via it's impact on the
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# upper left corner of the inverse information matrix.
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# Numbers 1 and 3 differ little for this dataset
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#
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predict(fit1, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
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fit2 <- survreg(Surv(time, status) ~ temp, data=imotor, scale=fit1$scale)
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predict(fit2, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
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fit3 <- fit2
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fit3$var <- fit1$var[1:2,1:2]
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predict(fit3, data.frame(temp=130), type='uquantile', p=c(.5, .1), se=T)
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pp <- seq(.05, .7, length=40)
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xx <- predict(fit1, data.frame(temp=130), type='uquantile', se=T,
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p=pp)
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#matplot(pp, cbind(xx$fit, xx$fit+2*xx$se, xx$fit - 2*xx$se), type='l')
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#
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# Now try out the various combinations of strata, #predicted, and
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# number of quantiles desired
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#
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fit1 <- survreg(Surv(time, status) ~ inst + strata(inst) + age + sex, lung)
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qq1 <- predict(fit1, type='quantile', p=.3, se=T)
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qq2 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T)
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aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
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aeq(qq1$fit, qq2$fit[,2])
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aeq(qq1$se.fit, qq2$se.fit[,2])
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qq3 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T,
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newdata= lung[1:5,])
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aeq(qq3$fit, qq2$fit[1:5,])
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qq4 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung[7,])
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aeq(qq4$fit, qq2$fit[7,])
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qq5 <- predict(fit1, type='quantile', p=c(.2, .3, .4), se=T, newdata=lung)
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aeq(qq2$fit, qq5$fit)
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aeq(qq2$se.fit, qq5$se.fit)
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