120 lines
4.2 KiB
Plaintext
120 lines
4.2 KiB
Plaintext
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R Under development (unstable) (2024-02-07 r85873) -- "Unsuffered Consequences"
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Copyright (C) 2024 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> #
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> # Verify that using multiple states + proportional baselines
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> # will mimic a factor covariate
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> #
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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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>
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> tdata <- subset(lung, ph.ecog < 3) # there is only one row with ph.ecog=3
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> tdata$state <- factor(tdata$status, 1:2, c("censor", "death"))
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> tdata$cstate<- factor(tdata$ph.ecog, 0:2, c("ph0", "ph1", "ph2"))
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> tdata$id <- 1:nrow(tdata)
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> survcheck(Surv(time, state) ~ 1, id=id, istate=cstate, tdata)
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Call:
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survcheck(formula = Surv(time, state) ~ 1, data = tdata, id = id,
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istate = cstate)
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Unique identifiers Observations Transitions
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226 226 163
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Transitions table:
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to
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from death (censored)
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ph0 37 26
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ph1 82 31
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ph2 44 6
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death 0 0
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Number of subjects with 0, 1, ... transitions to each state:
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count
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state 0 1
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death 63 163
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(any) 63 163
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>
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> # standard coxph fit, stratified by the ph0/1/2 groups
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> fit1 <- coxph(Surv(time, status) ~ age + sex + factor(ph.ecog), tdata,
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+ ties="breslow")
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> # multi-state fit, where ph0/1/2 are states with a shared hazard
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> fit2 <- coxph(list(Surv(time, state) ~1,
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+ 1:4 + 2:4 + 3:4~ age + sex/ common + shared),
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+ id=id, istate=cstate, data= tdata, ties="breslow")
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>
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> aeq(coef(fit1), coef(fit2)) # the names are quite different, values the same
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[1] TRUE
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> all.equal(fit1$loglik, fit2$loglik)
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[1] TRUE
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>
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> # Three curves in the usual way: ph0, 1, or 2 for all time, common baseline
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> csurv1 <- survfit(fit1, newdata=expand.grid(age=65, sex=1, ph.ecog=0:2))
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>
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> # Multistate: start in p0, p1, or p2 (the only place to go is death)
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> csurv2a <- survfit(fit2, newdata= list(age=65, sex=1), p0=c(1,0,0,0))
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> csurv2b <- survfit(fit2, newdata= list(age=65, sex=1), p0=c(0,1,0,0))
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> csurv2c <- survfit(fit2, newdata= list(age=65, sex=1), p0=c(0,0,1,0))
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>
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> aeq(csurv1[1]$surv, csurv2a$pstate[,1,1])
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[1] TRUE
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> aeq(csurv1[2]$surv, csurv2b$pstate[,1,2])
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[1] TRUE
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> aeq(csurv1[3]$surv, csurv2c$pstate[,1,3])
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[1] TRUE
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>
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> # Note that multi-state defaults to the Breslow, as it implements the Efron
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> # only imperfectly.
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>
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> # part 2: predicted survival for a multistate model that has a strata
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> mgus2$etime <- with(mgus2, ifelse(pstat==0, futime, ptime))
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> temp <- with(mgus2, ifelse(pstat==0, 2*death, 1))
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> mgus2$event <- factor(temp, 0:2, labels=c("censor", "pcm", "death"))
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>
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> dummy <- expand.grid(age=c(60, 80), mspike=1.2)
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>
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> cfit1 <- coxph(Surv(etime, event) ~ age + mspike +strata(sex), mgus2, id=id)
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>
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> csurv1 <- survfit(cfit1, newdata=dummy)
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>
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> cfit2 <- coxph(Surv(etime, event) ~ age + mspike, id=id,
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+ init= coef(cfit1), iter=0, data=mgus2, subset=(sex=='F'))
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> csurv3 <- survfit(cfit2, newdata= expand.grid(age=c(60, 80), mspike=1.2))
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> test <- c('n', 'time', 'n.risk', 'n.event', 'n.censor', 'pstate', 'cumhaz')
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> all.equal(unclass(csurv1[1,,])[test], unclass(csurv3)[test])
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[1] TRUE
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>
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>
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> # Part 3: compare a shared baseline to identical baseline
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> if (FALSE) {
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+ # not yet completed
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+ fit3 <- coxph(list(Surv(time, state) ~1,
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+ 1:4 + 2:4 + 3:4~ age + sex/ common + 1),
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+ id=id, istate=cstate, data= tdata)
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+ fit4 <- coxph(list(Surv(time, state) ~1,
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+ 1:4 + 2:4 + 3:4~ age + sex/ 1),
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+ id=id, istate=cstate, data= tdata)
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+
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+ fit0 <- coxph(Surv(time, status) ~ age + sex, tdata, ties="breslow")
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+
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+ survfit(fit3, newdata= list(age=65, sex=1))
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+ }
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>
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> proc.time()
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user system elapsed
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1.085 0.106 1.183
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