
R Under development (unstable) (2019-05-15 r76504) -- "Unsuffered Consequences"
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> ## check that the scale option to summary.survfit works
> ##  Marc Schwartz reported this as a bug in 2.35-3.
> library(survival)
> fit <- survfit(Surv(futime, fustat) ~rx, data=ovarian)
> temp1 <- summary(fit)
> temp2 <- summary(fit, scale=365.25)
> 
> all.equal(temp1$time/365.25, temp2$time)
[1] TRUE
> all.equal(temp1$rmean.endtime/365.25, temp2$rmean.endtime)
[1] TRUE
> all.equal(temp1$table[,5:6]/365.25,    temp2$table[,5:6])
[1] TRUE
> temp <- names(fit)
> temp <- temp[!temp  %in% c("time", "table", "rmean.endtime")]
> all.equal(temp1[temp], temp2[temp])
[1] TRUE
> 
> # Reprise, using the rmean option
> temp1 <- summary(fit, rmean=300)
> temp2 <- summary(fit, rmean=300, scale=365.25)
> all.equal(temp1$time/365.25, temp2$time)
[1] TRUE
> all.equal(temp1$rmean.endtime/365.25, temp2$rmean.endtime)
[1] TRUE
> all.equal(temp1$table[,5:6]/365.25,    temp2$table[,5:6])
[1] TRUE
> all.equal(temp1[temp], temp2[temp])
[1] TRUE
> 
> # Repeat using multi-state data.  Time is in months for mgus2
> etime <- with(mgus2, ifelse(pstat==0, futime, ptime))
> event <- with(mgus2, ifelse(pstat==0, 2*death, 1))
> event <- factor(event, 0:2, labels=c("censor", "pcm", "death"))
> mfit <- survfit(Surv(etime, event) ~ sex, mgus2)
> temp1 <- summary(mfit)
> temp2 <- summary(mfit, scale=12)
> 
> all.equal(temp1$time/12, temp2$time)
[1] TRUE
> all.equal(temp1$rmean.endtime/12, temp2$rmean.endtime)
[1] TRUE
> all.equal(temp1$table[,3]/12,    temp2$table[,3])
[1] TRUE
> temp <- names(temp1)
> temp <- temp[!temp  %in% c("time", "table", "rmean.endtime")]
> all.equal(temp1[temp], temp2[temp])
[1] TRUE
> 
> # Reprise, using the rmean option
> temp1 <- summary(mfit, rmean=240)
> temp2 <- summary(mfit, rmean=240, scale=12)
> all.equal(temp1$time/12, temp2$time)
[1] TRUE
> all.equal(temp1$rmean.endtime/12, temp2$rmean.endtime)
[1] TRUE
> all.equal(temp1$table[,3]/12,    temp2$table[,3])
[1] TRUE
> all.equal(temp1[temp], temp2[temp])
[1] TRUE
> 
> 
> # The n.risk values from summary.survfit were off when there are multiple
> #  curves (version 2.39-2)
> # Verify all components by subscripting
> m1 <- mfit[1,]
> m2 <- mfit[2,]
> s1 <- summary(m1, times=c(0,100, 200, 300))
> s2 <- summary(m2, times=c(0,100, 200, 300))
> s3 <- summary(mfit, times=c(0,100, 200, 300))
> 
> tfun <- function(what) {
+     if (is.matrix(s3[[what]]))
+         all.equal(rbind(s1[[what]], s2[[what]]), s3[[what]])
+     else all.equal(c(s1[[what]], s2[[what]]), s3[[what]])
+ }
> tfun('n')
[1] TRUE
> tfun("time")
[1] TRUE
> tfun("n.risk")
[1] TRUE
> tfun("n.event")
[1] TRUE
> tfun("n.censor")
[1] TRUE
> tfun("pstate")
[1] TRUE
> all.equal(rbind(s1$p0, s2$p0), s3$p0, check.attributes=FALSE)
[1] TRUE
> tfun("std.err")
[1] TRUE
> tfun("lower")
[1] TRUE
> tfun("upper")
[1] TRUE
> 
> # Check the cumulative sums
> temp <- rbind(0, 0,
+               colSums(m1$n.event[m1$time <= 100,]),
+               colSums(m1$n.event[m1$time <= 200, ]),
+               colSums(m1$n.event[m1$time <= 300, ]))
> all.equal(s1$n.event, apply(temp,2, diff))
[1] TRUE
> 
> temp <- rbind(0, 0,
+               colSums(m2$n.event[m2$time <= 100,]),
+               colSums(m2$n.event[m2$time <= 200, ]),
+               colSums(m2$n.event[m2$time <= 300, ]))
> all.equal(s2$n.event, apply(temp,2, diff))
[1] TRUE
> 
> temp <- c(0, 0,sum(m1$n.censor[m1$time <= 100]),
+                sum(m1$n.censor[m1$time <= 200]),
+                sum(m1$n.censor[m1$time <= 300]))
> all.equal(s1$n.censor, diff(temp))
[1] TRUE
>               
> # check the same with survfit objects
> s1 <- summary(fit[1], times=c(0, 200, 400, 600))
> s2 <- summary(fit[2], times=c(0, 200, 400, 600))
> s3 <- summary(fit, times=c(0, 200, 400, 600))
> tfun('n')
[1] TRUE
> tfun("time")
[1] TRUE
> tfun("n.risk")
[1] TRUE
> tfun("n.event")
[1] TRUE
> tfun("n.censor")
[1] TRUE
> tfun("surv")
[1] TRUE
> tfun("std.err")
[1] TRUE
> tfun("lower")
[1] TRUE
> tfun("upper")
[1] TRUE
> 
> f2 <- fit[2]
> temp <- c(0, 0, sum(f2$n.event[f2$time <= 200]),
+                 sum(f2$n.event[f2$time <= 400]),
+                 sum(f2$n.event[f2$time <= 600]))
> all.equal(s2$n.event, diff(temp))
[1] TRUE
> 
> f1 <- fit[1]
> temp <- c(0, 0,sum(f1$n.censor[f1$time <= 200]),
+                sum(f1$n.censor[f1$time <= 400]),
+                sum(f1$n.censor[f1$time <= 600]))
> all.equal(s1$n.censor, diff(temp))
[1] TRUE
> 
> #
> # A check on the censor option
> #
> s1 <- summary(fit[1])
> s2 <- summary(fit[2])
> s3 <- summary(fit)
> tfun('n')
[1] TRUE
> tfun("time")
[1] TRUE
> tfun("n.risk")
[1] TRUE
> tfun("n.event")
[1] TRUE
> tfun("n.censor")
[1] TRUE
> tfun("surv")
[1] TRUE
> tfun("std.err")
[1] TRUE
> tfun("lower")
[1] TRUE
> tfun("upper")
[1] TRUE
> 
> s1 <- summary(mfit[1,])
> s2 <- summary(mfit[2,])
> s3 <- summary(mfit)
> tfun('n')
[1] TRUE
> tfun("time")
[1] TRUE
> tfun("n.risk")
[1] TRUE
> tfun("n.event")
[1] TRUE
> tfun("n.censor")
[1] TRUE
> tfun("surv")
[1] TRUE
> tfun("std.err")
[1] TRUE
> tfun("lower")
[1] TRUE
> tfun("upper")
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  0.800   0.060   0.861 
