103 lines
4.3 KiB
Plaintext
103 lines
4.3 KiB
Plaintext
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R Under development (unstable) (2021-01-18 r79846) -- "Unsuffered Consequences"
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Copyright (C) 2021 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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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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> library(survival)
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> # Very simple tmerge example, for checking
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> data1 <- data.frame(idd = c(1,5,4,3,2,6), x1=1:6, age=50:55)
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> data2 <- data.frame(idd = c(2,5,1,2,1), x2=5:1, age=48:44)
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> test1 <- tmerge(data1, data1, id=idd, death=event(age))
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> test2 <- tmerge(test1, data2, id=idd, zed=tdc(age, x2))
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> all.equal(test2$idd, c(1,1,1,5,5,4,3,2,2,2,6))
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[1] TRUE
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> all.equal(test2$tstop, c(44, 46, 50, 47, 51, 52, 53, 45, 48, 54, 55))
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[1] TRUE
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> all.equal(test2$death, c(0,0,1,0,1,1,1,0,0,1,1))
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[1] TRUE
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> all.equal(test2$zed, c(NA, 1, 3,NA, 4, NA, NA, NA, 2, 5, NA))
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[1] TRUE
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>
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> #add in a cumtdc variable and cumevent variable
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> data3 <- data.frame(idd=c(5,5,1,1,6,4,3,2),
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+ age=c(45, 50, 44, 48, 53,-5,0,20),
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+ x = c(1,5,2,3,7, 4,6,8))
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> test3 <- tmerge(test2, data3, id=idd, x=cumtdc(age, x),
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+ esum = cumevent(age))
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> all.equal(test3$x, c(NA,2,2,5,NA, 1,1,6,4,6, NA, 8,8,8, NA,7))
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[1] TRUE
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> all.equal(test3$esum, c(1,0,2,0,1,0,2,0,0,0,1,0,0,0,1,0))
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[1] TRUE
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>
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>
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> # An example from Brendan Caroll
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> # It went wrong because the data is not sorted
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>
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> ages <- data.frame( id = c(1L, 2L, 5L, 6L, 9L, 10L, 12L, 13L, 14L, 15L, 16L,
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+ 17L, 18L, 20L, 21L, 24L, 26L, 27L, 28L, 29L, 30L, 31L, 34L, 35L, 36L, 37L,
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+ 38L, 39L, 40L, 42L, 45L, 46L, 43L, 48L, 49L, 50L, 51L, 52L, 54L, 55L, 57L,
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+ 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 68L, 69L, 70L, 71L, 72L, 73L,
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+ 74L, 75L, 8L, 19L, 22L, 23L, 33L, 41L),
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+ age = c(13668, 21550, 15249, 21550,
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+ 16045, 21550, 14976, 14976, 6574, 21550, 4463, 16927, 16927, 15706, 4567,
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+ 21306, 17235, 22158, 19692, 17632, 17597, 4383, 5811, 7704, 5063, 17351,
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+ 17015, 16801, 4383, 5080, 13185, 12604, 19784, 5310, 15369, 13239, 1638,
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+ 21323, 10914, 21262, 7297, 17214, 17508, 14199, 14062, 2227, 8434, 4593,
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+ 14429, 21323, 4782, 10813, 2667, 2853, 5709, 3140, 12237, 7882, 21550,
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+ 15553, 16466, 16621, 19534, 21842))
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>
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> transitions <- data.frame(id=c(2,2, 8, 19, 22, 23, 24, 31,
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+ 33, 41, 43, 52, 55, 66, 6, 10, 43),
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+ transition = c(18993, 13668, 15706,
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+ 11609, 4023, 9316, 16193, 1461,
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+ 4584, 17824, 11261, 16818,
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+ 10670, 15479, 15249, 15887,3713))
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>
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> # Unsorted
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> tdata <- tmerge(ages, ages, id=id, tstop=age)
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> newdata<- tmerge(tdata, transitions, id=id, enum=cumtdc(transition))
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>
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> # sorted
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> test1 <- ages[order(ages$id),]
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> test2 <- tmerge(test1, test1, id=id, tstop=age)
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> tran2 <- transitions[order(transitions$id, transitions$transition),]
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> test3 <- tmerge(test2, tran2, id=id, enum=cumtdc(transition))
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> all.equal(attr(newdata,'tcount'), attr(test3, 'tcount'))
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[1] TRUE
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>
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> test4 <- newdata[order(newdata$id, newdata$tstart),]
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> all.equal(test3, test4, check.attributes=FALSE) #rownames differ
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[1] TRUE
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>
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> # An extension of the first example, where the second data set has a surfeit
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> # of rows: some before the start, some doubled up in the middle
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> data1 <- data.frame(idd = c(1,5,4,3,2,6), x1=1:6, age=50:55)
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> data3 <- data.frame(idd = c(2,5,1,2,1,2,2,1,1,7,3,3),
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+ x2=c(5:1, 10:4), age=c(48:44, -4, -3, -1, -2, 35, 62,61))
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> test1 <- tmerge(data1, data1, id=idd, death=event(age))
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> test3 <- tmerge(test1, data3, id= idd, xx = tdc(age, x2), cx=cumtdc(age, x2, 2))
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> all.equal(test3$idd, c(1,1,1,5,5,4,3,2,2,2,6))
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[1] TRUE
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> all.equal(test3$xx, c(8, 1, 3, NA, 4, NA, NA, 9, 2, 5, NA))
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[1] TRUE
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> all.equal(test3$cx, c(17, 18, 21, 2, 6, 2,2, 21, 23, 28, 2))
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[1] TRUE
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>
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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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0.814 0.052 0.857
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