bethatkinson
commented
3 years ago You have 2 times that are 0. If you add .5 to those 2 subjects it will fix the analysis issue.
From: jgarces notifications@github.com Sent: Wednesday, December 9, 2020 6:38 AM To: bethatkinson/rpart rpart@noreply.github.com Cc: Atkinson, Elizabeth J. (Beth), M.S. atkinson@mayo.edu; Mention mention@noreply.github.com Subject: [EXTERNAL] [bethatkinson/rpart] Error in get(paste("rpart", method, sep = "."), envir = environment())(Y, : Observation time must be > 0 (#24)
Dear @bethatkinsonhttps://github.com/bethatkinson,
First, first things: thanks a lot for this useful package. My data has this structure...
structure(list(c(20, 24, 78, 8, 73, 77, 75, 73, 73, 28, 74, 75, 52, 76, 73, 74, 29, 72, 75, 72, 22, 12, 3, 47, 62, 9, 74, 73, 3, 72, 36, 71, 38, 71, 23, 71, 40, 28, 25, 70, 68, 73, 29, 0, 16, 70, 72, 73, 73, 69, 70, 59, 72, 48, 73, 73, 57, 62, 72, 32, 70, 70, 5, 69, 70, 70, 18, 67, 70, 71, 5, 53, 26, 55, 69, 52, 27, 67, 69, 9, 70, 67, 35, 9, 55, 36, 59, 66, 46, 25, 71, 7, 30, 66, 0, 61, 68, 49, 66, 70), c(1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0), structure(c(3L, 3L, 2L, 4L, 2L, 2L, 4L, 2L, 2L, 3L, 4L, 3L, 2L, 2L, 3L, 2L, 4L, 2L, 3L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 3L, 1L, 4L, 2L, 3L, 3L, 3L, 2L, 3L, 3L, 3L, 1L, 3L, 1L, 2L, 3L, 4L, 3L, 3L, 3L, 1L, 3L, 2L, 4L, 2L, 3L, 3L, 1L, 3L, 4L, 3L, 4L, 1L, 1L, 3L, 1L, 2L, 3L, 4L, 2L, 2L, 1L, 3L, 3L, 4L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 3L, 3L, 3L, 3L, 3L, 4L, 2L, 3L), .Label = c("0", "1", "2", "3"), class = "factor"), structure(c(2L, 2L, 1L, 2L, 2L, NA, 2L, 2L, 2L, 1L, 3L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, NA, NA, 2L, 2L, NA, 1L, 1L, 3L, NA, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, NA, 2L, 2L, NA, NA, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, NA, 2L, 2L, 3L, 2L, NA, 2L, 2L, 3L, 1L, 2L ), .Label = c("1", "2", "3"), class = "factor"), structure(c(2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 2L, 3L, 2L, 1L, 1L, 3L, 2L, 1L, 1L, 3L, 1L, 3L, 1L, 1L, 3L, NA, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 1L, 1L, 2L, 1L, 3L, 3L, 3L, 3L, 2L, 1L, 2L, 2L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 3L, 1L, 2L, 3L, 3L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 2L, 1L, 3L, 2L, 2L, 3L, 2L, 1L, 3L, 2L, 3L, 1L, 2L), .Label = c("1", "2", "3"), class = "factor"), structure(c(1L, 2L, 1L, 2L, NA, NA, 1L, 1L, 1L, 1L, 2L, 1L, 1L, NA, 1L, 1L, 2L, NA, NA, NA, 1L, 2L, NA, 1L, 1L, 2L, NA, 1L, 1L, 1L, 1L, 1L, 2L, 2L, NA, 1L, 1L, 2L, NA, 1L, 2L, NA, NA, 2L, 1L, 1L, 1L, 2L, 2L, NA, NA, 1L, 1L, 1L, 1L, 1L, NA, 1L, 2L, 1L, NA, NA, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, NA, 1L, 1L, 1L, 1L, 2L, NA, 2L, 1L, 1L, NA, 1L, 1L, 2L, 1L, 1L, 1L, NA, 2L, 1L, NA), .Label = c("0", "1"), class = "factor")), .Names = c("PFS", "PFS_c", "score", "Rscore", "grisk", NA), row.names = c(NA, 100L ), class = "data.frame")
... and I'm running rpart (the last version) with this code (and subsequent error):
tr <- rpart(Surv(PFS, PFS_c) ~ score + Rscore + grisk, data = df, method = "exp", control = rpart.control(cp = 0.001)) Error in get(paste("rpart", method, sep = "."), envir = environment())(Y, : Observation time must be > 0
I've seen this error could be coming from poisson method but I'd expect that, because I'm adding a formula with Surv(time... and specifying method = "exp"... could you help me, please? Am I missing something?
Thanks in advance.
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jgarces02
Dear @bethatkinson,
First, first things: thanks a lot for this useful package. My data has this structure...
... and I'm running
rpart(the last version) with this code (and subsequent error):I've seen this error could be coming from poisson method but I'd expect that, because I'm adding a formula with
Surv(time...and specifyingmethod = "exp"... could you help me, please? Am I missing something?Thanks in advance.