bethatkinson
commented
3 months ago If you put istate in the survcheck call you'll note that you have teleport errors. You're init_stat variable is causing you problems. Take a look at the istate variable created by survcheck to better understand how to define the variable. Generally I avoid trying to define istate unless people are entering the study with a different state because it can be tricky to get it right. My suggestion is to start with the istate created by survcheck, then modify it slightly as needed.
check <- survcheck( Surv( time = tstart, time2 = tstop, event = event, type = 'mstate' ) ~ 1, data = model_data, id = study_id, istate=init_stat)
check$teleport $row [1] 3 4 5 6 7 10 11 12 13 14 16 17 18 21
$id [1] 17 26 104
If I look at the natural istate values that come from the data check2 <- survcheck( Surv( time = tstart, time2 = tstop, event = event, type = 'mstate' ) ~ 1, data = model_data, id = study_id)
model_data$new_istate <- check2$istate
model_data[model_data$study_id==17,] study_id tstart tstop init_stat event new_istate 1 17 0 1 (s0) (s0) 2 17 1 7 (s0) Waitlisted (s0) 3 17 7 221 (s0) Waitlisted 4 17 221 248 (s0) Transplanted Waitlisted 5 17 248 249 (s0) Waitlisted Transplanted 6 17 249 251 (s0) Transplanted Waitlisted 7 17 251 253 (s0) Dead Transplanted
From: Demetri Pananos @.>
Sent: Wednesday, June 05, 2024 11:12 PM
To: therneau/survival @.>
Cc: Subscribed @.***>
Subject: [EXTERNAL] [therneau/survival] survift mentions survcheck flags>0, but survcheck returns no flags (Issue #258)
I have created a longitudinal dataset using tmerge. I've excluded time dependent covariates to isolate the problem, so there may be more rows than there are state transitions.
When I try to use survfit to fit a multistate model, I am met with an error stating Error in survfitCI(X, newY, weights = casewt, stype = stype, ctype = ctype, : one or more flags are >0 in survcheck. However, survcheck$ flags is all 0. See below for a reproducible example.
library(survival)
model_data <- structure(list(study_id = c(17, 17, 17, 17, 17, 17, 17, 26, 26,
26, 26, 26, 26, 26, 104, 104, 104, 104, 104, 104, 104), tstart = c(0,
1, 7, 221, 248, 249, 251, 0, 2, 7, 128, 129, 156, 164, 0, 629,
1044, 1045, 1057, 1373, 1666), tstop = c(1, 7, 221, 248, 249,
251, 253, 2, 7, 128, 129, 156, 164, 344, 629, 1044, 1045, 1057,
1373, 1666, 1724), init_stat = c("(s0)", "(s0)", "(s0)", "(s0)",
"(s0)", "(s0)", "(s0)", "(s0)", "(s0)", "(s0)", "(s0)", "(s0)",
"(s0)", "(s0)", "Waitlisted", "Waitlisted", "Waitlisted", "Waitlisted",
"Waitlisted", "Waitlisted", "Waitlisted"), event = c("", "Waitlisted",
"", "Transplanted", "Waitlisted", "Transplanted", "Dead", "",
"Waitlisted", "", "", "", "Transplanted", "Dead", "Removed from Waitlist",
"", "", "Waitlisted", "", "Removed from Waitlist", "Dead")), row.names = c(NA,
-21L), class = "data.frame")check <- survcheck( Surv(
time = tstart,
time2 = tstop,
event = event,
type = 'mstate'
) ~ 1, data = model_data, id = study_id)
check$flag
> overlap gap jump teleport duplicate
> 0 0 0 0 0
fit <- survfit(
Surv(
time = tstart,
time2 = tstop,
event = event,
type = 'mstate') ~ 1, data = model_data, id = study_id,
istate = init_stat
)
> Error in survfitCI(X, newY, weights = casewt, stype = stype, ctype = ctype, : one or more flags are >0 in survcheck
Created on 2024-06-06 with reprex v2.1.0https://reprex.tidyverse.org/
However, if I remove the istate argument, then the model fits. This suggests I've perhaps done something wrong with the istate variable.
Is this a problem with survfit, or a problem with what I pass to istate? How should this be rectified if it is a user error?
- Reply to this email directly, view it on GitHubhttps://github.com/therneau/survival/issues/258, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACWQG565QTGFHYX6TXBYEITZF7OPXAVCNFSM6AAAAABI35JTRWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZTOMRWHA2TIMY. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>
therneau
I have created a longitudinal dataset using
tmerge. I've excluded time dependent covariates to isolate the problem, so there may be more rows than there are state transitions.When I try to use
survfitto fit a multistate model, I am met with an error statingError in survfitCI(X, newY, weights = casewt, stype = stype, ctype = ctype, : one or more flags are >0 in survcheck. However,survcheck$flags is all 0. See below for a reproducible example.Created on 2024-06-06 with reprex v2.1.0
However, if I remove the
istateargument, then the model fits. This suggests I've perhaps done something wrong with theistatevariable.Is this a problem with
survfit, or a problem with what I pass toistate? How should this be rectified if it is a user error?