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Does psm::Surv handle interval2 data?
3 messages · Andrews, Chris, Frank E Harrell Jr
Chris, Thanks for sending the specifics. It appears that I've let Surv in rms fall behind recent versions of Surv in survival. It will take me a few days to get this fixed. I'll send a follow-up note then. Frank Andrews, Chris wrote
Does Surv in psm handle interval2 data? The argument list seems to
indicate it does but I get an error.
Thanks,
Chris
# code
library('survival')
left <- c(1, 3, 5, NA)
right <-c(2, 3, NA, 4)
Surv(left, right, type='interval2')
survreg(Surv(left, right, type='interval2') ~ 1)
library('rms')
Surv(left, right, type='interval2') # error
args(Surv)
psm(Surv(left, right, type='interval2') ~ 1) # same error (of course)
psm(survival::Surv(left, right, type='interval2') ~ 1) # runs
# output
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library('survival')
Loading required package: splines
left <- c(1, 3, 5, NA)
right <-c(2, 3, NA, 4)
Surv(left, right, type='interval2')
[1] [1, 2] 3 5+ 4-
survreg(Surv(left, right, type='interval2') ~ 1)
Call: survreg(formula = Surv(left, right, type = "interval2") ~ 1) Coefficients: (Intercept) 1.317943 Scale= 0.6098782 Loglik(model)= -5.3 Loglik(intercept only)= -5.3 n= 4
library('rms')
Loading required package: Hmisc
Hmisc library by Frank E Harrell Jr
Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.
NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting. To get the old behavior of Hmisc type dropUnusedLevels().
Attaching package: 'Hmisc'
The following object(s) are masked from 'package:survival':
untangle.specials
The following object(s) are masked from 'package:base':
format.pval, round.POSIXt, trunc.POSIXt, units
Attaching package: 'rms'
The following object(s) are masked from 'package:survival':
Surv
Surv(left, right, type='interval2') # error
Error in Surv(left, right, type = "interval2") : argument "event" is missing, with no default
args(Surv)
function (time, time2, event, type = c("right", "left", "interval",
"counting", "interval2"), origin = 0)
NULL
psm(Surv(left, right, type='interval2') ~ 1) # same error (of course)
Error in Surv(left, right, type = "interval2") : argument "event" is missing, with no default
psm(survival::Surv(left, right, type='interval2') ~ 1) # runs
Parametric Survival Model: Weibull Distribution
psm(formula = survival::Surv(left, right, type = "interval2") ~
1)
Model Likelihood Discrimination
Ratio Test Indexes
Obs 4 LR chi2 0.00 R2 0.000
Events 6 d.f. 0 g 0.000
sigma 0.6099 gr 1.000
Coef S.E. Wald Z Pr(>|Z|)
(Intercept) 1.3179 0.3598 3.66 0.0002
Log(scale) -0.4945 0.5977 -0.83 0.4081
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues
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______________________________________________
R-help@
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Does-psm-Surv-handle-interval2-data-tp4655472p4655475.html Sent from the R help mailing list archive at Nabble.com.
6 days later
Chris,
I've fixed Surv in rms. The fix will be in the next release. For now you
can do source('http://biostat.mc.vanderbilt.edu/tmp/Surv.s') after issuing
require(rms).
Frank
Frank Harrell wrote
Chris, Thanks for sending the specifics. It appears that I've let Surv in rms fall behind recent versions of Surv in survival. It will take me a few days to get this fixed. I'll send a follow-up note then. Frank Andrews, Chris wrote
Does Surv in psm handle interval2 data? The argument list seems to
indicate it does but I get an error.
Thanks,
Chris
# code
library('survival')
left <- c(1, 3, 5, NA)
right <-c(2, 3, NA, 4)
Surv(left, right, type='interval2')
survreg(Surv(left, right, type='interval2') ~ 1)
library('rms')
Surv(left, right, type='interval2') # error
args(Surv)
psm(Surv(left, right, type='interval2') ~ 1) # same error (of course)
psm(survival::Surv(left, right, type='interval2') ~ 1) # runs
# output
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library('survival')
Loading required package: splines
left <- c(1, 3, 5, NA)
right <-c(2, 3, NA, 4)
Surv(left, right, type='interval2')
[1] [1, 2] 3 5+ 4-
survreg(Surv(left, right, type='interval2') ~ 1)
Call: survreg(formula = Surv(left, right, type = "interval2") ~ 1) Coefficients: (Intercept) 1.317943 Scale= 0.6098782 Loglik(model)= -5.3 Loglik(intercept only)= -5.3 n= 4
library('rms')
Loading required package: Hmisc
Hmisc library by Frank E Harrell Jr
Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.
NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting. To get the old behavior of Hmisc type dropUnusedLevels().
Attaching package: 'Hmisc'
The following object(s) are masked from 'package:survival':
untangle.specials
The following object(s) are masked from 'package:base':
format.pval, round.POSIXt, trunc.POSIXt, units
Attaching package: 'rms'
The following object(s) are masked from 'package:survival':
Surv
Surv(left, right, type='interval2') # error
Error in Surv(left, right, type = "interval2") : argument "event" is missing, with no default
args(Surv)
function (time, time2, event, type = c("right", "left", "interval",
"counting", "interval2"), origin = 0)
NULL
psm(Surv(left, right, type='interval2') ~ 1) # same error (of course)
Error in Surv(left, right, type = "interval2") : argument "event" is missing, with no default
psm(survival::Surv(left, right, type='interval2') ~ 1) # runs
Parametric Survival Model: Weibull Distribution
psm(formula = survival::Surv(left, right, type = "interval2") ~
1)
Model Likelihood Discrimination
Ratio Test Indexes
Obs 4 LR chi2 0.00 R2 0.000
Events 6 d.f. 0 g 0.000
sigma 0.6099 gr 1.000
Coef S.E. Wald Z Pr(>|Z|)
(Intercept) 1.3179 0.3598 3.66 0.0002
Log(scale) -0.4945 0.5977 -0.83 0.4081
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues
[[alternative HTML version deleted]]
______________________________________________
R-help@
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Does-psm-Surv-handle-interval2-data-tp4655472p4656092.html Sent from the R help mailing list archive at Nabble.com.