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
>
>
>
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>
> Type 'contributors()' for more information and
>
> '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
>
> 'help.start()' for an HTML browser interface to help.
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> Type 'q()' to quit R.
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>
>
>> 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
>
>
>
> **********************************************************
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-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
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