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
>>
>>
>>
>> **********************************************************
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>>
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>> ______________________________________________
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-----
Frank Harrell
Department of Biostatistics, Vanderbilt University
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