[R] Does psm::Surv handle interval2 data?

[Frank Harrell]

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)
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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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