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

[Frank Harrell]

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
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> ISBN 3-900051-07-0
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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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