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-tp4655472p4655475.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org 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.