[R] [survMisc]: error message in examples of comp()

[David Winsemius]

On Oct 17, 2014, at 1:39 PM, Gerrit Eichner wrote:

> Hello, list members,
> 
> I have tried to contact the maintainer of the survMisc package, but my message could not be delivered. I can't get survMisc package to work as expected or documented, respectively. Maybe one of you has an idea regarding the following problem:
> 
> When, e.g., trying to executed the first few lines of code in the examples section of comp() (one of the package functions), i.e.,
> 
>> data(kidney,package="KMsurv")
>> s1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney)
>> comp(s1)
> 
> 
> I receive the following error message:
> 
> Error in parse(text = t2) : <text>:1:8: unexpected input
> 1: paste( ``
>            ^

I get the same error on a Mac in an English locale. I'm afraid the code in the offending function `.getTne` appears somewhat cobbled together. When I try to debug, I get a single row, 1920 column matrix for n1 which is numeric with all entries == 1. Object `t1` cannot be found.

{
    s <- Es <- .SD <- NULL
    n1 <- names(dt1)
    f1 <- function(x) paste(dQuote(paste(x, "=", sep = "")), 
        ", get(", dQuote(x), ")", sep = "")
    t1 <- paste(sapply(n1, f1), sep = ",")
    if (length(t1) > 1) {
        t1[2:length(t1)] <- sub("\"", "\"_", t1[2:length(t1)], 
            fixed = TRUE)
    }
    t1 <- paste(t1, collapse = ",")
    t2 <- paste("paste(", t1, ", sep='')")

# next line throw the error.

    p1 <- parse(text = t2)
    q <- quote(eval(p1))
    dt1[, `:=`("s", as.factor(eval(q, envir = .SD)))]
    stopifnot(attr(model.response(mf), "type") == "right")
    y <- data.table(unclass(model.response(mf, "numeric")))

I'm afraid I have been o help.

-- 
David.
> 
> 
> Could this be an encoding-related issue inside the code? Does somebody have an idea where to look for a solution for this problem?
> 
> Below you'll find my survMisc version and R session info. Thanks for any support!
> 
> Kind regards  --  Gerrit
> 
> ---------------------------------------------------------------------
> Dr. Gerrit Eichner                   Mathematical Institute, Room 212
> gerrit.eichner at math.uni-giessen.de   Justus-Liebig-University Giessen
> Tel: +49-(0)641-99-32104          Arndtstr. 2, 35392 Giessen, Germany
> Fax: +49-(0)641-99-32109        http://www.uni-giessen.de/cms/eichner
> ---------------------------------------------------------------------
> 
> 
>> citation( "survMisc")
> 
> To cite package .survMisc. in publications use:
> 
>  Chris Dardis (2014). survMisc: Miscellaneous functions for survival
>  data.. R package version 0.4.2.
>  http://CRAN.R-project.org/package=survMisc
> 
> 
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
> 
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] survMisc_0.4.2   rpart_4.1-8      data.table_1.9.2 ggplot2_1.0.0
> [5] survival_2.37-7  fortunes_1.5-2
> 
> loaded via a namespace (and not attached):
> [1] colorspace_1.2-4 digest_0.6.4     gam_1.09.1       grid_3.1.1
> [5] gtable_0.1.2     km.ci_0.5-2      KMsurv_0.1-5     MASS_7.3-33
> [9] munsell_0.4.2    plyr_1.8.1       proto_0.3-10     Rcpp_0.11.2
> [13] reshape2_1.4     scales_0.2.4     stringr_0.6.2    tools_3.1.1
> 
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David Winsemius
Alameda, CA, USA