[R] Error message in SIS package

[David Winsemius]

> On Oct 17, 2016, at 1:54 PM, Maity, Arnab K <akumar at stat.tamu.edu> wrote:
> 
> I try to run the following code:
> 
> sis.fit <- SIS(y = Surv(time = y[, 1], event = y[, 2]), x = x, family = "cox", penalty = "lasso", tune = "cv",
>                 nfolds = 10, type.measure = "deviance", nsis = min(dim(x)), iter = FALSE, seed = 334)
> 
> I get the following error:
> 
> Error in names(coef.beta) = paste("X", ix1, sep = "") :
>  'names' attribute [1] must be the same length as the vector [0].

You supplied a matrix as an argument to 'x' but the error message is suggesting to me that the code was written to expect a list (or dataframe). (On the other hand I suppose you could have a matrix accessioned with a length-1 'i' or 'j' argument that would return a "named"-vector.)

Reading the help page for SIS, one sees that x was supposed to be a "design matrix, of dimensions n * p, without an intercept." I cannot determine whether your 'x' argument qualifies as such. Others may be able to determine from the circumstantial evidence whether that is possibly the case. Rhelp's posting guide suggest that questions about unexpected behavior should be accompanied by a discussion that include prior correspondence with the package maintainer as well as data ojects from `dump` or `dput` that would allow replication of the error.

The code to obtain the maintainer's email address :

maintainer('SIS')

-- 
David.
> 
> here is some information about the data.
> 
>> head(y)
>  time status
> 1   24      1
> 2   31      0
> 3   39      0
> 4   64      1
> 5   72      1
> 6    6      0
>> str(y)
> num [1:46, 1:2] 24 31 39 64 72 6 87 17 53 54 ...
> - attr(*, "dimnames")=List of 2
>  ..$ : chr [1:46] "1" "2" "3" "4" ...
>  ..$ : chr [1:2] "time" "status"
>> str(x)
> num [1:46, 1:66] 0.59234 0.30042 0.28278 -0.00966 0.08189 ...
> - attr(*, "dimnames")=List of 2
>  ..$ : chr [1:46] "1" "2" "3" "4" ...
>  ..$ : chr [1:66] "EIF4EBP1" "TP53BP1" "AKT1.AKT2.AKT3" "AR" ...
>> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] survival_2.39-4 SIS_0.8-3       glmnet_2.0-5    foreach_1.4.3   Matrix_1.2-6
> 
> loaded via a namespace (and not attached):
> [1] tools_3.3.1      splines_3.3.1    codetools_0.2-14 grid_3.3.1       iterators_1.0.8  ncvreg_3.6-0     lattice_0.20-33
>> 
> 
> Please help!?
> 
> 
> 
> 
> Arnab Kumar Maity
> Department of Statistics
> Texas A&M University
> 3143 TAMU, Room 401A
> College Station, TX 77843
> akumar at stat.tamu.edu<mailto:arnabkrmaity at stat.tamu.edu>
> +1 779 777 3428<tel:%2B1%20779%20777%203428>
> 
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> 
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David Winsemius
Alameda, CA, USA