Re: [R] how does a valid subscript can produce an "subscript out of bounds" error?
I think you are somewhere between Circle 8.2.6 of 'The R Inferno' http://www.burns-stat.com/documents/books/the-r-inferno/ and the basics of subscripting http://www.burns-stat.com/documents/tutorials/impatient-r/more-r-subscript/ Pat On 05/07/2014 15:19, Witold E Wolski wrote: Thank you. You example helped to FIX IT. The problem is I guess somehow related to: class(msexp$pepinfo$transition_group_id) [1] "factor" and the whole R type conversion , riddle. For subscripts my intuition is: either require integer or do the "cast" to the rowname type (character). However, it seems that R somehow prefers to cast factors to integers... it seems that %in% "casts" both vectors to the same type. But to which one? Oh, I guess all this is neatly explained in the R standard ... but websearching for it just returns: standard deviation a frustrated R user. On 5 July 2014 02:18, Duncan Murdoch wrote: On 04/07/2014, 6:35 PM, Witold E Wolski wrote: how does a valid subscript (see first 2 lines) can produce an "subscript out of bounds" error (see line 4)? 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) [1] 0 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) [1] 0 3> class(msexp$rt) [1] "matrix" 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : subscript out of bounds x <- matrix(1,1,1) rownames(x) <- colnames(x) <- "23" 23 %in% rownames(x) [1] TRUE x[23,] Error in x[23, ] : subscript out of bounds -- Patrick Burns pbu...@pburns.seanet.com twitter: @burnsstat @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of: 'Impatient R' 'The R Inferno' 'Tao Te Programming') __ 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.
Re: [R] how does a valid subscript can produce an "subscript out of bounds" error?
On 05 Jul 2014, at 16:19 , Witold E Wolski wrote:
> Thank you. You example helped to FIX IT.
>
> The problem is I guess somehow related to:
>> class(msexp$pepinfo$transition_group_id)
> [1] "factor"
>
> and the whole R type conversion , riddle.
>
> For subscripts my intuition is: either require integer or do the
> "cast" to the rowname type (character).
> However, it seems that R somehow prefers to cast factors to integers...
>
> it seems that %in% "casts" both vectors to the same type. But to which one?
>
> Oh, I guess all this is neatly explained in the R standard ... but
> websearching for it just returns:
> standard deviation
>
>From help("[")
The index object ‘i’ can be numeric, logical, character or empty.
Indexing by factors is allowed and is equivalent to indexing by
the numeric codes (see ‘factor’) and not by the character values
which are printed (for which use ‘[as.character(i)]’).
One reason for hanging on to this convention is that it allows you to do
plot(x, y, col=c("red","blue")[sex])
Another reason is that it is the broader definition: It works for indexing
vectors that do not have names.
>
> a frustrated R user.
>
> On 5 July 2014 02:18, Duncan Murdoch wrote:
>> On 04/07/2014, 6:35 PM, Witold E Wolski wrote:
>>> how does a valid subscript (see first 2 lines) can produce an
>>> "subscript out of bounds" error (see line 4)?
>>>
>>>
>>> 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id)
>>> [1] 0
>>> 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt))
>>> [1] 0
>>> 3> class(msexp$rt)
>>> [1] "matrix"
>>> 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,])
>>> Error in msexp$rt[msexp$pepinfo$transition_group_id, ] :
>>> subscript out of bounds
>>>
>>
>>> x <- matrix(1,1,1)
>>> rownames(x) <- colnames(x) <- "23"
>>> 23 %in% rownames(x)
>> [1] TRUE
>>> x[23,]
>> Error in x[23, ] : subscript out of bounds
>>
>
>
>
> --
> Witold Eryk Wolski
>
> __
> 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.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how does a valid subscript can produce an "subscript out of bounds" error?
Thank you. You example helped to FIX IT. The problem is I guess somehow related to: > class(msexp$pepinfo$transition_group_id) [1] "factor" and the whole R type conversion , riddle. For subscripts my intuition is: either require integer or do the "cast" to the rowname type (character). However, it seems that R somehow prefers to cast factors to integers... it seems that %in% "casts" both vectors to the same type. But to which one? Oh, I guess all this is neatly explained in the R standard ... but websearching for it just returns: standard deviation a frustrated R user. On 5 July 2014 02:18, Duncan Murdoch wrote: > On 04/07/2014, 6:35 PM, Witold E Wolski wrote: >> how does a valid subscript (see first 2 lines) can produce an >> "subscript out of bounds" error (see line 4)? >> >> >> 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) >> [1] 0 >> 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) >> [1] 0 >> 3> class(msexp$rt) >> [1] "matrix" >> 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) >> Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : >> subscript out of bounds >>> >> > >> x <- matrix(1,1,1) >> rownames(x) <- colnames(x) <- "23" >> 23 %in% rownames(x) > [1] TRUE >> x[23,] > Error in x[23, ] : subscript out of bounds > -- Witold Eryk Wolski __ 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.
Re: [R] how does a valid subscript can produce an "subscript out of bounds" error?
On 04/07/2014, 6:35 PM, Witold E Wolski wrote: > how does a valid subscript (see first 2 lines) can produce an > "subscript out of bounds" error (see line 4)? > > > 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) > [1] 0 > 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) > [1] 0 > 3> class(msexp$rt) > [1] "matrix" > 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) > Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : > subscript out of bounds >> > > x <- matrix(1,1,1) > rownames(x) <- colnames(x) <- "23" > 23 %in% rownames(x) [1] TRUE > x[23,] Error in x[23, ] : subscript out of bounds __ 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.
Re: [R] how does a valid subscript can produce an "subscript out of bounds" error?
On 04/07/2014, 6:35 PM, Witold E Wolski wrote: > how does a valid subscript (see first 2 lines) can produce an > "subscript out of bounds" error (see line 4)? > > > 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) > [1] 0 > 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) > [1] 0 > 3> class(msexp$rt) > [1] "matrix" > 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) > Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : > subscript out of bounds >> > How are we supposed to know, since you didn't show us msexp$pepinfo$transition_group_id or the thing it was indexing, msexp$rt ? Please post reproducible examples. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how does a valid subscript can produce an "subscript out of bounds" error?
how does a valid subscript (see first 2 lines) can produce an "subscript out of bounds" error (see line 4)? 1> sum(!rownames(msexp$rt) %in% msexp$pepinfo$transition_group_id) [1] 0 2> sum(!msexp$pepinfo$transition_group_id %in% rownames(msexp$rt)) [1] 0 3> class(msexp$rt) [1] "matrix" 4> msexp$rt = as.matrix(msexp$rt[msexp$pepinfo$transition_group_id,]) Error in msexp$rt[msexp$pepinfo$transition_group_id, ] : subscript out of bounds > -- Witold Eryk Wolski __ 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.
