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 murdoch.dun...@gmail.com 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 05 Jul 2014, at 16:19 , Witold E Wolski wewol...@gmail.com 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 murdoch.dun...@gmail.com 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 __ 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?
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 murdoch.dun...@gmail.com 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.
[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.
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$rt ? Please post reproducible examples. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how does a valid subscript can produce an subscript out of bounds error?
On 04/07/2014, 6:35 PM, Witold E Wolski wrote: how does a valid subscript (see first 2 lines) can produce an subscript out of bounds error (see line 4)? 1 sum(!rownames(msexp$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.
