[R] parsing numeric values

[Gabor Grothendieck]

It only works if "some text" at the beginning has no digits, dots, E
characters or sign characters.

On Wed, Nov 18, 2009 at 12:44 PM, Bert Gunter <gunter.berton at gene.com> wrote:
> The previous elegant solutions required the use of the gsubfn package.
> Nothing wrong with that, of course, but I'm always curious whether still
> relatively simple base R solutions can be found, as they are often (but not
> always!) much faster. And anyway, it seems to be in the spirit of your query
> to try such a solution. So here is one base R approach that I believe works.
> I'll break it up into 2 lines so you can see what's going on.
>
> ## Using your example...
> ## First replace everything but the number with spaces
>
>> z <- gsub("[^[:digit:]E.+-]"," ",input)
>> z
> [1] "         "
> [2] "            1.3770E-03               3.4644E-07"
> [3] "            1.9412E-04               4.8840E-08"
> [4] ""
> [5] "          "
> [6] "              1.3770E-03                3.4644E-07"
> [7] "              1.9412E-04                4.8840E-08"
>
> ## Now it can be scanned to a numeric via
>
>> z<-scan(textConnection(z),what=0)
> Read 8 items
>> z
> [1] 1.3770e-03 3.4644e-07 1.9412e-04 4.8840e-08 1.3770e-03 3.4644e-07
> 1.9412e-04 4.8840e-08
>
> ########
> I believe this strategy is reasonably general, but I haven't checked it
> carefully and would appreciate folks pointing out where it trips up (e.g.
> perhaps with NA's).
>
> Best,
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
>  -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
> Behalf Of baptiste auguie
> Sent: Wednesday, November 18, 2009 3:57 AM
> To: r-help
> Subject: [R] parsing numeric values
>
> Dear list,
>
> I'm seeking advice to extract some numeric values from a log file
> created by an external program. Consider the following example,
>
> input <-
> readLines(textConnection(
> "some text
>  <ax> =    1.3770E-03     <bx> =    3.4644E-07
>  <ay> =    1.9412E-04     <by> =    4.8840E-08
>
> other text
>  <aax>  =    1.3770E-03     <bbx> =    3.4644E-07
>  <aay>  =    1.9412E-04     <bby> =    4.8840E-08"))
>
> ## this is what I want
> results <- c(as.numeric(strsplit(grep("<ax>", input,val=T), " ")[[1]][8]),
>             as.numeric(strsplit(grep("<ay>", input,val=T), " ")[[1]][8]),
>             as.numeric(strsplit(grep("<aax>", input,val=T), " ")[[1]][9]),
>             as.numeric(strsplit(grep("<aay>", input,val=T), " ")[[1]][9])
>             )
>
> ## [1] 0.00137700 0.00019412 0.00137700 0.00019412
>
> The use of strsplit is not ideal here as there is a different number
> of space characters in the lines containing <ax> and <aax> for
> instance (hence the indices 8 and 9 respectively).
>
> I tried to use gsubfn for a cleaner construct,
>
> strapply(input, "<ax> += +([0-9.]+)", c, simplify=rbind,combine=as.numeric)
>
> but I can't seem to find the correct regular expression to deal with
> the exponent.
>
>
> Any tips are welcome!
>
>
> Best regards,
>
> baptiste
>
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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.
>