[R] parsing numeric values

[Gabor Grothendieck]

Here is a slight variation:

> read.table(textConnection(grep("<aa?[xy]>", input, value = TRUE)),
+    colClasses = c("NULL", "NULL", "numeric"))
          V3         V6
1 0.00137700 3.4644e-07
2 0.00019412 4.8840e-08
3 0.00137700 3.4644e-07
4 0.00019412 4.8840e-08



On Wed, Nov 18, 2009 at 1:54 PM, baptiste auguie
<baptiste.auguie at googlemail.com> wrote:
> Hi,
>
> Thanks for the alternative approach. However, I should have made my
> example more complete in that other lines may also have numeric
> values, which I'm not interested in. Below is an updated problem, with
> my current solution,
>
> tc <- 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
>
> lots of other material,  including numeric values
>  1.23E-4 123E5 12.3E-4 123E5 123E-4 123E5
>  12.3E-4 123E5 12.3E-4 123E5 123E-4 123E5
> etc...")
>
> input <-
> readLines(tc)
> close(tc)
>
> ## I want to retrieve the values for
> ## <ax>, <ay>, <aax> and <aay> only
>
> results <- c(
> strapply(input, "<ax> += +(\\d+\\.\\d+E[-+]?\\d+)", as.numeric,
> simplify = rbind),
> strapply(input, "<ay> += +(\\d+\\.\\d+E[-+]?\\d+)", as.numeric,
> simplify = rbind),
> strapply(input, "<aax> += +(\\d+\\.\\d+E[-+]?\\d+)", as.numeric,
> simplify = rbind),
> strapply(input, "<aay> += +(\\d+\\.\\d+E[-+]?\\d+)", as.numeric,
> simplify = rbind))
>
> results
>
> Using the suggested base R solution, I've come up with this variation,
>
> z <- `, grep("<ax>|<ay>|<aax>|<aay>", input,
> value=TRUE))
>
> test <- scan(textConnection(z),what=0)
> test[seq(1, length(test), by=2)]
>
>
> Thanks again,
>
> baptiste
>
> 2009/11/18 Bert Gunter <gunter.berton at gene.com>:
>> 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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>> 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-help at 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.
>