Re: [R] regular expression for na.strings / read.table

From: jim holtman <jholtman_at_gmail.com>
Date: Tue, 12 Feb 2008 11:41:11 -0500

Here is one way of doing it:

> # read the file in as lines, do the convert and then re-read
> x <- readLines(textConnection(" X1 X.789 LNM. X78 X56 X89 X56.1 X100

+ 1  2   700  AUW  78  56   89    56  100
+ 2  3   400  TOC  78  56   89    56   10
+ 3  4   389  RMN  78  56   89    56  *89
+ 4  5   400  LNM  78  56 *452    56  100
+ 5  6   200  UTC  78 *40   89    56  100
+ 6  7   100  GAT  78  56    8    56 *100
+ 7  8    79 *LNM  78  56    9    56  100
+ 8  9    89  TCG  78  56  800    56 *100
+ 9 10   78*  LNM  78  56   89    56  100"))

> x.c <- gsub("\\*[[:alnum:]]*|[[:alnum:]]*\\*", "NA", x)
> x.new <- read.table(textConnection(x.c), header=TRUE)
> closeAllConnections()
>
> x.new

  X1 X.789 LNM. X78 X56 X89 X56.1 X100
1 2 700 AUW 78 56 89 56 100
2 3 400 TOC 78 56 89 56 10
3 4 389 RMN 78 56 89 56 NA
4 5 400 LNM 78 56 NA 56 100
5 6 200 UTC 78 NA 89 56 100
6 7 100 GAT 78 56 8 56 NA
7 8 79 <NA> 78 56 9 56 100
8 9 89 TCG 78 56 800 56 NA
9 10 NA LNM 78 56 89 56 100 On Feb 12, 2008 9:30 AM, <jessica.gervais_at_tudor.lu> wrote:
>
> Dear all,
>
> I am working with a csv file.
> Some data of the file are not valid and they are marked with a star '*'.
> For example : *789.
>
> I have attached with this email a example file (test.txt) that looks like
> the data I have to work with.
>
>
> I see 2 possibilities ..thast I cannot manage anyway in R:
>
> 1-first & easiest solution:
> Read the data with read.csv in R, and define as na strings all cells
> containing a star (*).
> Something which would looks like this ...
>
> >
> DATA<-read.csv("test.txt",na.strings=list(length(grep("\\*",DATA,value=T))==0))
>
> > DATA
> X1 X.789 LNM. X78 X56 X89 X56.1 X100
> 1 2 700 AUW 78 56 89 56 100
> 2 3 400 TOC 78 56 89 56 10
> 3 4 389 RMN 78 56 89 56 *89
> 4 5 400 LNM 78 56 *452 56 100
> 5 6 200 UTC 78 *40 89 56 100
> 6 7 100 GAT 78 56 8 56 *100
> 7 8 79 *LNM 78 56 9 56 100
> 8 9 89 TCG 78 56 800 56 *100
> 9 10 78* LNM 78 56 89 56 100
>
>
> ...but which would work (Stars are still there)! Do anyone knows how to do
> that ?
>
> 2-Second solution:
> - first read the file with DATA<-read.csv("test.txt")
> - then replace all fields containing a * with NA in applying the following
> function to the object DATA:
> DATA_cleaned<-apply(DATA,c(1,2),function(x){if(length(grep("\\*",x,value=TRUE))==1){x<-NA}})
> DATA_cleaned
> X1 X.789 LNM. X78 X56 X89 X56.1 X100
> [1,] NULL NULL NULL NULL NULL NULL NULL NULL
> [2,] NULL NULL NULL NULL NULL NULL NULL NULL
> [3,] NULL NULL NULL NULL NULL NULL NULL NA
> [4,] NULL NULL NULL NULL NULL NA NULL NULL
> [5,] NULL NULL NULL NULL NA NULL NULL NULL
> [6,] NULL NULL NULL NULL NULL NULL NULL NA
> [7,] NULL NULL NA NULL NULL NULL NULL NULL
> [8,] NULL NULL NULL NULL NULL NULL NULL NA
> [9,] NULL NA NULL NULL NULL NULL NULL NULL
>
> stars have deaseper, but all the rest too !
> The pb comes from the fact that if a field does not contain any *, the
> command
> if(length(grep("\\*",x,value=T))==1) return NULL instead of FALSE !
>
> I you have any idea, please let me know !
>
> Many thanks,
>
> Jessica
> ____________________________________
>
> Jessica Gervais
> Mail: jessica.gervais_at_tudor.lu
>
> Resource Centre for Environmental Technologies,
> Public Research Centre Henri Tudor,
> Technoport Schlassgoart,
> 66 rue de Luxembourg,
> P.O. BOX 144,
> L-4002 Esch-sur-Alzette, Luxembourg
>
> (See attached file: test.txt)
> ______________________________________________
> 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.
>
>
-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Received on Tue 12 Feb 2008 - 16:49:02 GMT

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