Re: [R] grep help needed

From: John Fox <jfox_at_mcmaster.ca>
Date: Tue 26 Jul 2005 - 22:48:35 EST


Dear Denis,

I don't believe that anyone fielded your question -- my apologies if I missed a response.

> -----Original Message-----
> From: r-help-bounces@stat.math.ethz.ch
> [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Denis Chabot
> Sent: Monday, July 25, 2005 9:46 PM
> To: R list
> Subject: [R] grep help needed
>
> Hi,
>
> In another thread ("PBSmapping and shapefiles") I asked for
> an easy way to read "shapefiles" and transform them in data
> that PBSmapping could use. One person is exploring some ways
> of doing this, but it is possible I'll have to do this "manually".
>
> With package "maptools" I am able to extract the information
> I need from a shapefile but it is formatted like this:
>
> [[1]]
> [,1] [,2]
> [1,] -55.99805 51.68817
> [2,] -56.00222 51.68911
> [3,] -56.01694 51.68911
> [4,] -56.03781 51.68606
> [5,] -56.04639 51.68759
> [6,] -56.04637 51.69445
> [7,] -56.03777 51.70207
> [8,] -56.02301 51.70892
> [9,] -56.01317 51.71578
> [10,] -56.00330 51.73481
> [11,] -55.99805 51.73840
> attr(,"pstart")
> attr(,"pstart")$from
> [1] 1
>
> attr(,"pstart")$to
> [1] 11
>
> attr(,"nParts")
> [1] 1
> attr(,"shpID")
> [1] NA
>
> [[2]]
> [,1] [,2]
> [1,] -57.76294 50.88770
> [2,] -57.76292 50.88693
> [3,] -57.76033 50.88163
> [4,] -57.75668 50.88091
> [5,] -57.75551 50.88169
> [6,] -57.75562 50.88550
> [7,] -57.75932 50.88775
> [8,] -57.76294 50.88770
> attr(,"pstart")
> attr(,"pstart")$from
> [1] 1
>
> attr(,"pstart")$to
> [1] 8
>
> attr(,"nParts")
> [1] 1
> attr(,"shpID")
> [1] NA
>
> I do not quite understand the structure of this data object
> (list of lists I think)

Actually, it looks like a list of matrices, each with some attributes (which, I gather, aren't of interest to you).

> but at this point I resorted to
> printing it on the console and imported that text into Excel
> for further cleaning, which is easy enough. I'd like to
> complete the process within R to save time and to circumvent
> Excel's limit of around 64000 lines. But I have a hard time
> figuring out how to clean up this text in R.
>

If I understand correctly what you want, this seems a very awkward way to proceed. Why not just extract the matrices from the list, stick on the additional columns that you want, stick the matrices together, name the columns, and then output the data to a file?

M1 <- Data[[1]]  # assuming that the original list is named Data
M2 <- Data[[2]]
M1 <- cbind(1, 1:nrow(M1), M1)
M2 <- cbind(2, 1:nrow(M2), M2)

M <- rbind(M1, M2)
colnames(M) <- c("PID", "POS", "X", "Y") write.table(M, "Data.txt", row.names=FALSE, quote=FALSE)

It wouldn't be hard to generalize this to any number of matrices and to automate the process.

I hope that this helps,
 John

> What I need to produce for PBSmapping is a file where each
> block of coordinates shares one ID number, called PID, and a
> variable POS indicates the position of each coordinate within
> a "shape". All other lines must disappear. So the above would become:
>
> PID POS X Y
> 1 1 -55.99805 51.68817
> 1 2 -56.00222 51.68911
> 1 3 -56.01694 51.68911
> 1 4 -56.03781 51.68606
> 1 5 -56.04639 51.68759
> 1 6 -56.04637 51.69445
> 1 7 -56.03777 51.70207
> 1 8 -56.02301 51.70892
> 1 9 -56.01317 51.71578
> 1 10 -56.00330 51.73481
> 1 11 -55.99805 51.73840
> 2 1 -57.76294 50.88770
> 2 2 -57.76292 50.88693
> 2 3 -57.76033 50.88163
> 2 4 -57.75668 50.88091
> 2 5 -57.75551 50.88169
> 2 6 -57.75562 50.88550
> 2 7 -57.75932 50.88775
> 2 8 -57.76294 50.88770
>
> First I imported this text file into R:
> test <- read.csv2("test file.txt",header=F, sep=";", colClasses =
> "character")
>
> I used sep=";" to insure there would be only one variable in
> this file, as it contains no ";"
>
> To remove lines that do not contain coordinates, I used the
> fact that longitudes are expressed as negative numbers, so
> with my very limited knowledge of grep searches, I thought of
> this, which is probably not the best way to go:
>
> a <- rep("-", length(test$V1))
> b <- grep(a, test$V1)
>
> this gives me a warning ("Warning message:
> the condition has length > 1 and only the first element will be used
> in: if (is.na(pattern)) {"
> but seems to do what I need anyway
>
> c <- seq(1, length(test$V1))
> d <- c %in% b
>
> e <- test$V1[d]
>
> Partial victory, now I only have lines that look like [1,]
> -57.76294 50.88770
>
> But I don't know how to go further: the number in square
> brackets can be used for variable POS, after removing the
> square brackets and the comma, but this requires a better
> knowledge of grep than I have.
> Furthermore, I don't know how to add a PID (polygon ID)
> variable, i.e. all lines of a polygon must have the same ID,
> as in the example above (i.e. each time POS == 1, a new
> polygon starts and PID needs to be incremented by 1, and PID
> is kept constant for lines where POS ! 1).
>
> Any help will be much appreciated.
>
> Sincerely,
>
> Denis Chabot



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