Yes, package:intervals uses the same idiom as my code. Mine allows Date and POSIXct objects as interval endpoints (which is why it represents the objects as data.frames instead of matrices). package:intervals has more than basic set opertions on the collections of intervals.
Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com From: Ben quant [mailto:ccqu...@gmail.com] Sent: Monday, May 14, 2012 1:19 PM To: Steve Lianoglou Cc: William Dunlap; r-help@r-project.org Subject: Re: [R] range segment exclusion using range endpoints Thank you Steve! This does everything I need (at this point): (this excludes ranges y2 from range y1) library('intervals') y1 = Intervals(c(-100,100)) y2 = Intervals(rbind( c(-100.5,30), c(0.77,10), c(25,35), c(70,80.3), c(90,95) )) interval_difference(y1,y2) Object of class Intervals_full 3 intervals over R: (35, 70) (80.3, 90) (95, 100] PS - I'm pretty sure William's solution worked as well, but opted for the package solution which is a bit more robust. Thanks everyone! Ben On Mon, May 14, 2012 at 1:06 PM, Steve Lianoglou <mailinglist.honey...@gmail.com<mailto:mailinglist.honey...@gmail.com>> wrote: Hi all, Nice code samples presented all around. Just wanted to point out that I think the stuff found in the `intervals` package might also be helpful: http://cran.at.r-project.org/web/packages/intervals/index.html HTH, -steve On Mon, May 14, 2012 at 2:54 PM, Ben quant <ccqu...@gmail.com<mailto:ccqu...@gmail.com>> wrote: > Yes, it is. I'm looking into understanding this now... > > thanks! > Ben > > On Mon, May 14, 2012 at 12:38 PM, William Dunlap > <wdun...@tibco.com<mailto:wdun...@tibco.com>> wrote: > >> To the list of function I sent, add another that converts a list of >> intervals >> into a Ranges object: >> as.Ranges.list <- function (x, ...) { >> stopifnot(nargs() == 1, all(vapply(x, length, 0) == 2)) >> # use c() instead of unlist() because c() doesn't mangle POSIXct and >> Date objects >> x <- unname(do.call(c, x)) >> odd <- seq(from = 1, to = length(x), by = 2) >> as.Ranges(bottoms = x[odd], tops = x[odd + 1]) >> } >> Then stop using get() and assign() all over the place and instead make >> lists of >> related intervals and convert them to Ranges objects: >> > x <- as.Ranges(list(x_rng)) >> > s <- as.Ranges(list(s1_rng, s2_rng, s3_rng, s4_rng, s5_rng)) >> > x >> bottoms tops >> 1 -100 100 >> > s >> bottoms tops >> 1 -250.50 30.0 >> 2 0.77 10.0 >> 3 25.00 35.0 >> 4 70.00 80.3 >> 5 90.00 95.0 >> and then compute the difference between the sets x and s (i.e., describe >> the points in x but not s as a union of intervals): >> > setdiffRanges(x, s) >> bottoms tops >> 1 35.0 70 >> 2 80.3 90 >> 3 95.0 100 >> and for a graphical check do >> > plot(x, s, setdiffRanges(x, s)) >> Are those the numbers you want? >> >> I find it easier to use standard functions and data structures for this >> than >> to adapt the cumsum/order idiom to different situations. >> >> Bill Dunlap >> Spotfire, TIBCO Software >> wdunlap tibco.com<http://tibco.com> >> >> >> > -----Original Message----- >> > From: r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org> >> > [mailto:r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] >> On Behalf >> > Of Ben quant >> > Sent: Monday, May 14, 2012 11:07 AM >> > To: jim holtman >> > Cc: r-help@r-project.org<mailto:r-help@r-project.org> >> > Subject: Re: [R] range segment exclusion using range endpoints >> > >> > Turns out this solution doesn't work if the s range is outside the range >> of >> > the x range. I didn't include that in my examples, but it is something I >> > have to deal with quite often. >> > >> > For example s1_rng below causes an issue: >> > >> > x_rng = c(-100,100) >> > s1_rng = c(-250.5,30) >> > s2_rng = c(0.77,10) >> > s3_rng = c(25,35) >> > s4_rng = c(70,80.3) >> > s5_rng = c(90,95) >> > >> > sNames <- grep("s[0-9]+_rng", ls(), value = TRUE) >> > queue <- rbind(c(x_rng[1], 1), c(x_rng[2], 1)) >> > for (i in sNames){ >> > queue <- rbind(queue >> > , c(get(i)[1], 1) # enter queue >> > , c(get(i)[2], -1) # exit queue >> > ) >> > } >> > queue <- queue[order(queue[, 1]), ] # sort >> > queue <- cbind(queue, cumsum(queue[, 2])) # of people in the queue >> > for (i in which(queue[, 3] == 1)){ >> > cat("start:", queue[i, 1L], ' end:', queue[i + 1L, 1L], "\n") >> > } >> > >> > Regards, >> > >> > ben >> > On Sat, May 12, 2012 at 12:50 PM, jim holtman >> > <jholt...@gmail.com<mailto:jholt...@gmail.com>> >> wrote: >> > >> > > Here is an example of how you might do it. It uses a technique of >> > > counting how many items are in a queue based on their arrival times; >> > > it can be used to also find areas of overlap. >> > > >> > > Note that it would be best to use a list for the 's' end points >> > > >> > > ================================ >> > > > # note the next statement removes names of the format 's[0-9]+_rng' >> > > > # it would be best to create a list with the 's' endpoints, but this >> is >> > > > # what the OP specified >> > > > >> > > > rm(list = grep('s[0-9]+_rng', ls(), value = TRUE)) # Danger Will >> > > Robinson!! >> > > > >> > > > # ex 1 >> > > > x_rng = c(-100,100) >> > > > >> > > > s1_rng = c(-25.5,30) >> > > > s2_rng = c(0.77,10) >> > > > s3_rng = c(25,35) >> > > > s4_rng = c(70,80.3) >> > > > s5_rng = c(90,95) >> > > > >> > > > # ex 2 >> > > > # x_rng = c(-50.5,100) >> > > > >> > > > # s1_rng = c(-75.3,30) >> > > > >> > > > # ex 3 >> > > > # x_rng = c(-75.3,30) >> > > > >> > > > # s1_rng = c(-50.5,100) >> > > > >> > > > # ex 4 >> > > > # x_rng = c(-100,100) >> > > > >> > > > # s1_rng = c(-105,105) >> > > > >> > > > # find all the names -- USE A LIST NEXT TIME >> > > > sNames <- grep("s[0-9]+_rng", ls(), value = TRUE) >> > > > >> > > > # initial matrix with the 'x' endpoints >> > > > queue <- rbind(c(x_rng[1], 1), c(x_rng[2], 1)) >> > > > >> > > > # add the 's' end points to the list >> > > > # this will be used to determine how many things are in a queue (or >> > > areas that >> > > > # overlap) >> > > > for (i in sNames){ >> > > + queue <- rbind(queue >> > > + , c(get(i)[1], 1) # enter queue >> > > + , c(get(i)[2], -1) # exit queue >> > > + ) >> > > + } >> > > > queue <- queue[order(queue[, 1]), ] # sort >> > > > queue <- cbind(queue, cumsum(queue[, 2])) # of people in the queue >> > > > print(queue) >> > > [,1] [,2] [,3] >> > > [1,] -100.00 1 1 >> > > [2,] -25.50 1 2 >> > > [3,] 0.77 1 3 >> > > [4,] 10.00 -1 2 >> > > [5,] 25.00 1 3 >> > > [6,] 30.00 -1 2 >> > > [7,] 35.00 -1 1 >> > > [8,] 70.00 1 2 >> > > [9,] 80.30 -1 1 >> > > [10,] 90.00 1 2 >> > > [11,] 95.00 -1 1 >> > > [12,] 100.00 1 2 >> > > > >> > > > # print out values where the last column is 1 >> > > > for (i in which(queue[, 3] == 1)){ >> > > + cat("start:", queue[i, 1L], ' end:', queue[i + 1L, 1L], "\n") >> > > + } >> > > start: -100 end: -25.5 >> > > start: 35 end: 70 >> > > start: 80.3 end: 90 >> > > start: 95 end: 100 >> > > > >> > > > >> > > ========================================= >> > > >> > > On Sat, May 12, 2012 at 1:54 PM, Ben quant >> > > <ccqu...@gmail.com<mailto:ccqu...@gmail.com>> wrote: >> > > > Hello, >> > > > >> > > > I'm posting this again (with some small edits). I didn't get any >> replies >> > > > last time...hoping for some this time. :) >> > > > >> > > > Currently I'm only coming up with brute force solutions to this issue >> > > > (loops). I'm wondering if anyone has a better way to do this. Thank >> you >> > > for >> > > > your help in advance! >> > > > >> > > > The problem: I have endpoints of one x range (x_rng) and an unknown >> > > number >> > > > of s ranges (s[#]_rng) also defined by the range endpoints. I'd like >> to >> > > > remove the x ranges that overlap with the s ranges. The examples >> below >> > > > demonstrate what I mean. >> > > > >> > > > What is the best way to do this? >> > > > >> > > > Ex 1. >> > > > For: >> > > > x_rng = c(-100,100) >> > > > >> > > > s1_rng = c(-25.5,30) >> > > > s2_rng = c(0.77,10) >> > > > s3_rng = c(25,35) >> > > > s4_rng = c(70,80.3) >> > > > s5_rng = c(90,95) >> > > > >> > > > I would get: >> > > > -100,-25.5 >> > > > 35,70 >> > > > 80.3,90 >> > > > 95,100 >> > > > >> > > > Ex 2. >> > > > For: >> > > > x_rng = c(-50.5,100) >> > > > >> > > > s1_rng = c(-75.3,30) >> > > > >> > > > I would get: >> > > > 30,100 >> > > > >> > > > Ex 3. >> > > > For: >> > > > x_rng = c(-75.3,30) >> > > > >> > > > s1_rng = c(-50.5,100) >> > > > >> > > > I would get: >> > > > -75.3,-50.5 >> > > > >> > > > Ex 4. >> > > > For: >> > > > x_rng = c(-100,100) >> > > > >> > > > s1_rng = c(-105,105) >> > > > >> > > > I would get something like: >> > > > NA,NA >> > > > or... >> > > > NA >> > > > >> > > > Ex 5. >> > > > For: >> > > > x_rng = c(-100,100) >> > > > >> > > > s1_rng = c(-100,100) >> > > > >> > > > I would get something like: >> > > > -100,-100 >> > > > 100,100 >> > > > or just... >> > > > -100 >> > > > 100 >> > > > >> > > > PS - You may have noticed that in all of the examples I am including >> the >> > > s >> > > > range endpoints in the desired results, which I can deal with later >> in my >> > > > program so its not a problem... I think leaving in the s range >> endpoints >> > > > simplifies the problem. >> > > > >> > > > Thanks! >> > > > Ben >> > > > >> > > > [[alternative HTML version deleted]] >> > > > >> > > > ______________________________________________ >> > > > R-help@r-project.org<mailto: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. >> > > >> > > >> > > >> > > -- >> > > Jim Holtman >> > > Data Munger Guru >> > > >> > > What is the problem that you are trying to solve? >> > > Tell me what you want to do, not how you want to do it. >> > > >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > R-help@r-project.org<mailto: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. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org<mailto: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. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact> [[alternative HTML version deleted]] ______________________________________________ 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.
