The dist() function works just fine in 2d or 3d or 100d. Your description of what you want to accomplish is not clear. Your code compares rows 1 and 2, then 2 and 3, then 3 and 4, and so on. You are comparing only adjacent points, but your description makes it sound like you want to compare point 1 to all the other points and see if they are in the same group and over 8 or in another group. If you type the following command you will see that your dat$X is just the diagonal of the distance matrix: 1 with 2, 2 with 3, 3 with 4 etc:
dist(dat[, 3:5]) ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Don McKenzie Sent: Thursday, August 21, 2014 1:44 PM To: Patzelt, Edward Cc: R-help@r-project.org Subject: Re: [R] Euclidean Distance in 3 Dimensions Ugh sorry. I misread your message obviously. Cc�ing back to the list (as is the protocol) I�m surprised no one else has replied. I�m a lightweight compared to others on the list. It looks as if the dist() function has compiled code, which suggests that there is some gnarly linear algebra underneath to speed it up even in 2D. Not for the faint-of-heart to hack. Others? �dist3D�? On Aug 21, 2014, at 11:34 AM, Patzelt, Edward <patz...@g.harvard.edu<mailto:patz...@g.harvard.edu>> wrote: > This function unfortunately does not work in 3d space. > > Thoughts? > > > On Wed, Aug 20, 2014 at 4:57 PM, Don McKenzie > <d...@u.washington.edu<mailto:d...@u.washington.edu>> wrote: > ?dist > > from the help > > dist {stats} R Documentation > Distance Matrix Computation > > Description > > This function computes and returns the distance matrix computed by using the > specified distance measure to compute the distances between the rows of a > data matrix. > > Is this what you want? Computing on a matrix whose rows are your x, y, and z > values? > > > On Aug 20, 2014, at 1:12 PM, Patzelt, Edward > <patz...@g.harvard.edu<mailto:patz...@g.harvard.edu>> wrote: > > > R Community - > > > > I am attempting to write a function that will calculate the distance > > between points in 3 dimensional space for unique regions (e.g. localized > > brain regions such as the frontal lobe). > > > > For example I'm looking to compare each point in region 45 to every other > > region in 45 to establish if they are a distance of 8 or more apart. I can > > do this linearly comparing each distance to the previous but this is not > > comparing all points. > > > > structure(list(Cluster.Index = c(46L, 46L, 46L, 46L, 46L, 45L, > > 45L, 45L, 45L, 45L, 44L, 44L, 44L, 44L, 44L, 43L, 43L, 43L, 43L, > > 43L), Value = c(8.21, 7.96, 7.85, 7.83, 7.8, 5.38, 4.56, 4.5, > > 4, 3.99, 5.42, 4.82, 4.21, 4.18, 3.91, 4.79, 4.27, 3.24, 3.06, > > 3.04), x = c(33L, 38L, 37L, 36L, 38L, 47L, 42L, 43L, 44L, 42L, > > 50L, 41L, 39L, 41L, 44L, 46L, 45L, 45L, 41L, 46L), y = c(15L, > > 12L, 12L, 13L, 13L, 91L, 84L, 84L, 95L, 96L, 69L, 70L, 65L, 65L, > > 59L, 41L, 40L, 46L, 44L, 47L), z = c(41L, 38L, 41L, 39L, 33L, > > 39L, 40L, 42L, 44L, 45L, 34L, 36L, 30L, 35L, 39L, 53L, 47L, 61L, > > 52L, 57L), X = c(NA, 6.557438524302, 3.16227766016838, 2.44948974278318, > > 6.32455532033676, 78.7464284904401, 8.66025403784439, 2.23606797749979, > > 11.2249721603218, 2.44948974278318, 30.2324329156619, 9.2736184954957, > > 8.06225774829855, 5.3851648071345, 7.81024967590665, 22.8910462845192, > > 6.16441400296898, 15.2315462117278, 10.0498756211209, 7.68114574786861 > > )), .Names = c("Cluster.Index", "Value", "x", "y", "z", "X"), row.names = > > c(NA, > > 20L), class = "data.frame") > > > > mainDat <- data.frame() > > for(i in 2:nrow(dat)){ > > tempDist <- (sqrt((dat$x[i] - dat$x[i-1])^2 + (dat$y[i] - dat$y[i-1])^2 + > > (dat$z[i] - dat$z[i-1])^2)) > > dat$X[i] <- c(tempDist) > > if(dat$Cluster.Index[i] != dat$Cluster.Index[i-1]){ > > mainDat <- rbind(mainDat, dat[i,]) > > } > > if((dat$Cluster.Index[i] == dat$Cluster.Index[i-1])) { > > if(tempDist > 8){ > > mainDat <- rbind(mainDat, dat[i,]) > > } > > } > > } > > > > > > > > > > -- > > > > *Edward H Patzelt | Clinical Science PhD StudentPsychology | Harvard > > University * > > > > [[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. > > Don McKenzie > Research Ecologist > Pacific Wildland Fire Sciences Lab > US Forest Service > > Affiliate Professor > School of Environmental and Forest Sciences > University of Washington > d...@uw.edu<mailto:d...@uw.edu> > > > > > > > > -- > Edward H Patzelt | Clinical Science PhD Student > Psychology | Harvard University > > Don McKenzie Research Ecologist Pacific Wildland Fire Sciences Lab US Forest Service Affiliate Professor School of Environmental and Forest Sciences University of Washington d...@uw.edu<mailto:d...@uw.edu> [[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 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.
