Your first description is correct with slight modification "compare point 1 to all the other points in that Cluster.Index and see if any of euclidean distances are greater than 8; do this for each point (i.e. point 2, point 3) in that specific Cluster.Index (i.e. 45)"
On Thu, Aug 21, 2014 at 3:35 PM, David L Carlson <dcarl...@tamu.edu> wrote: > 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> > 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> > 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> > 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 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 > > > > > > > > > > > > > > > > -- > > 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 > > > > > > [[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. > -- *Edward H Patzelt | Clinical Science PhD StudentPsychology | Harvard University * [[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.
