[R] Euclidean Distance in 3 Dimensions

Thu Aug 21 21:58:05 CEST 2014

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 <dcarlson at 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-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> *On Behalf Of *Don McKenzie
> *Sent:* Thursday, August 21, 2014 1:44 PM
> *To:* Patzelt, Edward
> *Cc:* R-help at 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 <patzelt at 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 <dmck at 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 <patzelt at 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 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.
> >
> > Don McKenzie
> > Research Ecologist
> > Pacific Wildland Fire Sciences Lab
> > US Forest Service
> >
> > Affiliate Professor
> > School of Environmental and Forest Sciences
> > University of Washington
> > dmck at 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
> dmck at uw.edu
>
>
>
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>

-- 

*Edward H Patzelt | Clinical Science PhD StudentPsychology | Harvard
University *

	[[alternative HTML version deleted]]