[R] Euclidean Distance in 3 Dimensions

[Don McKenzie]

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





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