R help - Nov 2009 - Concave hull

Dear friends,

Do you know how to calculate the CONCAVE hull of a set of points (2-
dimensional or n-dimensional)? is that possible in R? (With a
"smoothing"
parameter of course).

Best,
-- 
Corrado Topi

Global Climate Change & Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct529 at york.ac.uk

See the function 'convhulln' in the 'geometry' package. It uses
this
algorithm : http://www.qhull.org/



remko

-------------------------------------------------
Remko Duursma
Post-Doctoral Fellow

Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908
www.remkoduursma.com



On Thu, Nov 26, 2009 at 3:37 AM, Corrado <ct529 at york.ac.uk>
wrote:
> Dear friends,
>
> Do you know how to calculate the CONCAVE hull of a set of points (2-
> dimensional or n-dimensional)? is that possible in R? (With a
"smoothing"
> parameter of course).
>
> Best,
> --
> Corrado Topi
>
> Global Climate Change & Biodiversity Indicators
> Area 18,Department of Biology
> University of York, York, YO10 5YW, UK
> Phone: + 44 (0) 1904 328645, E-mail: ct529 at york.ac.uk
>
> ______________________________________________
> 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.
>

This is not a true convave hull, but a 2D density is something similar  
and perhaps more "statistical":

library(MASS)
  xx <- runif(100, 0, 1)
  xx <- runif(100, -1, 1)
  yy <- abs(xx)+rnorm(100,0,.2)
  dens2 <- kde2d(xx, yy, lims=c(min(xx)-sd(xx), max(xx)+sd(xx),  
min(yy)-sd(yy), max(yy)+sd(yy) )  )
  contour(dens2, add=TRUE)

#  You can pick a single contour if you like:

  contour(dens2, level=0.05, col="red", add=TRUE)
  contour(dens2, level=0.10, col="blue", add=TRUE)


Happy Valentine's
-- 
David

On Nov 25, 2009, at 11:37 AM, Corrado wrote:
> Dear friends,
>
> Do you know how to calculate the CONCAVE hull of a set of points (2-
> dimensional or n-dimensional)? is that possible in R? (With a  
> "smoothing"
> parameter of course).
>
> Best,
> -- 
> Corrado Topi
>
> Global Climate Change & Biodiversity Indicators
> Area 18,Department of Biology
> University of York, York, YO10 5YW, UK
> Phone: + 44 (0) 1904 328645, E-mail: ct529 at york.ac.uk
>
> ______________________________________________
> 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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Hi, I just want to add a possible solution to the problem in the special case
all the points must stay on the edge of the outline. THis is sometimes the
case when doing image analysis and you want to order the points along a
closed path.
In this specific case, you can use some algorithm like the traveling
salesman problem, which would give you the shortest path along all your
points.
In this scenario, if your points are xy, you may use the following:

library(TSP)
tsp <- TSP(dist(xy))
tour <- solve_TSP(tsp,method='farthest')
xy <- xy[tour,]

THis may not be the most economical solution (and you might also want
contrains such as never to intersect the path) and is not valid if your
boundary is not supposed to pass through all points.




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