[R-SIG-Mac] [R-sig-mac] trouble with point in polyhedron computation
Agustin Angel Diez Castillo
agustin.diez at uv.es
Thu Apr 3 11:25:58 CEST 2014
Hi,
If i got it right, the original question can be addressed somewhat with inashape3d (alphashape3d package), something like:
library(alphashape3d)
set1 <- matrix(rnorm(333)/2,ncol=3)
plot3d(set1)
ashape3d.obj <- ashape3d(set1, alpha = 2)
set2 <- matrix(rnorm(33)/2,ncol=3)
in3d <- inashape3d(ashape3d.obj, points = set2)
plot(ashape3d.obj, transparency = 0.2)
rgl.points(points[in3d,], col ="blue")
On Thursday, April 3, 2014 07:38 CEST, Don McKenzie <dmck at u.washington.edu> wrote:
> Thank you for the pointer. That’s quite a list, and I expect I will have to concede defeat, lacking the skill set to adapt my use of the package.
>
> On Apr 2, 2014, at 9:11 PM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>
> > Package ptinpoly has generated hangs/segfaults in its checks for years, across platforms. That is why there are all the exclusions at http://cran.r-project.org/web/checks/check_results_ptinpoly.html .
> >
> > On 03/04/2014 01:48, Don McKenzie wrote:
> >> I have a 3D ordination with two groups, and want to identify the points in one group that lie within the 3D convex hull of the other. I would appreciate any enlightenment about why the command at the end (below in a toy example) crashes R when I try to ID the points in the hull using pip3d(), from package ptinpoly. convhulln() is from package geometry. Have I not supplied the right “Faces” argument to pip3d()?
> >>
> >> The objects are not large and are reproduced at the bottom of this message.
> >>
> >> Thanks
> >>
> >> ------------------------
> >>> sessionInfo()
> >> R version 3.0.3 (2014-03-06)
> >> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods base
> >>
> >> other attached packages:
> >> [1] ptinpoly_2.0 misc3d_0.8-4 geometry_0.3-4 magic_1.5-6 abind_1.4-0
> >>
> >> loaded via a namespace (and not attached):
> >> [1] tools_3.0.3
> >>
> >> ——
> >>
> >>> set1 <- matrix(rnorm(99),ncol=3)
> >>> ch1 <- convhulln(set1)
> >>
> >> Output completed. Verifying that all points are below outer planes of
> >> all facets. Will make 594 distance computations.
> >>
> >>> set2 <- matrix(rnorm(33)/2,ncol=3)
> >>
> >>> temp.out <- pip3d(set1,ch1,set2)
> >>
> >> R CRASHES HERE
> >>
> >> ----------------------------------
> >>
> >>
> >> 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
> >>
> >>
> >>
> >> ————————————————
> >>
> >> set1
> >> [,1] [,2] [,3]
> >> [1,] -0.36381788 0.96624676 -1.09251167
> >> [2,] -1.09242946 -0.82002293 0.42005666
> >> [3,] 0.93852498 1.18059117 -0.34816811
> >> [4,] -0.77413132 1.06018374 -0.37589340
> >> [5,] -1.67759103 -1.52469985 0.85310979
> >> [6,] 0.81729494 -0.18900503 0.83172169
> >> [7,] 0.30546957 0.97549183 -1.30815121
> >> [8,] 0.22201517 -0.38260850 -0.05412764
> >> [9,] 0.48817331 1.30314678 0.19143994
> >> [10,] 1.89836307 -0.34575059 0.55599170
> >> [11,] 0.20776401 0.04977816 -0.78034565
> >> [12,] -0.76819740 0.24554574 0.40398017
> >> [13,] 0.38369531 1.07688341 -0.22686023
> >> [14,] 0.31806928 1.15482656 -0.99259846
> >> [15,] 1.07142182 -1.03495199 -0.15650968
> >> [16,] -1.24667302 -0.35217160 0.71090188
> >> [17,] -0.92079326 -1.44075490 -0.42838857
> >> [18,] 0.16907840 0.37587569 1.34994069
> >> [19,] 0.50947015 1.81852997 -1.83315646
> >> [20,] 0.52015187 1.56904146 0.90679914
> >> [21,] -0.04261864 -1.22145642 0.51953397
> >> [22,] -0.86611946 -1.21106313 -0.86571463
> >> [23,] -0.13147715 0.07893287 0.83513033
> >> [24,] -0.63488792 -0.89396994 0.70103420
> >> [25,] -0.11370015 2.00351619 -0.17652412
> >> [26,] -1.04527261 -0.14570830 1.64893662
> >> [27,] 0.46238598 -0.07990767 0.16431874
> >> [28,] -0.72396505 1.45081393 -0.91068823
> >> [29,] -0.48892499 -1.05289633 1.36531224
> >> [30,] 1.83781721 1.50964339 1.85100986
> >> [31,] 1.00023790 -0.92779325 -2.16783507
> >> [32,] -0.51429532 -1.44766548 -1.41456589
> >> [33,] -0.93249545 -0.21845332 0.75023990
> >>
> >>> ch1
> >> [,1] [,2] [,3]
> >> [1,] 15 31 10
> >> [2,] 29 30 10
> >> [3,] 29 15 10
> >> [4,] 26 28 25
> >> [5,] 26 29 5
> >> [6,] 26 29 30
> >> [7,] 32 15 31
> >> [8,] 19 28 25
> >> [9,] 19 32 31
> >> [10,] 19 32 28
> >> [11,] 19 30 25
> >> [12,] 19 31 10
> >> [13,] 19 30 10
> >> [14,] 21 29 5
> >> [15,] 21 29 15
> >> [16,] 21 32 5
> >> [17,] 21 32 15
> >> [18,] 20 30 25
> >> [19,] 20 26 25
> >> [20,] 20 26 30
> >> [21,] 16 28 5
> >> [22,] 16 26 5
> >> [23,] 16 26 28
> >> [24,] 22 28 5
> >> [25,] 22 32 5
> >> [26,] 22 32 28
> >>
> >>> set2
> >> [,1] [,2] [,3]
> >> [1,] 0.061298933 0.561676607 -0.29029312
> >> [2,] -0.227292687 0.980185118 0.21751216
> >> [3,] 0.182482967 0.913803801 -0.08308208
> >> [4,] -0.143596376 -0.007469921 -0.33050543
> >> [5,] -0.354096826 0.023132113 0.45463150
> >> [6,] 0.006247011 0.183155253 0.97496500
> >> [7,] 0.128600720 -0.249603537 -0.24710206
> >> [8,] -0.418782299 -0.325201099 0.28908138
> >> [9,] 0.231829464 0.343250895 0.65134735
> >> [10,] -0.392597726 0.126741875 0.21411363
> >> [11,] -0.051290704 -1.007826669 0.92808143
> >>
> >> _______________________________________________
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >
> >
> > --
> > Brian D. Ripley, ripley at stats.ox.ac.uk
> > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> > University of Oxford, Tel: +44 1865 272861 (self)
> > 1 South Parks Road, +44 1865 272866 (PA)
> > Oxford OX1 3TG, UK Fax: +44 1865 272595
>
> 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]]
>
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