[R-SIG-Mac] [R-sig-mac] trouble with point in polyhedron computation

Don McKenzie dmck at u.washington.edu
Thu Apr 3 15:54:39 CEST 2014


Thanks Augustin.  I will give that a try.

Don

On Apr 3, 2014, at 2:25 AM, Agustin Angel Diez Castillo <agustin.diez at uv.es> wrote:

> 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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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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