[R-sig-Geo] density /diversity of points
Matevž Pavlič
matevz.pavlic at gi-zrmk.si
Tue May 17 16:47:05 CEST 2011
Thanks for the help marcelino!
-----Original Message-----
From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of Marcelino de la Cruz
Sent: Tuesday, May 17, 2011 2:28 PM
To: Mathieu Rajerison
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] density /diversity of points
On 17/05/2011 14:00, Mathieu Rajerison wrote:
> Many thanks for the code!
>
> What are the units of R in marktable? I didn't find the information in
> the documentation.
>
The same units of x and y coordinates in your ppp object.
Cheers,
Marcelino
> 2011/5/17 Marcelino de la Cruz<marcelino.delacruz at upm.es>
>
>
>> On 16/05/2011 10:27, Matevž PavliÄ? wrote:
>>
>>
>>> Hi all,
>>>
>>> I read (just now) about the Simpson idex. This would probably be a
>>> good thing to try in my case. Do you have any ideas of how to create
>>> a diversity map using Simpson index?
>>>
>>>
>>>
>> library(vegan)
>> simpson<- diversity(lansing.tab, "simpson")
>> lansing.simpson<- setmarks(lansing,simpson)
>> lansing.simpson.s<-smooth.ppp(lansing.simpson)
>> plot(lansing.simpson.s)
>>
>>
>> . I have just a few more questions about the code :
>>
>>> The line below as I understand sets a table for each point with the
>>> type of points that are in the near in the radius R=350 units?
>>> mol.tab<- marktable(mol.ppp,R=350)
>>>
>>>
>>>
>> Yes.
>> To resolve questions like this about the arguments of the functions,
>> please read the help pages, e.g.
>> help(marktable)
>>
>>
>> And this line creates a surface(map) of diversity ?
>>
>>> lansing.div.s<-smooth.ppp(lansing.div)
>>>
>>>
>> Yes again.
>> help(smooth.ppp); help(density.ppp)
>>
>>
>>
>>> I think this map that is created with smooth.ppp is to rough giving
>>> to little detail on the diversity. Would it be possible to use
>>> kriging to create diversity map?
>>>
>>>
>>>
>> It depends on what do you think is "too rough". You may control
>> the"roughnes" of the map changing the "dimyx" argument (that controls
>> the final grid of the smoothed surface). You may be also interested
>> in setting the argument "sigma" (that controls the bandwith of the smoothing kernel).
>> Although it is possible to krige the results, I think that in this
>> case is preferable to trust the smoothed surface.
>>
>> Cheers,
>> Marcelino
>>
>>
>>
>>
>> Thanks for the help,
>>
>>> m
>>>
>>> -----Original Message-----
>>> From: marcelino.delacruz at upm.es [mailto:marcelino.delacruz at upm.es]
>>> Sent: Monday, May 16, 2011 9:59 AM
>>> To: Matevž PavliÄ?
>>> Cc: r-sig-geo at r-project.org
>>> Subject: RE: [R-sig-Geo] density /diversity of points
>>>
>>> Con fecha 15/5/2011, "Matevž Pavlič"<matevz.pavlic at gi-zrmk.si>
>>> escribió:
>>>
>>>
>>>
>>>
>>>> Hi Marcelino,
>>>>
>>>> Was out of the office for a while...
>>>> Thanks for the help. I think this could work...but can you tell me
>>>> what this line does?
>>>>
>>>> diversity<- apply(mol.tab,1,function(x) sum(x>0))
>>>>
>>>>
>>>>
>>> mol.tab is a table with the number of occurrences of each type
>>> (columns) in the neighborhood of each point (rows). This line
>>> computes for each row (i.e. for each point) the number of types whose value is ">0"
>>> (i.e. types that are present in the neighborhood). This is a very
>>> simple definition of diversity (i.e. "richness"). From that table
>>> you could also compute Shannon or Simpson diversity indices, if you
>>> would prefer that.
>>>
>>>
>>> Marcelino
>>>
>>>
>>>
>>>
>>>> i cant figure out how diversity is calculated here?
>>>>
>>>> Thanks again for the help,
>>>>
>>>> matevz
>>>>
>>>> -----Original Message-----
>>>> From: Marcelino de la Cruz [mailto:marcelino.delacruz at upm.es]
>>>> Sent: Thursday, May 12, 2011 2:03 PM
>>>> To: MatevÃ...¾ PavliÃ" Cc: r-sig-geo at r-project.org
>>>> Subject: Re: [R-sig-Geo] density /diversity of points
>>>>
>>>> On 12/05/2011 13:12, MatevÃ...¾ PavliÃ" wrote:
>>>>
>>>>
>>>>
>>>>> Hi all,
>>>>>
>>>>>
>>>>>
>>>>> I have a point data set (SHP) with coordinates and a attribute (i.e.
>>>>> type of point).
>>>>>
>>>>> These points are scattered around a fairly big area. What i would
>>>>> like to do is to find a sub-area where density of points sombined
>>>>> with the diversity of type is the biggest.
>>>>>
>>>>> Does anyone have any idea iff this is somehowe possible to do in R?
>>>>> Any idea would be greatly aprpeciated,
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> To your first question:
>>>>
>>>> library(fortunes)
>>>> fortune("Yoda")
>>>>
>>>> ;-)
>>>>
>>>> More seriously, you could transform your shp data in a ppp object
>>>> with spatstat. See the vignette in spatstat. Then you can use some
>>>> functions there, for example (with the data set lansing):
>>>>
>>>> library(spatstat)
>>>> data(lansing)
>>>> plot(lansing)
>>>> # get an estimate of point density
>>>> lansing.den<- density.ppp(lansing)
>>>> plot(lansing.den)
>>>>
>>>> # get an estimate of point diversity (here, for the shake of
>>>> brevity, at the points themselves)
>>>> lansing.tab<- marktable(lansing,R=0.05)
>>>> diversity<- apply(lansing.tab,1,function(x) sum(x>0)) lansing.div<-
>>>> setmarks(lansing,diversity) lansing.div.s<-smooth.ppp(lansing.div)
>>>>
>>>> plot(lansing.div.s)
>>>>
>>>> # select areas with arbitrary high values of density and diversity plot(
>>>> eval.im(lansing.div.s>4.5& (lansing.den/max(lansing.den))>0.9))
>>>>
>>>>
>>>> HTH. Cheers,
>>>>
>>>> Marcelino
>>>>
>>>>
>>>>
>>>> --
>>>> _________________________________
>>>>
>>>> Marcelino de la Cruz Rot
>>>> Departamento de Biologia Vegetal
>>>> E.U.T.I. Agricola
>>>> Universidad Politecnica de Madrid
>>>> 28040 Madrid
>>>> Tel: 34913365654
>>>> _________________________________
>>>>
>>>>
>>>>
>>>>
>>>
>> --
>> _________________________________ Marcelino de la Cruz Rot
>> Departamento de Biologia Vegetal E.U.T.I. Agricola Universidad
>> Politecnica de Madrid 28040 Madrid Tel: 34913365654
>> _________________________________
>>
>>
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--
_________________________________ Marcelino de la Cruz Rot Departamento de Biologia Vegetal E.U.T.I. Agricola Universidad Politecnica de Madrid
28040 Madrid Tel: 34913365654 _________________________________
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