[R-sig-Geo] density /diversity of points
Matevž Pavlič
matevz.pavlic at gi-zrmk.si
Tue May 17 18:39:48 CEST 2011
Hi again,
I managed (with your help) to find the areas of my interest. But now i would like to export thist plot (of arbitrary hig values of diversity and density) to a tiff (with projection).
I used to do that with rgdal library (writeGDAL) but here it is not possible since this the object needs to be SpatialPointsGrid. Is it possible to create Tiff from, ppp object?
Thanks for the help,
m
-----Original Message-----
From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of Matevž Pavlič
Sent: Tuesday, May 17, 2011 4:47 PM
To: marcelino.delacruz at upm.es; Mathieu Rajerison
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] density /diversity of points
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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>>
>>
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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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