[R-sig-Geo] density /diversity of points

[Matevž Pavlič]

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)) 

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: Matevž Pavlič
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] density /diversity of points

On 12/05/2011 13:12, Matevž Pavlič 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
  _________________________________