On 16/05/2011 10:27, Matevž Pavlič 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: [email protected] [mailto:[email protected]]
Sent: Monday, May 16, 2011 9:59 AM
To: Matevž Pavlič
Cc: [email protected]
Subject: RE: [R-sig-Geo] density /diversity of points
Con fecha 15/5/2011, "Matevž Pavlič"<[email protected]>
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:[email protected]]
Sent: Thursday, May 12, 2011 2:03 PM
To: Matevž PavliÄ
Cc: [email protected]
Subject: Re: [R-sig-Geo] density /diversity of points
On 12/05/2011 13:12, Matevž PavliÄ 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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