[R-sig-eco] nearest neighbours

[Anna Marburg]

Hi Katia -


The spdep package has a variety of functions to count neighbors, as  
well as functions to combine neighborhoods.
You will first need to extract the coordinates of your .ppp into a  
matrix

Here's a quick example:

library(spatstat)
data(amacrine)

ama.split <- split(amacrine) # make one .ppp for each mark
summary(ama.split)

coords <- cbind(ama.split[["on"]]$x, ama.split[["on"]]$y)
class(coords)			# a matrix of co-ordinates

rn <- 1:nrow(coords)	# if your points have meaningful ids put them here

# find 4 nearest neighbors:
k4 <- knn2nb(knearneigh(coords, k = 4), row.names = rn)

# look at result
summary(k4, coords)
plot(k4, coords)

# calculate distances from each point to its neighbors
dsts <- nbdists(k4, coords)
summary(unlist(dsts))

# find all neighbors closer than some threshold
close.nb <- dnearneigh(coords, 0, 0.12330, row.names=rn)

# test the effect of different set logic
summary(intersect.nb(k4, close.nb), coords)

summary(union.nb(k4, close.nb), coords)

If you are doing more spatial analyses within R, you may want to check  
out the following references. There's also a dedicated mailing list  
for questions about "geographical data and mapping", R-sig-Geo.

Bivand, R. S., E. J. Pebesma, and V. Gómez-Rubio. 2008. Applied  
spatial data analysis with R. Springer Verlag, NY.

Baddeley, A. 2008. Analysing spatial point patterns in R. Workshop  
Notes [available from http://www.csiro.au/resources/Spatial-Point-Patterns-in-R.html 
]

HTH,

Anna

Dr. Anna E.  Marburg
Ecosystem Processes Team
Landcare Research
P O Box 40
Lincoln 7640
NEW ZEALAND

phone + 64  3 321 9729
MarbugA at landcareresearch.co.nz


>
> Message: 1
> Date: Fri, 25 Sep 2009 11:31:08 -0400
> From: K?tia Emidio <kat.emidio at gmail.com>
> Subject: [R-sig-eco] nearest neighbours
> To: r-sig-ecology at r-project.org
> Message-ID:
> 	<cf3004ea0909250831n38dfd0bbl853e43d4b382da8d at mail.gmail.com>
> Content-Type: text/plain
>
> Hi, What function should I use to find out who are my 5 nearest  
> neigbours(N)
> or in a specified radius,  in a .ppp (object) where the marks are  
> factors?
> thanks
> Katia
>
> -- 
> K?tia Em?dio da Silva MSc
> Eng. Florestal
> Pesquisador
> Embrapa Amaz?nia Ocidental
>
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