At 21:05 09/11/2009, Raya A. Pruner wrote:
>I have another question for everyone related to the spatstat package 
>and model fitting.
>
>A brief background on my question of interest: We are interested in 
>the spatial aggregation of snowy plover nests on a barrier island 
>system in response to nest fates.  We hypothesize a greater level of 
>aggregation in response to a positive nest fate.  Given this, we are 
>also interested in underlying covariates.  So we have data for human 
>activity, predator activity, and prey availability. We would like to 
>see how these covariates influence the aggregation of nests as 
>well.  Currently I have been trying to create a list of images, but 
>was unsuccessful.  So I used based on what I have been able to 
>figure out and did each separately.  This was the only way I could 
>figure out in associating a continuous covariate with a pixel inmage:
>
>nests.extra <- read.csv("CIE 2009 covariates.csv", header = T)
>extra.chop <- subset(nests.extra, select = c(Id, 
>X,Y,Tracks,Predator_T, Invert_Tra))
>
>
>covH.ppp <- ppp(extra.chop[,2], extra.chop[,3], marks 
>=extra.chop[,4],window = area1)
>human.act=density.ppp(covH.ppp)
>human.act
>
>covP.ppp <- ppp(extra.chop[,2], extra.chop[,3], marks 
>=extra.chop[,5]_T,window = area1)
>predator.act=density.ppp(covP.ppp)
>predator.act
>
>covI.ppp <- ppp(extra.chop[,2], extra.chop[,3], marks 
>=extra.chop[,6],window = area1)
>invert.act=density.ppp(covI.ppp)
>invert.act
>
>using this allows me to fit models such as this using multiple covariate:
>cov2.cord.model=ppm(nestsF.ppp, ~x+y+Tracks+Pred, covariates = 
>list(Tracks=human.act,Pred=predator.act ))
>
>However, I don???t think it is working right.  I tried to plot 
>human.act and it doesn???t seem to relate to the data provided in 
>plotting covH.ppp.  The way that I collected the covariate data was 
>systematic by counting human and predator tracks every 500m linearly 
>along the beach.  So I want to be able to look at how the human 
>intensity value effects nesting aggregation and not the density of 
>covariate points themselves which is what I think it is doing 
>currently.  I am interested in the value behind the point.
>If anyone has any insight on this, please let me know!


 From the help page of density.ppp:
"
"To perform spatial interpolation of values that were observed at the 
points of a point pattern, use 
<mk:@MSITStore:C:\ARCHIV~1\R\R-29~1.2\library\spatstat\chtml\spatstat.chm::/smooth.ppp.html>smooth.ppp." 


So, instead of :

human.act=density.ppp(covH.ppp)

use :

human.act <- smooth.ppp(covH.ppp)

And if the results don't fit your expectations,  try to control the 
smooth parameters with the argument "sigma"


HTH

Marcelino



>Cheers!!!
>Raya
>
>
>--
>Raya A Pruner - Graduate Student
>University of Florida
>Department of Wildlife Ecology and Conservation
>PO Box 110430
>Gainesville, FL 32611-0430
>352-214-3262
>
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