[R-sig-Geo] Problem with tripGrid when some segments lie outside the study area

[Michael Sumner]

I'm not totally sure what you are asking here since as you say and as
reported by pixellate.psp (from within tripGrid) your tracks do not
all lie entirely within the grid.

 tgrid <- tripGrid(tr, grid = gt)
Error: 7 segments do not lie entirely inside the window.

You either need to expand the grid to encompass the data or trim the
data to lie within the grid - this is not done automatically.

It's also not documented in much detail so if that is the source of
confusion I apologise.

An easy way to make a grid is to use ?makeGridTopology, which will
choose defaults based on a lot of varying input data. You can
initialize the extents by doing

 makeGridTopology(tr)

and you can control the exact options with arguments for cells.dim and so on.

Cheers, Mike.


On Wed, Nov 23, 2011 at 10:22 PM, Pinaud David <pinaud at cebc.cnrs.fr> wrote:
> Dear all,
>
> I'm calculating time spent per cell over a grid (study area) with the
> package "trip", for satellite-tracked seabirds.
> Some birds bred outside the area of interest (Kerguelen Plateau, to design
> marine protected areas), so their trips didn't lie entirely in the grid. In
> this case, it seems that time is added in some cells that are not visited by
> the bird (tipically in the border of the grid).
> This problem seems coming from pixellate(), and because I need to set
> spatstat.options(checksegments=F)...
>
> Any solution?
>
> Many thanks
> David
>
> Here a reproducible exemple:
>
> library(trip)
> Le chargement a nécessité le package : sp
> Le chargement a nécessité le package : spatstat
> Le chargement a nécessité le package : mgcv
> This is mgcv 1.7-6. For overview type 'help("mgcv-package")'.
> Le chargement a nécessité le package : deldir
> deldir 0.0-15
>
> Please note: The process for determining duplicated points
> has changed from that used in version 0.0-9 (and previously).
>
> spatstat 1.23-4
> Type ‘help(spatstat)’ for an overview of spatstat
> ‘latest.news()’ for news on latest version
> ‘licence.polygons()’ for licence information on polygon calculations
>
> spatstat.options(checksegments=F) # to allow segment outside the window
>
> # a trip with some parts outside the study area :
> d <- data.frame(x = 1:10, y = c(1, 1.5, 2, 4, 5, 5.5, 8, 8, 6, 10), tms =
> Sys.time() + seq(10,100, 10), id = rep(1, 10))
> coordinates(d) <- ~x+y
> tr <- trip(d, c("tms", "id"))
>
> # the sutdy area :
> gridaa <- expand.grid(Long=seq(-0.5, 10.5, by=1), Lat=seq(3.5, 6.5, by=1))
> coordinates(gridaa) <- ~ Long + Lat
> gridded(gridaa) <- T
> fullgrid(gridaa) <- T
> gt <- getGridTopology(gridaa)
>
> # time spent per cell
> tgrid <- tripGrid(tr, grid = gt)
>
> image(tgrid, axes=T)
> points(coordinates(tr), t="l", col="blue")
> points(gridaa, pch="+")
> text(x= midpoints.psp(as.psp(tr)), col="green", pos=3, labels=1:9)
>
> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] trip_1.1-10 spatstat_1.23-4 deldir_0.0-15 mgcv_1.7-6
> [5] sp_0.9-88
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1 lattice_0.19-30 Matrix_0.9996875-3 nlme_3.1-101
>
> --
> ***************************************************
> Dr. David PINAUD
> Ingénieur de Recherche "Analyses spatiales"
>
> Centre d'Etudes Biologiques de Chizé - CNRS UPR1934
> 79360 Villiers-en-Bois, France
> poste 485
> Tel: +33 (0)5.49.09.35.58
> Fax: +33 (0)5.49.09.65.26
> http://www.cebc.cnrs.fr/
>
> ***************************************************
>
>
>
>
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-- 
Michael Sumner
Institute for Marine and Antarctic Studies, University of Tasmania
Hobart, Australia
e-mail: mdsumner at gmail.com