On Fri, 23 Nov 2007, Sisi wrote:
Dear all,
Thanks for your quick reply!
For Roger, I checked the sessioninfo and mine is same as yours. My object
size is indeed quite big, it is 275608. So I simplified the polygon
and erased all the small islands, only hold the main land of Asia, Europe
and Africa. After I loaded the polygon window and points, I checked the
object size. It becomes 86768, which seems quite ok (compared with yours
57760). I ran the function again, and still doesn't work, the code and
errors are as follow:
sessionInfo()
R version 2.6.0 (2007-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.0-2 spatstat_1.12-1 mgcv_1.3-27
maptools_0.6-19 sp_0.9-16
[6] foreign_0.8-23
loaded via a namespace (and not attached):
[1] grid_2.6.0 lattice_0.16-5 tools_2.6.0
#Enlarge the memory
memory.limit(size=4095)
# creat polygon to be used as a window in ppp
library(maptools)
library(sp)
library(spatstat)
a <- readShapePoly("D:/5Bird/Result/New2Project.shp"[1])
plot(a)
# Define the window
W <- as(as(a, "SpatialPolygons"), "owin")
plot(W)
# Import point data and creat ppp
cases <- coordinates(readShapePoints("D:/5Bird/Result/BirdPoint.shp"))
str(cases)
#num [1:3345, 1:2] 5431396 5305812 5343499 1975828 2128985 ...
#- attr(*, "dimnames")=List of 2
#..$ : NULL
#..$ : chr [1:2] "coords.x1" "coords.x2"
colnames(cases)<-c("x","y")
p1 <- ppp(cases[,1], cases[,2], window=W)
plot(p1)
points(cases, pch=20,col="red")
object.size(p1)
#[1] 86768
#Ripley's K function
K <- Kest(p1,nlarge=Inf)
#Error: cannot allocate vector of size 38.6 Mb
plot(K)
#Generate envelope
en <- envelope(p1, fun=Kest(p1,nlarge=3500), nsim=10)
#Error: cannot allocate vector of size 38.6 Mb
plot(en, main="Envelopes of K function based on CSR")
For the question about the geographical coordinates, the projection system
I'm using is Equidistant Cylindrical , the unit is meter. Just considering
this projection has no distortion in distance.
For Don, when I set nlarge=3500, the error was: "Error: cannot allocate
vector of size 381.8 Mb". When I set nlarge=Inf, the error became:"Error:
cannot allocate vector of size 38.6 Mb". I cannot figure out the cause
of the errors. When you mentioned edge correction, I get a question to
consult. Do I still need edge correction if my study area
covers Asia, Europe and Africa continents. I mean the boundary is the real
boundary, and beyond it is the sea.
The edge correction is the real issue. K is measuring the number of points
within areas of distance bands adjusted for the area within the edges. So
you have to correct - but shorelines may not be appropriate for birds -
how far can your birds fly over water? Have you considered using a raster
mask which would permit contact over channels between islands?
Roger
Thank you for your time and best regards,
Sisi
On Thu, 22 Nov 2007, Roger Bivand wrote:
This number is not large in itself, and:
set.seed(1)
xy <- runifpoint(3500)
res <- Kest(xy, nlarge=3500)
works without any problems on a 1GB system:
sessionInfo()
R version 2.6.0 (2007-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian
(Bokmål)_Norway.1252;LC_MONETARY=Norwegian
(Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] spatstat_1.12-3 mgcv_1.3-29
(it is always helpful to include the output of sessionInfo())
However note that here:
xy
planar point pattern: 3500 points
window: rectangle = [0, 1] x [0, 1] units
object.size(xy)
[1] 57760
only has the simplest window, and my guess is that your window mask is
much richer (continental shorelines? raster landmass mask?). If so, edge
correction will probably involve much more memory use. If you are using a
vector shoreline, and this is the reason for the problems, have you tried
using a raster mask instead?
I have tried using coarse GSHHS shorelines without difficulties (Rgshhs in
maptools), but very possibly with a shoreline with too many details, you
might see problems, or with a raster mask with too high resolution.
Have you considered the problems involved in using geographical
coordinates?
Roger
On 22/11/2007, Putler, Dan <[EMAIL PROTECTED]> wrote:
Hi Sisi,
By setting nlarge to 3500 you are creating problems (given that you have
just over 3300 observations) since you may be using either the isotropic or
Ripley's method for border correction. You want to use the border method
(which is what was used when nlarge was at its original value of 3000). To
quote the documentation of the function:
If the point pattern X contains more than about 3000 points, the isotropic
and translation edge cor-
rections can be computationally prohibitive. The computations for the
border method are much
faster, and are statistically efficient when there are large numbers of
points. Accordingly, if the
number of points in X exceeds the threshold nlarge, then only the border
correction will be com-
puted. Setting nlarge=Inf will prevent this from happening. Setting
nlarge=0 is equivalent
to selecting only the border correction with correction="border".
My guess is that Roger's suggested approach of simplifying the boundaries
is correct (my experience is that his suggestions are always on target),
which would allow you to take advantage of the other methods, but the using
the border method only can be justified in your case (and a lot easier to
implement).
Dan
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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