Converting spatialPointsDataFrame into ppp
On Fri, 16 Sep 2011, GodinA wrote:
Dear all, I am new to spatial and point process analysis (as well as R), however most of my Ph.D. will rely heavily on these tools *sighs :) I am starting a new chapter where I intend to model elasmobranch i.e., shark and skate catch in the Northwest Atlantic Canadian waters using point process modeling. I am interested in investigating the spatial, temporal, and space?time clustering of catch events conditioned upon the distribution of fishing locations. I have been following the R-sig-geo mails and found many great reading suggestions, which were very helpful! Thank you. I would like to do some exploratory data analysis on a small subset of my database i.e., solely shark catch for the year 2009 (546 observations), but I am running (not surprisingly) into errors and warnings! Would be grateful to anyone's help! I am trying to convert my SpatialPointsDataFrame into a ppp. Right now, I would just like to make a ppp with "catch" as a mark (this is the catch size in kg).
class(SHK09)
[1] "SpatialPointsDataFrame" attr(,"package") [1] "sp" #SHK09 looks as follow
head(as.data.frame(SHK09))
year month day tripID setID gear NAFO x y kept discard fmonth
fgear
1 2009 8 17 345 16 5 22 55.41 -58.46 0 227 Aug
GN
2 2009 2 1 3 2 1 23 52.36 -51.24 0 450 Feb
OT
3 2009 7 28 296 4 5 9 68.37 -59.34 0 250 Jul
GN
4 2009 9 5 339 29 5 9 68.27 -59.53 0 10 Sep
GN
5 2009 8 28 316 44 5 9 68.38 -64.36 0 1400 Aug
GN
6 2009 9 1 316 49 5 9 69.26 -64.50 0 200 Sep
GN
fNAFO t.spp.name t.spp.category elasmo.name
elasmo.category
1 2H GREENLAND HALIBUT 0 SHARKS,DOGFISH (NS)
1
2 2J GREENLAND HALIBUT 0 SHARK,GREENLAND
1
3 BaffinIsd GREENLAND HALIBUT 0 SHARK,GREENLAND
1
4 BaffinIsd GREENLAND HALIBUT 0 SHARK,GREENLAND
1
5 BaffinIsd GREENLAND HALIBUT 0 SHARK,GREENLAND
1
6 BaffinIsd GREENLAND HALIBUT 0 SHARK,GREENLAND
1
catch logcatch
1 227 5.429346
2 450 6.111467
3 250 5.525453
4 10 2.397895
5 1400 7.244942
6 200 5.303305
#I tried to do the following as suggested by prior email, however, I get
this following error message
coordinates(SHK09) = ~x+y
Error in `coordinates<-`(`*tmp*`, value = ~x + y) : setting coordinates cannot be done on Spatial objects, where they have already been set
Well, that is what you would expect.
#so decided to proceed as follow
catch <- as(SHK09["catch"], "ppp")
Error in as(SHK09["catch"], "ppp") : no method or default for coercing "SpatialPointsDataFrame" to "ppp"
Did you look at the vignette for the spatstat package about handling shapefiles? You would note that you need the maptools package, which also contains the as() coercion functions. They are there, rather than in sp or spatstat, to try to avoid unwanted dependencies between packages. However, I doubt whether your data are a marked point process - the catch positions were decided by someone, not, say, the fish? Have you thought of trying the bubble() function in sp? Roger
Ideas? Thank you very much in advance! ~~Aurelie Aurelie Cosandey-Godin Ph.D. Candidate, Department of Biology, Dalhousie University Industrial Graduate Fellow, WWF-Canada Email: godina at dal.ca | Web: wormlab.biology.dal.ca ----------------------------------------------------------------------------------------------------- Want to learn more about sharks in Atlantic Canada? Visit ShARCC! www.atlanticsharks.org -- View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Converting-spatialPointsDataFrame-into-ppp-tp2764866p6801137.html Sent from the R-sig-geo mailing list archive at Nabble.com.
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Roger Bivand Department of Economics, NHH Norwegian School of Economics, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: Roger.Bivand at nhh.no