Folkes, Michael
2008-Nov-04 23:28 UTC
[R] contour plot, failing to interpolate through all data
I'm having trouble making contour lines for this attached, sparse dataset (low data:NA ratio!). Is it the high number of NA's, or funny layout of the densities, or something else that's causing this? This is a subsample of the dataset, and I get the same problem when using the full data. The only reason I get any contours is because I'm forcing specific levels. If no levels are declared, no contours are generated. Please excuse my hack job at coding. thanks in advance! Michael ####start data to be in file='testmatrix.csv' "0.5","1","1.5","2","2.5","3" "-0.833",NA,NA,NA,NA,NA,21.05 "-0.8",NA,NA,NA,NA,10.62,NA "-0.75",NA,NA,NA,5.13,NA,NA "-0.667",NA,NA,2.24,NA,NA,11.68 "-0.6",NA,NA,NA,NA,5.69,NA "-0.5",NA,0.74,NA,2.53,NA,5.81 "-0.4",NA,NA,NA,NA,2.59,NA "-0.333",NA,NA,0.86,NA,NA,2.59 "-0.25",NA,NA,NA,0.89,NA,NA "-0.2",NA,NA,NA,NA,0.9,NA "-0.167",NA,NA,NA,NA,NA,0.9 "0",0,0,0,0,0,0 "0.2",NA,NA,NA,NA,-0.47,NA "0.25",NA,NA,NA,-0.47,NA,NA "0.333",NA,NA,-0.47,NA,NA,NA "0.5",NA,-0.46,NA,-0.72,NA,NA "0.667",NA,NA,-0.72,NA,NA,NA "1",-0.42,-0.72,-0.85,NA,NA,NA "1.5",NA,-0.85,NA,NA,NA,NA "2",-0.69,-0.92,NA,NA,NA,NA "3",-0.84,NA,NA,NA,NA,NA "4",-0.91,NA,NA,NA,NA,NA "5",-0.95,NA,NA,NA,NA,NA ####End data ####start code junk2<-as.matrix(read.csv(file='testmatrix.csv')) colnames(junk2)<-as.character(seq(.5,3,by=.5)) contour(ylim=c(-1,1),as.numeric(rownames(junk2)),as.numeric(colnames(jun k2)), junk2,levels=c(seq(-1,0,by=.1),seq(1,23,by=2))) junk3<-cbind(as.numeric(colnames(junk2)[as.vector(col(junk2))]),as.numer ic(row.names(junk2)[as.vector(row(junk2))]),as.numeric(as.vector(junk2)) ) text(junk3[,1],junk3[,2],junk3[,3],cex=.5) #### End code _______________________________________________________ Michael Folkes Salmon Stock Assessment Canadian Dept. of Fisheries & Oceans Pacific Biological Station 3190 Hammond Bay Rd. Nanaimo, B.C., Canada V9T-6N7 Ph (250) 756-7264 Fax (250) 756-7053 Michael.Folkes at dfo-mpo.gc.ca
Dieter Menne
2008-Nov-05 07:44 UTC
[R] contour plot, failing to interpolate through all data
Folkes, Michael <Michael.Folkes <at> dfo-mpo.gc.ca> writes:> I'm having trouble making contour lines for this attached, sparse > dataset (low data:NA ratio!). Is it the high number of NA's, or funny > layout of the densities, or something else that's causing this? > > ####start data to be in file='testmatrix.csv' > > "0.5","1","1.5","2","2.5","3" > "-0.833",NA,NA,NA,NA,NA,21.05 > "-0.8",NA,NA,NA,NA,10.62,NA > "-0.75",NA,NA,NA,5.13,NA,NA > "-0.667",NA,NA,2.24,NA,NA,11.68contour needs a more data, it's rather a plotting workhorse and not so good for interpolation. There are examples for spatial statistics in library/MASS/scripts/ch15.R and in "the book" by Venables/Ripley. You might also search for "geo" in the packages, because your problem is fairly common in geographical ecology. Dieter