[R-sig-Geo] adding points to spplot grid

[Nick Matzke]

On 11/6/10 3:03 AM, Edzer Pebesma wrote:
 >
 >
 > On 11/06/2010 01:37 AM, Nick Matzke wrote:
 >> Hi,
 >>
 >> I have been working with spplot.  I can get continuous 
grids to plot
 >> with spplot, but what do I do if I want to plot some 
points with x,y
 >> coordinates on top of the image?
 >>
 >> Cheers!
 >> Nick
 >>
 >>
 > http://r-spatial.sourceforge.net/gallery/


Thanks! This helped although it took some digging.  For 
others with this question:

=================================
# I start with some (randomly generated for now)
# * TRUE/FALSE values (samp_hits)
# * x & y columns giving sample locations (sample_locs)

# generate the tmpdata for species #1 (samp_hits, column #1)
tmpdata = as.data.frame(cbind(sample_locs[,1], 
sample_locs[,2], samp_hits[,1]))

names(tmpdata) = c("x", "y", "sp1")
coordinates(tmpdata) = ~x+y
# set projection to lon (x) & lat (y), i.e. unprojected;
# find projections with Terminal: proj -lp
proj4string(tmpdata) = CRS("lonlat")

hits = tmpdata[tmpdata$sp1 == 1, ]
misses = tmpdata[tmpdata$sp1 == 0, ]


#plot points for kicks
plot(0,0, xlim=minmax_literal(sample_locs[, 1]), 
ylim=minmax_literal(sample_locs[, 2]) )

points(hits, col="blue", pch=19)
points(misses, col="blue", pch=1)


# Make variogram

default_vgm = vgm(0.15, "Exp", 80, 0)
gs = gstat(id="sp001", formula=sp1~1, data=tmpdata, beta = 
0.1,  model=default_vgm)
vg = variogram(gs)
plot(vg)


# Make a tmpgrid
xs=xmin:xmax
ys=ymin:ymax

# use expand.grid to make all possible combinations of inputs
tmpgrid = expand.grid(xs, ys)
names(tmpgrid) = c("x", "y")
gridded(tmpgrid) = ~x+y
# set projection to lon (x) & lat (y), i.e. unprojected;
# find projections with Terminal: proj -lp
proj4string(tmpgrid) = CRS("lonlat")



# Fit a variogram model to the empirical variogram
# for single variogram
sp1_vgm = fit.variogram(vg, model=default_vgm)

plot(vg, model=default_vgm)
plot(vg, model=sp1_vgm)

# simple kriging
sk = krige(sp1~1, tmpdata, tmpgrid, sp1_vgm, nsim=0, 
indicators = TRUE, nmax = 40)

# plot the result
print(spplot(sk, cuts=1, col.regions=grey.colors(2, 0.6, 
0.90, 2.2)))
print(spplot(sk))


alphaChannelSupported = function()
	{
	!is.na(match(names(dev.cur()), c("pdf")))
	}

spplot_hits = list("sp.points", hits, pch=19, col="black", 
alpha = ifelse(alphaChannelSupported(), .5, 1))
spplot_misses = list("sp.points", misses, pch=21, cex=0.75, 
col="black", alpha = ifelse(alphaChannelSupported(), .5, 1))

# col.regions does color scale for grid
# sp.layout contains a list of the various points, text, 
etc. to plot
# at=seq() does limits of the color bar
spplot(sk["var1.pred"], scales=list(draw = TRUE), 
col.regions=rev(rainbow(100)[1:75]), 
sp.layout=list(spplot_hits, spplot_misses), at=seq(0, 1, 1/75))

=================================





-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Graduate Student Instructor, IB200A
Principles of Phylogenetics: Systematics
http://ib.berkeley.edu/courses/ib200a/index.shtml

Lab websites:
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http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

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