Thanks, that is a big help.
David Winsemius wrote:
On Oct 13, 2009, at 3:46 PM, Gavin Simpson wrote:
On Mon, 2009-10-12 at 22:20 -0400, David Winsemius wrote:
On Oct 12, 2009, at 8:20 PM, Jason Gasper wrote:
<snip />
# contour examples.... vis.gam(g,
view=c("x1","x2"),plot.type="contour",color="heat", nlevels=20)
Warning messages:
1: In plot.window(...) : "nlevels" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "nlevels" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
"nlevels" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
"nlevels" is not a graphical parameter
5: In box(...) : "nlevels" is not a graphical parameter
6: In title(...) : "nlevels" is not a graphical parameter
# This does result in warnings that do not seem correct (since nlevels
is listed as a graphics parameter in the help page of contour)
They are correct for a certain definition of "graphical parameter", and
'nlevels' is an argument to contour. IIRC this really refers to things
in ?par and is a common issue that I have come across when coding
function that pass some arguments in '...' to other functions and some
to plotting functions. There are ways around this, but I don't have the
details to hand - Prof. Ripley suggested one solution that is used
within base R to get round this problem, and which we subsequently used
in the vegan package.
This the case. Looking at the code it appears the vis.gam function may
have been written with the persp plotting case in mind. There is some
minimal processing of parameters when the call is for "contour", and
nlevels is not a named argument within vis.gam. If you make it one,
and then pass it to the contour call within the eval(parse(text= ))
dispatching strategy, you can avoid the warnings:
vis.gam2(g, view=c("x1","x2"),plot.type="contour",color="heat",
nlevels=20)
#no warnings
#after defining the function
vis.gam2 <- function (x, view = NULL, cond = list(), n.grid = 30,
too.far = 0,
col = NA, color = "heat", contour.col = NULL, se = -1, type =
"link", nlevels=10,
plot.type = "persp", zlim = NULL, nCol = 50, ...)
{
---snipped unchanged code-----
if (plot.type == "contour") {
stub <- paste(ifelse("xlab" %in% dnm, "", ",xlab=view[1]"),
ifelse("ylab" %in% dnm, "", ",ylab=view[2]"),
ifelse("main" %in% dnm, "", ",main=zlab"), ",...)",
sep = "")
if (color != "bw") {
txt <- paste("image(m1,m2,z,col=pal,zlim=c(min.z,max.z)",
stub, sep = "")
eval(parse(text = txt))
txt <-
paste("contour(m1,m2,z,col=contour.col,zlim=c(min.z,max.z)",
ifelse("add" %in% dnm, "", ",add=TRUE"), ", nlevels=
nlevels, ...)",
sep = "")
eval(parse(text = txt))
}
else {
txt <- paste("contour(m1,m2,z,col=1,zlim=c(min.z,max.z)",
stub, sep = "")
eval(parse(text = txt))
}
}
---snipped more unchanged code-------
}
HTH
G
but the
desired effect seems to be occurring. I have seen such warnings many
times before an have learned to ignore them. Whether that is the
correct posture to assume, I am not sure.
Thanks
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
--
Jason Gasper
National Marine Fisheries Service
Alaska Region, Sustainable Fisheries Division
709 W. 9th St. Juneau, Alaska 99801
Juneau, Alaska 99801
Phone 907-586-7237
Fax 907-586-7249
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
