[R] Query on contour plots

Jim Lemon drj|m|emon @end|ng |rom gm@||@com
Wed Jun 3 00:50:13 CEST 2020

Hi Bruce & Abby,
Here is a start on merging the two plots.
Abby - I had to cheat on the legend colors as I could not work out
from the help pages how to specify the range of colors. Also I don't
know the range of densities. Both should be easy to fix. While I
specified xlab and ylab, they don't seem to make it to the plotting
functions. More study needed.
Bruce - The following code gives general idea of how to automate
plotting from a single data set. let me know whether you want
automated adjustment of axes, etc.
Both - I suspect that the constraints forming the diagonal lines are
due to characteristics of the bat larynx.

# split out what you want to identify the plot
# define the plot sequence
plot_ds <- function (dataset, main="", xlim, ylim, ..., k1=1, k2=1)
    {   names <- names (dataset)
        fh <- kbvpdf (dataset [,1], dataset [,2], k1 * bw.nrd (dataset
[,1]), k2 * bw.nrd (dataset [,2]) )
        plot (fh, main=main, xlab = names [1], ylab = names [2],
            xlim=xlim, ylim=ylim,
# open the device
# leave space for the color legend
plot_ds (bfs[,c("Fc","Sc")],
 main=paste(species,"characteristic bat call"),
 xlab="Frequency (kHz)",ylab="Characteristic slope (octaves/s)",
 ,k1=1.25, k2=1.25)


On Wed, Jun 3, 2020 at 6:22 AM Neotropical bat risk assessments
<neotropical.bats using gmail.com> wrote:
> Hi Abby,
> The contour lines are actually useful to see groupings.
> However w/o a legend for density it is not possible to see what is
> presented.
> >> Very nice
> > Jim, thank you.
> > However, the (deterministic, or near-deterministic) diagonal lines in
> > the plot, make me question the suitability of this approach.
> > In my plot, the contour lines could be removed, and brighter colors
> > could be used.
> >
> > But perhaps, a better approach would be to model those lines...
> > And it's not clear from the plot, if all the observations fall on a
> > diagonal line...
> >
> >
> > P.S.
> > I'm not sure why there's a white line on the plot.
> > Most of my testing was with PDF output, I will need to do some more
> > testing with PNG output.
> --
> Bruce W. Miller, PhD.
> Neotropical bat risk assessments
> Conservation Fellow - Wildlife Conservation Society
> If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet
> Using acoustic sampling to identify and map species distributions
> and pioneering acoustic tools for ecology and conservation of bats for >25 years.
> Key projects include providing free interactive identification keys and call fact sheets for the vocal signatures of New World Bats

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