# [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
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
species<-unlist(strsplit("Procen_sample.csv","_"))[1]
library(bivariate)
# 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,
ncontours=2)
}
# open the device
png(paste0(species,".png"))
# leave space for the color legend
par(mar=c(6,4,4,2))
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)
library(plotrix)
xylim<-par("usr")
color.legend(xylim[1],xylim[3]-(xylim[4]-xylim[3])/7,
xylim[1]+(xylim[2]-xylim[1])/4,xylim[3]-(xylim[4]-xylim[3])/10,
legend=seq(0,10,length.out=5),
rect.col=color.scale(0:4,extremes=c("#7be6bd","#bdb3df")),align="rb")
text(xylim[1]+(xylim[2]-xylim[1])/8,
xylim[3]-(xylim[4]-xylim[3])/5,
"Density",xpd=TRUE)
dev.off()

Jim

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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