Tnx Jim,
Yes if there is a way to first extract the ranges of each data files Fc
range and Sc ranges and then link to the plot that would be stellar.
I will look at this code and see how it is working so far.
Thanks a million.
Bruce
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.
bfs<-read.csv("Procen_sample.csv")
# 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.b...@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
--
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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