Atlantic puffin close up, by user john-289283 from pexels.com
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This vignette has two goals:
lightr parsers produce the same output
as the official softwarelightrFor this, we use spectral data of the beak of the atlantic puffin, Fratercula arctica. This data was collected by Dr Claire Doutrelant, using an OceanOptics spectrometer.
Atlantic puffin close up, by user john-289283 from pexels.com
By default, OceanInsight spectrometers produce .ProcSpec
files, which R cannot readily import. To help with this, OceanInsight
official software, SpectraSuite has a conversion feature, which turns
.ProcSpec files into tab separated values files
(.txt).
So, let’s start by comparing the .ProcSpec spectra
imported by lightr and the .txt files produced
by OceanOptics.
raw_files <- lr_get_spec(file.path("data", "puffin"), ext = "ProcSpec")
#> 2 files found; importing spectra:
txt_files <- lr_get_spec(file.path("data", "puffin"), ext = "txt")
#> 2 files found; importing spectra:We can visually inspect these two file using the dedicated S3
function pavo::plot.rspec():
library(pavo)
plot(raw_files, main = "Raw ProSpec files")
plot(txt_files, main = "Exported txt files")
Spectra imported by lightr and converted by SpectraSuite
look pretty similar upon visual inspection and we can confirm this
with
One possibly biologically relevant question would be to look at the interspecific variability in beak colour. I.e., do all puffin individuals have roughly the same colour or are some individuals brighter, more colourful than others?
For this, we will look at the difference in hue and brightness on the
red part of the beak for two individuals, with
pavo::summary.rspec() function (after smoothing with
pavo::procspec()):
beak <- procspec(raw_files, opt = "smooth")
#> processing options applied:
#> smoothing spectra with a span of 0.25
summary(beak, subset = c("B2", "H5"))
#> B2 H5
#> BR_PF26_1 26.23823 569
#> BR_PF27_3 21.78785 581Okay, these two individuals seem to differ quite a lot in terms of
hue and brightness. Now, one might ask if these difference can be
perceived in bird vision. We can test this with the
pavo::coldist() function.
vis_beak <- vismodel(beak, visual = "avg.uv", achromatic = "ch.dc")
tcs_beak <- colspace(vis_beak)
coldist(tcs_beak, achromatic = TRUE)
#> Quantum catch are relative, distances may not be meaningful
#> Calculating unweighted Euclidean distances and Weber luminance contrast
#> patch1 patch2 dS dL
#> 1 BR_PF26_1 BR_PF27_3 0.005867583 0.2004935The values of dS and dL are below the 1 JND
(just
noticeable differences) threshold, which means that the colour of
the two individuals, in spite of their difference, looks the same to the
birds.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.