README.md

In thomased/spec.vis: A Spectral Sensitivity and Ocular Transmission Database

spec.vis

Spectral sensitivity data package

spec.vis is a mini-database and R data package of receptor absorbance and ocular transmission spectra with metadata, useful for visual/colorspace modelling among other things. It currently contains 410 spectra from 119 species.

Installation

To download the development version of spec.vis, you can:

• use the remotes package:

# install.packages("remotes")
remotes::install_github("thomased/spec.vis")

• download files from GitHub and install using $R CMD INSTALL or, from within R:

install.packages(path, type = "source", repos = NULL)

Browsing and searching spectra

The entire database can be loaded into memory by simply calling data(specvis_spectra), along with the metadata data(specvis_meta) and dictionary data(specvis_dict).

Alternately, the specvis_search() function allows you to query the available data and return a select subset based on search terms (e.g. specvis_search(genus == 'bombus')), with the option of returning either raw spectra or metadata via the return.spectra argument.

Finally, if you’re not an R person, the ‘database’ boils down to a few text files located in the data.raw/ directory, which you’re free to download and use as you please.

Example

# Load packages
library(spec.vis)
library(pavo)

# Grab some spectra
apis <- specvis_search(genus == 'apis', species == 'mellifera', return.spectra = TRUE)
canis <- specvis_search(genus == 'canis', species == 'familiaris', return.spectra = TRUE)
bluetit <- specvis_search(genus == 'cyanistes', species == 'caeruleus', return.spectra = TRUE)

# Plot them
par(mfrow=c(1,3))
plot(as.rspec(canis), main = 'Canis familiaris', ylab = 'Absorbance', xlab = '')
plot(as.rspec(apis), ylab = '', main = 'Apis mellifera (f)')
plot(as.rspec(bluetit), ylab = '', main = 'Cyanistes caeruleus', xlab = '')

Contributing

Contributions of spectra to the package are most welcome. There are a few ways to do so, from most- to least-involved:

• via pull request
  • Install the spec.vis package in the usual manner.
  • Fork and clone the package repository.
  • Append your spectra to the data-raw/specvis_spectra.csv file, and complete all metadata fields in the data-raw/specvis_meta.csv file. Spectra should follow the naming convention <species>_<genus>.<integer>, where <integer> begins at 1 and proceeds from the shortest- to longest- wavelength sensitive receptor.
  • Run the function specvis_rebuild() to rebuild the database (i.e. to save the raw data as .rda files.
  • Commit and push your changes, and submit a pull request.
• via email, v1
  • Take a look at the structure of the package’s spectral data (data(specvis_spectra)) and metadata (data(specvis_meta)).
  • Email me your data in as similar a format as possible (but I’ll take anything).
• via email, v2
  • Email me a paper containing data that you’d like added (containing either lambda-max values or plotted absorbance curves, at a minimum).

Citing

If you find the package useful, please cite the original data source(s)and the spec.vis package (see citation("spec.vis") for the reference).

thomased/spec.vis documentation built on May 26, 2019, 10:36 a.m.