Modeling spectral sensitivity — sensmodel • pavo

Models spectral sensitivity (with oil droplets; optional) based on peak cone sensitivity according to the models of Govardovskii et al. (2000) and Hart & Vorobyev (2005).

sensmodel(
  peaksens,
  range = c(300, 700),
  lambdacut = NULL,
  Bmid = NULL,
  oiltype = NULL,
  beta = TRUE,
  om = NULL,
  integrate = TRUE,
  sensnames = NULL
)

Arguments

peaksens	(required) a vector with peak sensitivities for the cones to model.
range	a vector of length 2 for the range over which to calculate the spectral sensitivities (defaults to 300nm to 700nm).
lambdacut	a vector of same length as peaksens that lists the cut-off wavelength value for oil droplets. Needs either `Bmid` or `oiltype` to also be entered. See Hart and Vorobyev (2005).
Bmid	a vector of same length as peaksens that lists the gradient of line tangent to the absorbance spectrum of the oil droplets. See Hart and Vorobyev (2005).
oiltype	a list of same length as peaksens that lists the oil droplet types (currently accepts only "T", C", "Y", "R", "P") when Bmid is not known. Calculates Bmid based on the regression equations found in Hart ad Vorobyev (2005).
beta	logical. If `TRUE` the sensitivities will include the beta peak See Govardovskii et al.(2000) (defaults to `TRUE`).
om	a vector of same length as `range1`-`range2` that contains ocular media transmission data. If included, cone sensitivity will be corrected for ocular media transmission. Currently accepts "bird" using values from Hart et al. (2005), or user-defined values.
integrate	logical. If `TRUE`, each curve is transformed to have a total area under the curve of 1 (best for visual models; defaults to `TRUE`). NOTE: integration is applied before any effects of ocular media are considered, for compatibility with visual model procedures.
sensnames	A vector equal in length to `peaksens`, specifying custom names for the resulting sensitivity curves (e.g. c('s', 'm', 'l') for short-, medium- and long-wavelength sensitive receptors.)

Value

A data frame of class rspec containing each cone model as a column.

References

Govardovskii VI, Fyhrquist N, Reuter T, Kuzmin DG and Donner K. 2000. In search of the visual pigment template. Visual Neuroscience 17:509-528, doi: 10.1017/S0952523800174036

Hart NS, and Vorobyev M. 2005. Modeling oil droplet absorption spectra and spectral sensitivities of bird cone photoreceptors. Journal of Comparative Physiology A. 191: 381-392, doi: 10.1007/s00359-004-0595-3

Hart NS, Partridge JC, Cuthill IC, Bennett AT (2000) Visual pigments, oil droplets, ocular media and cone photoreceptor distribution in two species of passerine bird: the blue tit (Parus caeruleus L.) and the blackbird (Turdus merula L.). J Comp Physiol A 186:375-387, doi: 10.1007/s003590050437

Author

Pierre-Paul Bitton bittonp@uwindsor.ca

Chad Eliason cme16@zips.uakron.edu

Examples

# Blue tit visual system based on Hart et al (2000)
bluesens <- sensmodel(c(371, 448, 502, 563),
  beta = FALSE,
  lambdacut = c(330, 413, 507, 572),
  oiltype = c("T", "C", "Y", "R"), om = TRUE
)

# Danio aequipinnatus based on Govardovskii et al. (2000)
daniosens <- sensmodel(c(357, 411, 477, 569))