pavo (version 2.9.0)

sensmodel: Modeling spectral sensitivity

Description

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).

Usage

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

Value

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

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.)

Author

Pierre-Paul Bitton

Chad Eliason

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, tools:::Rd_expr_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, tools:::Rd_expr_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, tools:::Rd_expr_doi("10.1007/s003590050437")

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))