vismodel {pavo}R Documentation

Visual models

Description

Calculates quantum catches at each photoreceptor. Both raw and relative values can be returned, for use in a suite of colourspace and non-colourspace models.

Usage

vismodel(
  rspecdata,
  visual = c("avg.uv", "avg.v", "bluetit", "ctenophorus", "star", "pfowl", "apis",
    "canis", "cie2", "cie10", "musca", "drosophila", "segment", "habronattus",
    "rhinecanthus"),
  achromatic = c("none", "bt.dc", "ch.dc", "st.dc", "md.r1", "dm.r1", "ra.dc", "cf.r",
    "ml", "l", "all"),
  illum = c("ideal", "bluesky", "D65", "forestshade"),
  trans = c("ideal", "bluetit", "blackbird"),
  qcatch = c("Qi", "fi", "Ei"),
  bkg = c("ideal", "green"),
  vonkries = FALSE,
  scale = 1,
  relative = TRUE
)

Arguments

rspecdata

(required) a data frame, possibly of class rspec, which contains a column containing a wavelength range, named 'wl', and spectra data in remaining columns.

visual

the visual system to be used. Options are:

  • a data frame such as one produced containing by sensmodel(), containing user-defined sensitivity data for the receptors involved in colour vision. The data frame must contain a 'wl' column with the range of wavelengths included, and the sensitivity for each other cone as a column.

  • 'apis': Honeybee Apis mellifera.

  • 'avg.uv': average avian UV system (default).

  • 'avg.v': average avian V system.

  • 'bluetit': Blue tit Cyanistes caeruleus.

  • 'canis': Canid Canis familiaris.

  • 'cie2': 2-degree colour matching functions for CIE models of human colour vision. Functions are linear transformations of the 2-degree cone fundamentals of Stockman & Sharpe (2000), as ratified by the CIE (2006).

  • 'cie10': 10-degree colour matching functions for CIE models of human colour vision. Functions are linear transformations of the 10-degree cone fundamentals of Stockman & Sharpe (2000), as ratified by the CIE (2006).

  • 'ctenophorus': Ornate dragon lizard Ctenophorus ornatus.

  • 'musca': Housefly Musca domestica.

  • 'drosophila': Vinegar fly Drosophila melanogaster (Sharkey et al. 2020).

  • 'pfowl': Peafowl Pavo cristatus.

  • 'segment': Generic tetrachromat 'viewer' for use in the segment analysis of Endler (1990).

  • 'star': Starling Sturnus vulgaris.

  • 'habronattus': Jumping spider Habronattus pyrrithrix.

  • 'rhinecanthus': Triggerfish Rhinecanthus aculeatus.

achromatic

the sensitivity data to be used to calculate luminance (achromatic) receptor stimulation. Either a vector containing the sensitivity for a single receptor, or one of the options:

  • 'none': no achromatic stimulation calculated (default).

  • 'bt.dc': Blue tit Cyanistes caeruleus double cone.

  • 'ch.dc': Chicken Gallus gallus double cone.

  • 'st.dc': Starling Sturnus vulgaris double cone.

  • 'md.r1': Housefly Musca domestica R1-6 photoreceptor.

  • 'dm.r1': Vinegar fly Drosophila melanogaster R1-6 photoreceptor.

  • 'ra.dc': Triggerfish Rhinecanthus aculeatus double cone.

  • 'cf.r': Canid Canis familiaris cone.

  • 'ml': the summed response of the two longest-wavelength photoreceptors.

  • 'l': the longest-wavelength photoreceptor.

  • 'all': the summed response of all photoreceptors.

illum

either a vector containing the illuminant, or one of the options:

  • 'ideal': homogeneous illuminance of 1 across wavelengths (default)

  • 'bluesky' open blue sky.

  • 'D65': standard daylight.

  • 'forestshade' forest shade.

trans

either a vector containing the ocular or environmental transmission spectra, or one of the options:

  • 'ideal': homogeneous transmission of 1 across all wavelengths (default)

  • 'bluetit': blue tit Cyanistes caeruleus ocular transmission (from Hart et al. 2000).

  • 'blackbird': blackbird Turdus merula ocular transmission (from Hart et al. 2000).

qcatch

Which quantal catch metric to return. Options are:

  • 'Qi': Quantum catch for each photoreceptor (default)

  • 'fi': Quantum catch according to Fechner's law (the signal of the receptor channel is proportional to the logarithm of the quantum catch)

  • 'Ei': Hyperbolic-transformed quantum catch, where Ei = Qi / (Qi + 1).

bkg

background spectrum. Note that this will have no effect when vonkries = FALSE. Either a vector containing the spectral data, or one of the options:

  • 'ideal': homogeneous illuminance of 1 across all wavelengths (default).

  • 'green': green foliage.

vonkries

logical. Should the von Kries colour correction transformation be applied? (defaults to FALSE).

scale

a value by which the illuminant will be multiplied. Useful for when the illuminant is a relative value (i.e. transformed to a maximum of 1 or to a percentage), and does not correspond to quantum flux units (μmol.s-1.m-2). Useful values are, for example, 500 (for dim light) and 10000 (for bright illumination). Note that if vonkries = TRUE this transformation has no effect.

relative

should relative quantum catches be returned (i.e. is it a colour space model? Defaults to TRUE).

Value

An object of class vismodel containing the photon catches for each of the photoreceptors considered. Information on the parameters used in the calculation are also stored and can be called using the summary.vismodel() function.

Note

Built-in visual, achromatic, illum, bkg and trans are only defined on the 300 to 700nm wavelength range. If you wish to work outside this range, you will need to provide your own data.

Author(s)

Thomas E. White thomas.white026@gmail.com

Rafael Maia rm72@zips.uakron.edu

References

Vorobyev, M., Osorio, D., Bennett, A., Marshall, N., & Cuthill, I. (1998). Tetrachromacy, oil droplets and bird plumage colours. Journal Of Comparative Physiology A-Neuroethology Sensory Neural And Behavioral Physiology, 183(5), 621-633.

Hart, N. S., Partridge, J. C., Cuthill, I. C., Bennett, A. T. D. (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.). Journal of Comparative Physiology A, 186, 375-387.

Hart, N. S. (2001). The visual ecology of avian photoreceptors. Progress In Retinal And Eye Research, 20(5), 675-703.

Barbour H. R., Archer, M. A., Hart, N. S., Thomas, N., Dunlop, S. A., Beazley, L. D, Shand, J. (2002). Retinal characteristics of the Ornate Dragon Lizard, Ctenophorus ornatus.

Stoddard, M. C., & Prum, R. O. (2008). Evolution of avian plumage color in a tetrahedral color space: A phylogenetic analysis of new world buntings. The American Naturalist, 171(6), 755-776.

Endler, J. A., & Mielke, P. (2005). Comparing entire colour patterns as birds see them. Biological Journal Of The Linnean Society, 86(4), 405-431.

Chittka L. (1992). The colour hexagon: a chromaticity diagram based on photoreceptor excitations as a generalized representation of colour opponency. Journal of Comparative Physiology A, 170(5), 533-543.

Stockman, A., & Sharpe, L. T. (2000). Spectral sensitivities of the middle- and long-wavelength sensitive cones derived from measurements in observers of known genotype. Vision Research, 40, 1711-1737.

CIE (2006). Fundamental chromaticity diagram with physiological axes. Parts 1 and 2. Technical Report 170-1. Vienna: Central Bureau of the Commission Internationale de l' Eclairage.

Neitz, J., Geist, T., Jacobs, G.H. (1989) Color vision in the dog. Visual Neuroscience, 3, 119-125.

Sharkey, C. R., Blanco, J., Leibowitz, M. M., Pinto-Benito, D., & Wardill, T. J. (2020). The spectral sensitivity of Drosophila photoreceptors. Scientific reports, 10(1), 1-13.

See Also

sensdata() to retrieve or plot in-built spectral sensitivity data used in vismodel()

Examples

# Dichromat (dingo)
data(flowers)
vis.dingo <- vismodel(flowers, visual = "canis")
di.dingo <- colspace(vis.dingo, space = "di")

# Trichromat (honeybee)
data(flowers)
vis.bee <- vismodel(flowers, visual = "apis")
tri.bee <- colspace(vis.bee, space = "tri")

# Tetrachromat (blue tit)
data(sicalis)
vis.bluetit <- vismodel(sicalis, visual = "bluetit")
tcs.bluetit <- colspace(vis.bluetit, space = "tcs")

# Tetrachromat (starling), receptor-noise model
data(sicalis)
vis.star <- vismodel(sicalis, visual = "star", achromatic = "bt.dc", relative = FALSE)
dist.star <- coldist(vis.star, achromatic = TRUE)

# Estimate quantum catches using a custom trichromatic visual phenotype
custom <- sensmodel(c(330, 440, 550))
names(custom) <- c("wl", "s", "m", "l")
vis.custom <- vismodel(flowers, visual = custom)
tri.custom <- colspace(vis.custom, space = "tri")
[Package pavo version 2.9.0 Index]