pavo (version 0.5-6)

vismodel: Visual Models

Description

Applies the visual models of Vorobyev et al. (1998) to calculate quantum catches at each photoreceptor. Relative values may also be obtained, in which case the model reduces to the color space as described in Endler & Mielke (2005) and Stoddard & Prum (2008).

Usage

vismodel(rspecdata, qcatch = c("Qi", "fi"), visual = c("avg.uv", "avg.v", "bluetit", "star", "pfowl"), achromatic = c("bt.dc", "ch.dc", "st.dc", "ml", "none"), illum = c("ideal", "bluesky", "D65", "forestshade"), vonkries = F, scale = 1, bkg = "ideal", relative = TRUE)

Arguments

rspecdata

(required) a data frame, possibly an object of class rspec that has wavelength range in the first column, named 'wl', and spectral measurements in the remaining columns.

qcatch

Which quantal catch metric to return. Options are:

• Qi: Quantum catch for each photoreceptor
• fi: Quantum catch according to Fechner law (the signal of the receptor channel is proportional to the logarithm of the quantum catch)

visual

the visual system to be used. Options are:

• a data frame such as one produced containing by sensmodel, containing sensitivity for the user-defined visual system. The data frame must contain a 'wl' column with the range of wavelengths included, and the sensitivity for each other cone as a column
• avg.uv: average avian UV system
• avg.v: average avian V system
• bluetit: Blue tit Cyanistes caeruleus visual system
• star: Starling Sturnus vulgaris visual system
• pfowl: Peafowl Pavo cristatus visual system

achromatic

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

• bt.dc: Blue tit Cyanistes caeruleus double cone
• ch.dc: Chicken Gallus gallus double cone
• st.dc: Starling Sturnus vulgaris double cone
• ml: sum of the two longest-wavelength cones
• none

illum

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

• ideal: homogeneous illuminance of 1 accross wavelengths (default)
• 'bluesky'
• 'D65': standard daylight
• 'forestshade'

vonkries

logical. Should the von Kries color 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 ($umol*s^-1*m^-2$). Useful values are, for example, 500 (for dim light) and 10000 (for bright illumination). Note that if vonkries=TRUE this transformation has no effect.

bkg

either a vector containing the background spectra, or an ideal (white) background is used (Default assumes an idealized homogeneous background).

relative

should relative quantum catches be returned (i.e. is it a color 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.

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

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.

Examples

## Not run: 
# data(sicalis)
# vis.sicalis <- vismodel(sicalis, visual='avg.uv')
# tcs.sicalis <- tcs(vis.sicalis)## End(Not run)