pavo (version 0.3-1)

coldist: Color distances

Description

Applies the visual models of Vorobyev et al. (1998) to calculate color distances with receptor noise based on relative photoreceptor densities.

Usage

coldist(vismodeldata, qcatch = c("Qi", "fi"),
    vis = c("tetra", "tri", "di"),
    noise = c("neural", "quantum"), subset = NULL,
    achro = TRUE, n1 = 1, n2 = 2, n3 = 2, n4 = 4, v = 0.1)

Arguments

vismodeldata

(required) quantum catch color data. Can be either the result from vismodel or independently calculated data (in the form of a data frame with four columns, representing the avian cones).

qcatch

if the object is of class vismodel, such as one generated using pavo, this argument is ignored. If the object is a data frame of quantal catches from another source, this argument is used to specify what type of quantum c

vis

visual system phenotype to use in the model:

• tetra: Tetrachromatic color vision (default)
• tri: Trichromatic color vision
• di: Dichromatic color vision

subset

If only some of the comparisons should be returned, a character vector of length 1 or 2 can be provided, indicating which samples are desired. The subset vector must match the labels of the imput samples, but partial matching (and regular expressi

achro

logical. If TRUE, last column of the data frame is used to calculate the achromatic contrast, with noise based on the Weber fraction calculated using n4

n1,n2,n3,n4

tetrachromatic photoreceptor densities for u, s, m & l (default to blue tit Cyanistes caeruleus densities: 1:2:2:4). If vis does not equal 'tetra', only n1 and n2 (vis='di')

v

Noise-to-signal ratio of a single cone (defaults to 0.1, so that under the default densities, the Weber fraction for the large cone will be 0.05, as estimated from behavioral experiment with the Perkin robin, Leiothrix lutea)

noise

how the noise will be calculated:

• neural: noise is proportional to the Weber fraction and is independent of the intensity of the signal received.
• quantum: noise is the sum of the neural noise and receptor no

Value

• A data frame containing 4 columns. The first two (patch1, patch2) refer to the two colors being contrasted; dS is the chromatic contrast (delta S, in JNDs) and dL is the achromatic contrast (delta L, in JNDs)

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.

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

data(sicalis)
vis.sicalis <- vismodel(sicalis, visual='avg.uv', relative=FALSE)
coldist.sicalis <- coldist(vis.sicalis, vis='tetra')