"summary"(object, subset = FALSE, wlmin = NULL, wlmax = NULL, ...)rspec,
with a column with wavelength data, named 'wl', and the remaining column containing
spectra to process.FALSE (the default), TRUE, or a character vector.
If FALSE, all variables calculated are returned. If TRUE, only a subset
of the complete ouput (composed of B2, S8 and H1; the variables described in
Andersson and Prager 2006) are returned. Finally, a user-specified string of variable
names can be used in order to filter and show only those variables.rspec object).subset = TRUE) variables described
in Montgomerie (2006) with spectra name as row names.
The colorimetric variables calculated by this function are
described in Montgomerie (2006) with corrections included in the README CLR
file from the May 2008 distribution of the CLR sofware. Authors should reference
both this package,Montgomerie (2006), and the original reference(s).
Description and notes on the measures:B1 (Total brightness): Sum of the relative reflectance over the entire spectral
range (area under the curve). Frequently used but should be discouraged because
values are difficult to compare across studies (B2 is preferred). REF 1-3, 7, 9-11,
13B2 (Mean brightness): Mean relative reflectance over the entire spectral range.
This is prefered to B1 since values are easier to compare across studies. REF 4, 12B3 (Intensity): Maximum relative reflectance (Reflectance at wavelength of maximum
reflectance). Note that may be sensitive to noise near the peak. REF 1, 5, 6S1 (Chroma): Relative contribution of a spectral range to the total brightness (B1)
S1 is arbitrarily devided in 6 measures of chroma based on the wavelength ranges
normally associated with specific hues. The values are calculated using the
following ranges: S1U (UV, if applicable): lambda min-400nm;
S1v (Violet) lambda min-415nm; S1B (Blue) 400nm-510nm; S1G (Green) 510nm-605nm;
S1Y (Yellow) 550nm-625nm; S1R (Red) 605nm-lambda max. REF 2, 7, 8, 11-13S2 (Spectral saturation): Rmax/Rmin This measure is sensitive to spectral noise.
Proper interpretation of this value may be difficult for spectra with multiple
peaks in the range of interest. REF 1S3 (Chroma): Reflectance over the Rmax +- 50nm range divided by B1. Values for peaks
within 50nm of either the minimum or maximum range of the data will not be comparable
since the area under the curve for the area of interest will not always
be based on the same wavelength range. Therefore, S3 should be interpreted
with caution for peaks in the UV or Red range. REF 11S4 (Spectral purity): |bmaxneg| , calculated by approximating the derivative
of the spectral curve. As such, it is very sensitive to noise and should only
be considered when data is adequately smoothed. NAs are returned for curves which
do not, at any range of wavelength, decrease in intensity. Therefore, reflectance
curves for brown and red surfaces, for example, should not generate a values. REF 1S5 (Chroma): Similar in design to segment classification measures (see Montgomerie 2006)
for details. REF 10S6 (Contrast): Rmax - Rmin. Because it uses both Rmin and Rmax, this measure may be
sensitive to spectral noise. REF 5, 6S7 (Spectral saturation): Relative reflectance between the area around the peak with
reflectance equal to or larger to half of that of the peak (an approximation to the
full-width at half maxima. See Montgomerie (2006) for details). Somewhat sensitive
to noise and can be misleading when more than one maxima and/or minima are present.
REF 3, 9S8 (Chroma): (Rmax - Rmin)/B2. Because it uses both Rmin and Rmax, this measure may be
sensitive to spectral noise. REF 3, 13S9 (Carotenoid chroma): (R450 - R700)/R700. Should only be used when the color
of the surface is clearly due to carotenoid pigmentation and R450 is lower than
R700. Could be sensitive to noise. REF 8S10 (Peaky chroma): (Rmax - Rmin)/B2 x |bmaxneg|. Should be used with properly
smoothed curves. REF 7H1 (Peak wavelength, hue): Wavelength of maximum reflectance. May be sensitive to noise
and may be variable if there is more than one maxima. REF 1, 2, 4, 6, 7, 10-13H2 (Hue): Wavelength at bmaxneg. Should be calculated using smoothed data. REF 2, 13H3 (Hue): Wavelength at Rmid. Sensitive to noisy spectra and may be variable if there are
more than one maxima and minima. REF 3, 9, 13H4 (Hue): Similar in design to segment classification measures see Montgomerie
(2006) for details. REF 10H5 (Hue): Wavelength at bmax. Sensitive to noise and may be variable if there is
more than one maxima and minima. REF 5
References describing variables:
1- Andersson, S. 1999. Morphology of uv reflectance in a whistling-thrush: Implications for the study of structural colour signalling in birds. Journal of Avian Biology 30:193-204.
2- Andersson, S., J. Ornborg, and M. Andersson. 1998. Ultraviolet sexual dimorphism and assortative mating in blue tits. Proceedings of the Royal Society B 265:445-450.
3- Andersson, S., S. Pryke, J. Ornborg, M. Lawes, and M. Andersson. 2002. Multiple receivers, multiple ornaments, and a trade-off between agonistic and epigamic signaling in a widowbird. American Naturalist 160:683-691.
4- Delhey, K., A. Johnsen, A. Peters, S. Andersson, and B. Kempenaers. 2003. Paternity analysis reveals opposing selection pressures on crown coloration in the blue tit (parus caeruleus). Proceedings of the Royal Society B 270:2057-2063.
5- Keyser, A. and G. Hill. 1999. Condition-dependent variation in the blue-ultraviolet coloration of a structurally based plumage ornament. Proceedings of the Royal Society B 266:771-777.
6- Keyser, A.J. and G. Hill. 2000. Structurally based plumage coloration is an honest signal of quality in male blue grosbeaks. Behavioural Ecology 11:202-209.
7- Ornborg, J., S. Andersson, S. Griffith, and B. Sheldon. 2002. Seasonal changes in a ultraviolet structural colour signal in blue tits, parus caeruleus. Biological Journal of the Linnean Society 76:237-245.
8- Peters, A., A. Denk, K. Delhey, and B. Kempenaers. 2004. Carotenoid-based bill colour as an indicator of immunocompetence and sperm performance in male mallards. Journal of Evolutionary Biology 17:1111-1120.
9- Pryke, S., M. Lawes, and S. Andersson. 2001. Agonistic carotenoid signalling in male red-collared widowbirds: Aggression related to the colour signal of both the territory owner and model intruder. Animal Behaviour 62:695-704.
10- Saks, L., K. Mcgraw, and P. Horak. 2003. How feather colour reflects its carotenoid content. Functional Ecology 17:555-561.
11- Shawkey, M., A. Estes, L. Sieffereman, and G. Hill. 2003. Nanostructure predicts intraspecific variation in ultraviolet-blue plumage colour. Proceedings of the Royal Society B 270:1455-1460.
12- Siefferman, L. and G. Hill. 2005. Uv-blue structural coloration and competition for nestboxes in male eastern bluebirds. Animal Behaviour 69:67-72.
13- Smiseth, P., J. Ornborg, S. Andersson, and T. Amundsen. 2001. Is male plumage reflectance correlated with paternal care in bluethroats? Behavioural Ecology 12:164-170.
## Not run:
# data(sicalis)
# summary(sicalis)
# summary(sicalis, subset = TRUE)
# summary(sicalis, subset = c('B1', 'H4'))
# ## End(Not run)
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