pavo (version 2.9.0)

simulate_spec: Simulate a spectrum

Description

Simulate a naturalistic reflectance, radiance, irradiance, or transmission spectrum. Curves may have sigmoidal (s-shaped) and/or Gaussian (bell-shaped) features. Multiple Gaussian and sigmoidal curves can be combined in a single spectrum, to simulate more complex spectral functions.

Usage

simulate_spec(
  wl_inflect = NULL,
  wl_peak = NULL,
  width_sig = 20,
  width_gauss = 70,
  skew_gauss = 0,
  xlim = c(300, 700),
  ylim = c(0, 100)
)

Value

An object of class rspec.

Arguments

wl_inflect

A numeric vector specifying the wavelength location (in nm) for one or more inflection point(s) for a 'sigmoid' shaped curve, if desired.

wl_peak

A numeric vector specifying the wavelength location (in nm) for one or more inflection point(s) for a 'Gaussian' (or 'bell') shaped curve, if desired.

width_sig

A numeric value or vector (if multiple wl_inflect values are specified) specifying the steepness of the change, for any sigmoidal curve(s). Required when wl_peak is specified. Defaults to 20 nm.

width_gauss

A numeric value or vector specifying the the full-width at half-maximum of any Gaussian curve(s). Required when wl_peak is specified. Defaults to 70 nm.

skew_gauss

Skewness parameter for controlling the direction and magnitude of skew, when simulating for Gaussian curves (ignored when simulating only sigmoidal curves). Curves will have no skew when skew_gauss = 0 (default), right skew when skew_gauss > 0, and left skew when skew_gauss < 0. The parameter corresponds to 'alpha' in the the skew-normal distribution (Azzalini 1985).

xlim

A vector specifying the wavelength range of the simulated spectra. Defaults to 300-700nm (c(300, 700)).

ylim

A vector specifying the minimum and maximum reflectance values of the resulting curve. Defaults to 0 - 100 % (c(0, 100)). Note: sigmoidal curves, by default, move from low to high reflectance. But if high-to-low sigmoidal curves are desired this can be controlled by the ordering of the values given to ylim(). E.g. c(0, 100) will generate a low-to-high sigmoidal curve, whereas c(100, 0) will generate a high- to-low curve. The ordering of values has no effect on the Gaussian portions of the final curve.

Author

Thomas White

Hugo Gruson

References

Azzalini A (1985). A class of distributions which includes the normal ones. Scan. J. Stat. 171-178.

Examples

# Single ideal 'grey' reflectance spectrum, with 50% reflectance across 300 - 700 nm.
reflect0 <- simulate_spec(ylim = c(0, 50))

# Single sigmoidal spectrum, with a low-to-high inflection at 550 nm.
reflect1 <- simulate_spec(wl_inflect = 550)

# Single Gaussian spectrum, with a peak at 400 nm
reflect2 <- simulate_spec(wl_peak = 400)

# Combination of both Gaussian (with peak at 340 nm) and sigmoidal (with inflection
# at 560 nm)
reflect3 <- simulate_spec(wl_inflect = 560, wl_peak = 340)

# Double-Gaussian peaks of differing widths
reflect4 <- simulate_spec(wl_peak = c(340, 560), width_gauss = c(12, 40))

# Complex spectrum with single sigmoidal peak and multi-Gaussian peaks
reflect5 <- simulate_spec(wl_inflect = 575, wl_peak = c(340, 430), width_gauss = c(20, 60))

# Simulate a set of Gaussian reflectance curves with peaks varying between 400-600nm
# in increments of 10, then combine into a single rspec object, and plot the result
peaks <- seq(400, 600, 10)  # Peak locations
reflectances <- lapply(seq_along(peaks), function(x) simulate_spec(wl_peak = peaks[x]))  # Simulate
reflectances <- Reduce(merge, reflectances)  # Combine
plot(reflectances)  # Plot

# Simulate a set of Gaussian reflectance curves with a single peak at 500 nm, but
# with maximum reflectance varying from 30 to 90% in 10% increments, then combine
# into a single rspec object, and plot the result
ymax <- lapply(seq(30, 90, 10), function(x) c(0, x))  # Varying reflectance maxima
reflectances2 <- lapply(ymax, function(x) simulate_spec(wl_peak = 500, ylim = x))  # Simulate
reflectances2 <- Reduce(merge, reflectances2)  # Combine
plot(reflectances2)  # Plot

# To simulate non-reflectance spectra (like irradiances or radiances), it's often useful
# to explore more 'extreme' parameters. Here's a simple example which simulates
# natural daylight, as represented by the D65 standard daylight spectrum.
D65_real <- procspec(sensdata(illum = 'D65'), opt = 'smooth')  # Official D65 daylight spectrum
D65_sim <- simulate_spec(wl_peak = 400,
                         width_gauss = 1300,
                         skew_gauss = 10,
                         ylim = c(0, 1))  # Simulated D65
cor.test(D65_real$D65, D65_sim$spec_p400)  # >0.99 correlation
plot(merge(D65_real, D65_sim), lty = 1:2, ylab = 'Irradiance (%)')  # Merge and plot the two spectra