Package index • luxR

Package & app

Package overview and the interactive Shiny explorer.

luxR-package luxR: luxR: Underwater Light Analysis and Visual Ecology
run_app(): Launch the luxR Shiny explorer.

Unit conversions

Convert between radiometric and photometric quantities.

photon2W(): Convert photon counts to watts at a given wavelength.
W2photon(): Convert watts to photon counts at a given wavelength.
n2W_spec_irradiance(): Convert photon-count spectral irradiance to Watts/m^2/nm.
W2mol_spec_irradiance(): Convert energy spectral irradiance to molar photon flux.
reflectance_to_radiance(): Convert spectral reflectance to spectral radiance
wavelength_in_medium(): Wavelength of light inside an optical medium.
ft2m(): Convert feet to metres.
m2ft(): Convert metres to feet.

Photometric quantities

Compute illuminance and PAR from spectral irradiance.

irradiance2lux(): Provide lux values for measures of spectral irradiance.
scotopic_lux(): Compute scotopic illuminance (V'(lambda) weighting).
lux2irradiance(): Distribute integrated lux across a reference spectral shape.
broadband2spectrum(): Convert a broadband scalar reading into a plausible spectrum.
par_irradiance(): PAR irradiance from a spectral irradiance measurement.
par_fraction(): Fraction of spectral irradiance in the PAR window.

Spectral data sources

Accessors for bundled reference spectra and field data import. lux_spectrum-returning wrappers (from_naples, from_solar, from_trios, from_ocean_optics) are listed under Spectral abstraction.

solar_irradiance(): Reference solar spectral irradiance under standard conditions.
read_trios(): Read a TriOS RAMSES spectroradiometer data file
read_ocean_optics(): Strictly parse an Ocean Optics / Ocean Insight spectrum file
read_instrument_spectrum(): Parse one instrument spectrum with lightr
read_spectrum(): Read a declared, calibrated spectrum with lightr

Depth propagation

Beer-Lambert attenuation through the water column.

attenuate_spectrum(): Propagate a surface spectrum through the water column.
attenuate_depth(): Beer-Lambert attenuation at a single wavelength.
propagate_depth(): Propagate a known irradiance to any other depth (bidirectional).
propagate_spectrum(): Propagate a known spectrum to any other depth(s) (bidirectional).
band_irradiance(): Band-integrated irradiance at one or more depths
photic_depth(): Depth at which a given fraction of surface light remains.
fit_Kd(): Estimate the diffuse attenuation coefficient from two irradiance readings.
jerlov_Kd(): Diffuse attenuation coefficient for Jerlov optical water types.
light_at_depth(): In-water downwelling spectral irradiance at a single depth.

Optical visibility

Secchi depth, diver/camera visual range, image contrast, and object-vs-background detection.

secchi_depth(): Secchi depth from diffuse attenuation coefficient(s).
visual_range(): Heuristic horizontal visual-range estimate in water.
michelson_contrast(): Michelson contrast
weber_contrast(): Weber contrast
inherent_contrast(): Inherent (zero-distance) contrast of an object against its background.
contrast_at_distance(): Heuristic scalar contrast remaining after a sighting path through water.
detection_range(): Scenario estimate of object-background threshold-crossing distance.
detectability(): Object-vs-background detection summary.

Inherent optical properties & interface

Beam attenuation, Beer-Lambert transmittance/absorbance, and the air-water boundary.

beam_attenuation(): Beam attenuation coefficient from absorption and scattering.
single_scattering_albedo(): Single-scattering albedo.
transmittance(): Beer-Lambert transmittance over a path.
absorbance(): Absorbance (optical density) from transmittance.
snells_window(): Snell's window half-angle.
fresnel_reflectance(): Fresnel reflectance at the air-water interface.
surface_transmittance(): Fraction of downwelling irradiance transmitted across the water surface.

Polarization

Linear polarization of the underwater light field (single-scattering model) and Stokes-parameter descriptors.

underwater_polarization(): Tunable Rayleigh-like approximation to underwater polarization
polarization_contrast(): Polarization contrast between a target and its background
degree_of_polarization(): Degree of polarization from Stokes parameters
angle_of_polarization(): Angle of polarization (e-vector orientation) from Stokes parameters
scattering_angle(): Angle between a line of sight and the solar beam
refracted_solar_angle(): Refracted zenith angle of the sun beneath the surface

Species perception

Visual pigment templates, quantum catch, and colour discrimination.

govardovskii_template(): Govardovskii et al. (2000) visual-pigment template.
receptor_absorptance(): Photoreceptor absorptance from a normalised absorbance template (self-screening).
fit_sensitivity(): Fit a Govardovskii visual-pigment template to measured spectral sensitivity.
species_LEF(): Spectral sensitivity for a named species and photoreceptor class.
quantum_catch(): Sensitivity-weighted photon irradiance.
species_brightness(): Per-species sensitivity-weighted photon irradiance.
colour_jnd(): Chromatic distance between two illuminants (Vorobyev-Osorio model).
species_sensitivity_matrix(): Photoreceptor sensitivity matrix for colourvision

Geometry

Radiance/irradiance conversion with solid-angle geometry.

irradiance2radiance(): Convert irradiance to radiance under a geometry assumption.
radiance2irradiance(): Convert radiance to irradiance under a geometry assumption.

Datasets

Reference data bundled with the package.

CIE1931: CIE Photopic Luminous Efficiency Function
CIE_scotopic: CIE Scotopic Luminous Efficiency Function
Naples: Example downwelling irradiance from Mare Chiaro, Gulf of Naples
jerlov_types: Diffuse attenuation coefficients for Jerlov optical water types.
solar_spectra: ASTM G173-03 reference solar spectral irradiance.
species_sensitivities: Photoreceptor spectral sensitivities for selected species.
species_channels: Validated visual-channel memberships for selected species.
species_channel_support: Species visual-channel support decisions.

Spectral abstraction

lux_spectrum S3 class, coercers, format readers, and unit conversion.

lux_spectrum(): Create a lux_spectrum object
as_lux_spectrum(): Coerce an object to lux_spectrum
as_rspec(): Convert luxR spectra to a pavo rspec object
as_colourvision(): Convert luxR spectra to a colourvision input data frame
as_source_spct(): Convert luxR spectra to photobiology spectral classes
as_reflector_spct(): Convert luxR reflectance to a photobiology reflector_spct
convert_unit(): Convert a lux_spectrum to a different unit
resample_spectrum(): Resample a spectrum to a new wavelength grid
plot_spectra(): Plot a list of lux_spectrum objects as overlaid lines.
from_naples(): Load a Naples depth spectrum as a lux_spectrum
from_solar(): Load a reference solar spectrum as a lux_spectrum
from_trios(): Read a TriOS RAMSES file as calibrated radiance spectra
from_ocean_optics(): Read a calibrated Ocean Optics spectrum as a lux_spectrum