{ "_id": "6ab8f51c99f7aa8c6aa38ede", "Package": "luxR", "Type": "Package", "Title": "Underwater Light Analysis and Visual Ecology", "Version": "0.1.1", "Date": "2026-07-29", "Authors@R": "person(given = c(\"John\", \"D\"),\nfamily = \"Kirwan\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jkirwan+luxR@pm.me\")", "Description": "Tools for quantifying and modelling underwater light\nenvironments. Propagates spectral irradiance through the water\ncolumn via Beer-Lambert attenuation, computes\nphotosynthetically active radiation (PAR), and converts between\nenergy and photon-flux units. Provides the 'lux_spectrum' S3\nclass for unit-safe spectral arithmetic and format readers for\nTriOS RAMSES and Ocean Optics instruments. The optional\n'lightr' package parses further instrument formats into strict\nnative records; explicit measurement, scale, calibration, and\nresampling policies govern conversion via read_spectrum().\nSpectra convert to and from the generic spectral classes of the\noptional 'photobiology' package, which also serves as the\nreference implementation luxR's integration and photometry are\nvalidated against. Includes visual ecology utilities:\nGovardovskii (2000) visual-pigment templates, photoreceptor\nquantum catch, Vorobyev-Osorio colour discrimination (JND),\nSecchi depth, and explicitly unvalidated contrast-threshold\ndistance scenarios.", "License": "GPL (>= 3)", "URL": "https://johnkirwan.github.io/luxR/,\nhttps://github.com/JohnKirwan/luxR", "BugReports": "https://github.com/JohnKirwan/luxR/issues", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "8.0.0", "RdMacros": "Rdpack", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Repository": "https://johnkirwan.r-universe.dev", "Date/Publication": "2026-07-29 21:25:56 UTC", "RemoteUrl": "https://github.com/JohnKirwan/luxR", "RemoteRef": "HEAD", "RemoteSha": "75ae5c201a47cf658f3ea43bb9ef75689be01158", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-27 10:46:18 UTC", "User": "root" }, "Author": "John D Kirwan [aut, cre]", "Maintainer": "John D Kirwan ", "_user": "johnkirwan", "_type": "src", "_file": "luxR_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/2cb4696c9497c2c5a4113116a7e5989450b63db45d722a7edf630d59d3490578", "_filesize": 3093056, "_sha256": "2cb4696c9497c2c5a4113116a7e5989450b63db45d722a7edf630d59d3490578", "_expires": "2027-01-05T10:51:06.000Z", "_created": "2026-09-27T10:46:18.000Z", "_published": "2026-09-27T10:51:08.592Z", "_jobs": [ { "job": 108604124600, "time": 236, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10930405148" }, { "job": 108604124574, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10929797372" }, { "job": 108604124641, "time": 109, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10930111297" }, { "job": 108604124606, "time": 97, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10929871907" }, { "job": 108603506521, "time": 247, "config": "source", "r": "4.6.1", "check": "OK", "artifact": 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D Kirwan", "email": "jkirwan+luxr@pm.me" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "shiny", "version": ">= 1.7.0", "role": "Suggests" }, { "package": "lightr", "version": ">= 2.0.0", "role": "Suggests" }, { "package": "pavo", "version": ">= 2.9.0", "role": "Suggests" }, { "package": "photobiology", "version": ">= 0.11.0", "role": "Suggests" }, { "package": "colourvision", "version": ">= 2.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" } ], "_owner": "johnkirwan", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-30", "n": 5 }, { "week": "2026-31", "n": 5 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-07-24" }, { "name": "v0.1.1", "date": "2026-07-29" } ], "_stars": 1, "_contributors": [ { "user": "johnkirwan", "count": 24, "uuid": 3696221 } ], "_userbio": { "uuid": 3696221, "type": "user", "name": "John Kirwan", "followers": 6 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/luxR" }, "_devurl": "https://github.com/johnkirwan/luxr", "_pkgdown": "https://johnkirwan.github.io/luxR/", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/luxR.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "absorbance", "angle_of_polarization", "as_colourvision", "as_lux_spectrum", "as_reflector_spct", "as_rspec", "as_source_spct", "attenuate_depth", "attenuate_spectrum", "band_irradiance", "beam_attenuation", "broadband2spectrum", "colour_jnd", "contrast_at_distance", "convert_unit", "degree_of_polarization", "detectability", "detection_range", "fit_Kd", "fit_sensitivity", "fresnel_reflectance", "from_naples", "from_ocean_optics", "from_solar", "from_trios", "ft2m", "govardovskii_template", "inherent_contrast", "irradiance2lux", "irradiance2radiance", "jerlov_Kd", "light_at_depth", "lux_spectrum", "lux2irradiance", "m2ft", "michelson_contrast", "n2W_spec_irradiance", "par_fraction", "par_irradiance", "photic_depth", "photon2W", "plot_spectra", "polarization_contrast", "propagate_depth", "propagate_spectrum", "quantum_catch", "radiance2irradiance", "read_instrument_spectrum", "read_ocean_optics", "read_spectrum", "read_trios", "receptor_absorptance", "reflectance_to_radiance", "refracted_solar_angle", "resample_spectrum", "run_app", "scattering_angle", "scotopic_lux", "secchi_depth", "single_scattering_albedo", "snells_window", "solar_irradiance", "species_brightness", "species_LEF", "species_sensitivity_matrix", "surface_transmittance", "transmittance", "underwater_polarization", "unit_expression", "unit_label", "visual_range", "W2mol_spec_irradiance", "W2photon", "wavelength_in_medium", "weber_contrast" ], "_datasets": [ { "name": "CIE_scotopic", "title": "CIE Scotopic Luminous Efficiency Function", "object": "CIE_scotopic", "class": [ "data.frame" ], "fields": [ "lambda", "W" ], "rows": 401, "table": true, "tojson": true }, { "name": "CIE1931", "title": "CIE Photopic Luminous Efficiency Function", "object": "CIE1931", "class": [ "data.frame" ], "fields": [ "lambda", "W" ], "rows": 471, "table": true, "tojson": true }, { "name": "jerlov_types", "title": "Diffuse attenuation coefficients for Jerlov optical water types.", "object": "jerlov_types", "class": [ "data.frame" ], "fields": [ "type", "lambda", "Kd" ], "rows": 120, "table": true, "tojson": true }, { "name": "Naples", "title": "Example downwelling irradiance from Mare Chiaro, Gulf of Naples", "object": "Naples", "class": [ "data.frame" ], "fields": [ "wv", "depth_0m", "depth_5m", "depth_10m" ], "rows": 103, "table": true, "tojson": true }, { "name": "solar_spectra", "title": "ASTM G173-03 reference solar spectral irradiance.", "object": "solar_spectra", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "species_channel_support", "title": "Species visual-channel support decisions.", "object": "species_channel_support", "class": [ "data.frame" ], "fields": [ "species", "channel_role", "status", "reason", "source" ], "rows": 16, "table": true, "tojson": true }, { "name": "species_channels", "title": "Validated visual-channel memberships for selected species.", "object": "species_channels", "class": [ "data.frame" ], "fields": [ "species", "channel", "channel_role", "receptor", "weight", "is_default", "source" ], "rows": 13, "table": true, "tojson": true }, { "name": "species_sensitivities", "title": "Photoreceptor spectral sensitivities for selected species.", "object": "species_sensitivities", "class": [ "data.frame" ], "fields": [ "species", "receptor", "lambda_max", "chromophore", "channel_role", "source" ], "rows": 27, "table": true, "tojson": true } ], "_help": [ { "page": "luxR-package", "title": "luxR: Underwater Light Analysis and Visual Ecology", "topics": [ "luxR-package", "luxR" ] }, { "page": "absorbance", "title": "Absorbance (optical density) from transmittance.", "topics": [ "absorbance" ] }, { "page": "angle_of_polarization", "title": "Angle of polarization (e-vector orientation) from Stokes parameters", "topics": [ "angle_of_polarization" ] }, { "page": "as_colourvision", "title": "Convert luxR spectra to a colourvision input data frame", "topics": [ "as_colourvision", "as_colourvision.list", "as_colourvision.lux_spectrum" ] }, { "page": "as_lux_spectrum", "title": "Coerce an object to lux_spectrum", "topics": [ "as_lux_spectrum", "as_lux_spectrum.data.frame", "as_lux_spectrum.lux_instrument_spectrum", "as_lux_spectrum.lux_spectrum", "as_lux_spectrum.numeric", "as_lux_spectrum.reflector_spct", "as_lux_spectrum.rspec", "as_lux_spectrum.source_spct" ] }, { "page": "as_reflector_spct", "title": "Convert luxR reflectance to a photobiology reflector_spct", "topics": [ "as_reflector_spct", "as_reflector_spct.list", "as_reflector_spct.lux_spectrum" ] }, { "page": "as_rspec", "title": "Convert luxR spectra to a pavo 'rspec' object", "topics": [ "as_rspec", "as_rspec.list", "as_rspec.lux_spectrum" ] }, { "page": "as_source_spct", "title": "Convert luxR spectra to photobiology spectral classes", "topics": [ "as_source_spct", "as_source_spct.list", "as_source_spct.lux_spectrum" ] }, { "page": "attenuate_depth", "title": "Beer-Lambert attenuation at a single wavelength.", "topics": [ "attenuate_depth" ] }, { "page": "attenuate_spectrum", "title": "Propagate a surface spectrum through the water column.", "topics": [ "attenuate_spectrum", "attenuate_spectrum.lux_spectrum", "attenuate_spectrum.numeric" ] }, { "page": "band_irradiance", "title": "Band-integrated irradiance at one or more depths", "topics": [ "band_irradiance", "band_irradiance.lux_spectrum", "band_irradiance.numeric" ] }, { "page": "beam_attenuation", "title": "Beam attenuation coefficient from absorption and scattering.", "topics": [ "beam_attenuation" ] }, { "page": "broadband2spectrum", "title": "Convert a broadband scalar reading into a plausible spectrum.", "topics": [ "broadband2spectrum" ] }, { "page": "CIE_scotopic", "title": "CIE Scotopic Luminous Efficiency Function", "topics": [ "CIE_scotopic" ] }, { "page": "CIE1931", "title": "CIE Photopic Luminous Efficiency Function", "topics": [ "CIE1931" ] }, { "page": "colour_jnd", "title": "Chromatic distance between two illuminants (Vorobyev-Osorio model).", "topics": [ "colour_jnd" ] }, { "page": "contrast_at_distance", "title": "Heuristic scalar contrast remaining after a sighting path through water.", "topics": [ "contrast_at_distance" ] }, { "page": "convert_unit", "title": "Convert a lux_spectrum to a different unit", "topics": [ "convert_unit" ] }, { "page": "degree_of_polarization", "title": "Degree of polarization from Stokes parameters", "topics": [ "degree_of_polarization" ] }, { "page": "detectability", "title": "Object-vs-background detection summary.", "topics": [ "detectability" ] }, { "page": "detection_range", "title": "Scenario estimate of object-background threshold-crossing distance.", "topics": [ "detection_range" ] }, { "page": "fit_Kd", "title": "Estimate the diffuse attenuation coefficient from two irradiance readings.", "topics": [ "fit_Kd", "fit_Kd.lux_spectrum", "fit_Kd.numeric" ] }, { "page": "fit_sensitivity", "title": "Fit a Govardovskii visual-pigment template to measured spectral sensitivity.", "topics": [ "fit_sensitivity" ] }, { "page": "fresnel_reflectance", "title": "Fresnel reflectance at the air-water interface.", "topics": [ "fresnel_reflectance" ] }, { "page": "from_naples", "title": "Load a Naples depth spectrum as a lux_spectrum", "topics": [ "from_naples" ] }, { "page": "from_ocean_optics", "title": "Read a calibrated Ocean Optics spectrum as a lux_spectrum", "topics": [ "from_ocean_optics" ] }, { "page": "from_solar", "title": "Load a reference solar spectrum as a lux_spectrum", "topics": [ "from_solar" ] }, { "page": "from_trios", "title": "Read a TriOS RAMSES file as calibrated radiance spectra", "topics": [ "from_trios" ] }, { "page": "ft2m", "title": "Convert feet to metres.", "topics": [ "ft2m" ] }, { "page": "govardovskii_template", "title": "Govardovskii et al. (2000) visual-pigment template.", "topics": [ "govardovskii_template" ] }, { "page": "inherent_contrast", "title": "Inherent (zero-distance) contrast of an object against its background.", "topics": [ "inherent_contrast" ] }, { "page": "irradiance2lux", "title": "Provide lux values for measures of spectral irradiance.", "topics": [ "irradiance2lux", "irradiance2lux.default", "irradiance2lux.lux_spectrum", "irradiance2lux.numeric" ] }, { "page": "irradiance2radiance", "title": "Convert irradiance to radiance under a geometry assumption.", "topics": [ "irradiance2radiance" ] }, { "page": "jerlov_Kd", "title": "Diffuse attenuation coefficient for Jerlov optical water types.", "topics": [ "jerlov_Kd" ] }, { "page": "jerlov_types", "title": "Diffuse attenuation coefficients for Jerlov optical water types.", "topics": [ "jerlov_types" ] }, { "page": "light_at_depth", "title": "In-water downwelling spectral irradiance at a single depth.", "topics": [ "light_at_depth" ] }, { "page": "lux_spectrum", "title": "Create a lux_spectrum object", "topics": [ "*.lux_spectrum", "+.lux_spectrum", "-.lux_spectrum", "/.lux_spectrum", "as.data.frame.lux_spectrum", "lux_spectrum", "plot.list", "plot.lux_spectrum", "print.lux_spectrum", "summary.lux_spectrum", "[.lux_spectrum" ] }, { "page": "lux2irradiance", "title": "Distribute integrated lux across a reference spectral shape.", "topics": [ "lux2irradiance" ] }, { "page": "m2ft", "title": "Convert metres to feet.", "topics": [ "m2ft" ] }, { "page": "michelson_contrast", "title": "Michelson contrast", "topics": [ "michelson_contrast" ] }, { "page": "n2W_spec_irradiance", "title": "Convert photon-count spectral irradiance to W m^-2 nm^-1.", "topics": [ "n2W_spec_irradiance", "n2W_spec_irradiance.lux_spectrum", "n2W_spec_irradiance.numeric" ] }, { "page": "Naples", "title": "Example downwelling irradiance from Mare Chiaro, Gulf of Naples", "topics": [ "Naples" ] }, { "page": "par_fraction", "title": "Fraction of spectral irradiance in the PAR window.", "topics": [ "par_fraction", "par_fraction.lux_spectrum", "par_fraction.numeric" ] }, { "page": "par_irradiance", "title": "PAR irradiance from a spectral irradiance measurement.", "topics": [ "par_irradiance", "par_irradiance.lux_spectrum", "par_irradiance.numeric" ] }, { "page": "photic_depth", "title": "Depth at which a given fraction of surface light remains.", "topics": [ "photic_depth" ] }, { "page": "photon2W", "title": "Convert photon counts to watts at a given wavelength.", "topics": [ "photon2W" ] }, { "page": "plot_spectra", "title": "Plot a list of lux_spectrum objects as overlaid lines.", "topics": [ "plot_spectra" ] }, { "page": "polarization_contrast", "title": "Polarization contrast between a target and its background", "topics": [ "polarization_contrast" ] }, { "page": "propagate_depth", "title": "Propagate a known irradiance to any other depth (bidirectional).", "topics": [ "propagate_depth" ] }, { "page": "propagate_spectrum", "title": "Propagate a known spectrum to any other depth(s) (bidirectional).", "topics": [ "propagate_spectrum", "propagate_spectrum.lux_spectrum", "propagate_spectrum.numeric" ] }, { "page": "quantum_catch", "title": "Sensitivity-weighted photon irradiance.", "topics": [ "quantum_catch" ] }, { "page": "radiance2irradiance", "title": "Convert radiance to irradiance under a geometry assumption.", "topics": [ "radiance2irradiance" ] }, { "page": "read_instrument_spectrum", "title": "Parse one instrument spectrum with lightr", "topics": [ "read_instrument_spectrum" ] }, { "page": "read_ocean_optics", "title": "Strictly parse an Ocean Optics / Ocean Insight spectrum file", "topics": [ "read_ocean_optics" ] }, { "page": "read_spectrum", "title": "Read a declared, calibrated spectrum with lightr", "topics": [ "read_spectrum" ] }, { "page": "read_trios", "title": "Read a TriOS RAMSES spectroradiometer data file", "topics": [ "read_trios" ] }, { "page": "receptor_absorptance", "title": "Photoreceptor absorptance from a normalised absorbance template (self-screening).", "topics": [ "receptor_absorptance" ] }, { "page": "reflectance_to_radiance", "title": "Convert spectral reflectance to spectral radiance", "topics": [ "reflectance_to_radiance", "reflectance_to_radiance.lux_spectrum", "reflectance_to_radiance.numeric" ] }, { "page": "refracted_solar_angle", "title": "Refracted zenith angle of the sun beneath the surface", "topics": [ "refracted_solar_angle" ] }, { "page": "resample_spectrum", "title": "Resample a spectrum to a new wavelength grid", "topics": [ "resample_spectrum", "resample_spectrum.lux_spectrum", "resample_spectrum.numeric" ] }, { "page": "run_app", "title": "Launch the luxR Shiny explorer.", "topics": [ "run_app" ] }, { "page": "scattering_angle", "title": "Angle between a line of sight and the solar beam", "topics": [ "scattering_angle" ] }, { "page": "scotopic_lux", "title": "Compute scotopic illuminance (V'(lambda) weighting).", "topics": [ "scotopic_lux", "scotopic_lux.default", "scotopic_lux.lux_spectrum", "scotopic_lux.numeric" ] }, { "page": "secchi_depth", "title": "Secchi depth from diffuse attenuation coefficient(s).", "topics": [ "secchi_depth" ] }, { "page": "single_scattering_albedo", "title": "Single-scattering albedo.", "topics": [ "single_scattering_albedo" ] }, { "page": "snells_window", "title": "Snell's window half-angle.", "topics": [ "snells_window" ] }, { "page": "solar_irradiance", "title": "Reference solar spectral irradiance under standard conditions.", "topics": [ "solar_irradiance" ] }, { "page": "solar_spectra", "title": "ASTM G173-03 reference solar spectral irradiance.", "topics": [ "solar_spectra" ] }, { "page": "species_brightness", "title": "Per-species sensitivity-weighted photon irradiance.", "topics": [ "species_brightness" ] }, { "page": "species_channel_support", "title": "Species visual-channel support decisions.", "topics": [ "species_channel_support" ] }, { "page": "species_channels", "title": "Validated visual-channel memberships for selected species.", "topics": [ "species_channels" ] }, { "page": "species_LEF", "title": "Spectral sensitivity for a named species and photoreceptor class.", "topics": [ "species_LEF" ] }, { "page": "species_sensitivities", "title": "Photoreceptor spectral sensitivities for selected species.", "topics": [ "species_sensitivities" ] }, { "page": "species_sensitivity_matrix", "title": "Photoreceptor sensitivity matrix for colourvision", "topics": [ "species_sensitivity_matrix" ] }, { "page": "surface_transmittance", "title": "Fraction of downwelling irradiance transmitted across the water surface.", "topics": [ "surface_transmittance" ] }, { "page": "transmittance", "title": "Beer-Lambert transmittance over a path.", "topics": [ "transmittance" ] }, { "page": "underwater_polarization", "title": "Tunable Rayleigh-like approximation to underwater polarization", "topics": [ "underwater_polarization" ] }, { "page": "unit_expression", "title": "Render a unit string as a plotmath expression", "topics": [ "unit_expression" ] }, { "page": "unit_label", "title": "Render a unit string for display", "topics": [ "unit_label" ] }, { "page": "visual_range", "title": "Heuristic horizontal visual-range estimate in water.", "topics": [ "visual_range" ] }, { "page": "W2mol_spec_irradiance", "title": "Convert energy spectral irradiance to molar photon flux.", "topics": [ "W2mol_spec_irradiance", "W2mol_spec_irradiance.lux_spectrum", "W2mol_spec_irradiance.numeric" ] }, { "page": "W2photon", "title": "Convert watts to photon counts at a given wavelength.", "topics": [ "W2photon" ] }, { "page": "wavelength_in_medium", "title": "Wavelength of light inside an optical medium.", "topics": [ "wavelength_in_medium" ] }, { "page": "weber_contrast", "title": "Weber contrast", "topics": [ "weber_contrast" ] } ], "_pkglogo": "https://github.com/JohnKirwan/luxR/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/JohnKirwan/luxR/raw/HEAD/README.md", 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