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photobiology  

Photobiological Calculations
View on CRAN: Click here


Download and install photobiology package within the R console
Install from CRAN:
install.packages("photobiology")

Install from Github:
library("remotes")
install_github("cran/photobiology")

Install by package version:
library("remotes")
install_version("photobiology", "0.14.1")



Attach the package and use:
library("photobiology")
Maintained by
Pedro J. Aphalo
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-02-01
Latest Update: 2025-07-31
Description:
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) .
How to cite:
Pedro J. Aphalo (2016). photobiology: Photobiological Calculations. R package version 0.14.1, https://cran.r-project.org/web/packages/photobiology. Accessed 05 Mar. 2026.
Previous versions and publish date:
0.9.4 (2016-02-01 21:11), 0.9.5 (2016-02-03 01:21), 0.9.6 (2016-04-02 23:46), 0.9.7 (2016-04-07 01:37), 0.9.8 (2016-05-19 23:28), 0.9.9 (2016-08-01 19:13), 0.9.11 (2016-09-11 14:02), 0.9.12 (2016-10-21 21:27), 0.9.13 (2016-12-18 11:23), 0.9.14 (2017-03-20 18:34), 0.9.15 (2017-04-29 19:41), 0.9.16 (2017-06-25 17:40), 0.9.17 (2017-08-27 18:21), 0.9.18-1 (2017-12-18 20:06), 0.9.19 (2018-03-05 12:29), 0.9.20 (2018-04-02 20:36), 0.9.21 (2018-06-28 07:05), 0.9.22 (2018-07-09 11:30), 0.9.23 (2018-08-30 09:50), 0.9.24 (2018-09-23 19:30), 0.9.25 (2018-12-11 07:40), 0.9.26 (2019-02-12 11:50), 0.9.27 (2019-04-25 10:40), 0.9.28 (2019-06-08 14:10), 0.9.29 (2019-09-11 09:00), 0.9.30 (2020-01-09 15:20), 0.10.0 (2020-04-02 14:20), 0.10.1 (2020-04-17 14:40), 0.10.2 (2020-04-27 15:50), 0.10.3 (2020-06-03 12:30), 0.10.4 (2020-06-07 07:40), 0.10.5 (2020-08-28 00:50), 0.10.6 (2021-04-04 18:00), 0.10.7 (2021-09-29 14:20), 0.10.8 (2021-12-08 12:50), 0.10.9 (2022-02-04 12:30), 0.10.10 (2022-03-25 17:00), 0.10.11 (2022-07-11 10:30), 0.10.12 (2022-08-05 13:50), 0.10.13 (2022-10-05 22:40), 0.10.14 (2022-10-16 02:20), 0.10.15 (2023-01-07 17:40), 0.10.16 (2023-04-02 21:30), 0.10.17 (2023-05-27 22:50), 0.11.0 (2023-10-21 02:00), 0.11.1 (2024-02-26 12:40), 0.11.2 (2024-03-31 17:30), 0.11.3 (2024-08-25 23:00), 0.11.4 (2024-11-30 14:30), 0.12.0 (2025-02-03 00:10), 0.13.0 (2025-06-07 00:10), 0.13.1 (2025-06-23 20:20), 0.13.2 (2025-08-01 01:50), 0.14.0 (2025-09-27 00:50)
Other packages that cited photobiology R package
View photobiology citation profile
Other R packages that photobiology depends, imports, suggests or enhances
Complete documentation for photobiology
Functions, R codes and Examples using the photobiology R package
Some associated functions: A.illuminant.spct . A2T . Afr2T . D2.UV586 . D2.UV653 . D2.UV654 . D2_spectrum . D65.illuminant.spct . ET_ref . FEL.BN.9101.165 . FEL_spectrum . Ler_leaf.spct . Ler_leaf_rflt.spct . Ler_leaf_trns.spct . Ler_leaf_trns_i.spct . MathFun . Rfr_fraction . Rfr_from_n . Rfr_normdiff . Rfr_ratio . T2A . T2Afr . Tfr_fraction . Tfr_normdiff . Tfr_ratio . Trig . absorbance . absorbance_spct . absorptance . absorptance_spct . adaptive_smoothing . add_attr2tb . any2T . as.calibration_mspct . as.calibration_spct . as.chroma_mspct . as.chroma_spct . as.cps_mspct . as.cps_spct . as.filter_mspct . as.filter_spct . as.generic_mspct . as.generic_spct . as.matrix-mspct . asject_mspct . asject_spct . as.raw_mspct . as.raw_spct . as.reflector_mspct . as.reflector_spct . as.response_mspct . as.response_spct . as.solar_date . as.solute_mspct . as.solute_spct . as.source_mspct . as.source_spct . as_energy . as_quantum . as_quantum_mol . as_tod . auto_hinges . average_spct . beesxyzCMF.spct . black_body.spct . c . calc_multipliers . calc_source_output . ccd.spct . checkMspctVersion . checkSpctVersion . checkTimeUnit . check_and_rename_vars . check_spct . check_spectrum . check_w.length . ciev10.spct . ciev2.spct . ciexyzCC10.spct . ciexyzCC2.spct . ciexyzCMF10.spct . ciexyzCMF2.spct . class_spct . clean . clean_spct . clear.spct . clear_body.spct . clear_photobio.cache . clip_wl . collect2mspct . color_of . compare_spct . cone_fundamentals10.spct . convertTfrType . convertThickness . convertTimeUnit . convolve_each . copy_attributes . cps2irrad . day_night . defunct . despike . diffraction_single_slit . dim.generic_mspct . div-.generic_spct . div_spectra . drop_user_cols . e2q . e2qmol_multipliers . e2quantum_multipliers . e_fluence . e_fraction . e_irrad . e_ratio . e_response . enable_check_spct . energy_as_default . energy_irradiance . energy_ratio . eq_ratio . expanse . extract . extract_mspct . f_dispatcher_spct . filter_cps.mspct . findMultipleWl . find_peaks . find_spikes . find_wls . fit_peaks . fluence . format.solar_time . format.tod_time . formatted_range . fscale . fscale_spct . fshift . fshift_spct . generic_mspct . getBSWFUsed . getFilterProperties . getHowMeasured . getIdFactor . getInstrDesc . getInstrSettings . getKType . getMspctVersion . getMultipleWl . getNormalized . getResponseType . getRfrType . getScaled . getSoluteProperties . getSpctVersion . getTfrType . getTimeUnit . getWhatMeasured . getWhenMeasured . getWhereMeasured . get_attributes . get_peaks . green_leaf.spct . head_tail . illuminance . insert_hinges . insert_spct_hinges . integrate_spct . integrate_xy . interpolate_spct . interpolate_spectrum . interpolate_wl . irrad . irrad_extraterrestrial . irradiance . is.generic_mspct . is.generic_spct . is.old_spct . is.solar_time . is.summary_generic_spct . is.waveband . isValidInstrDesc . isValidInstrSettings . is_absorbance_based . is_effective . is_mole_based . is_normalized . is_photon_based . is_scaled . is_tagged . join_mspct . julian_day . l_insert_hinges . labels . log . make_wl_consistent . max . merge2object_spct . merge_attributes . midpoint . min . minus-.generic_spct . mod-.generic_spct . msmsply . mspct_classes . na.omit . net_irradiance . normalization . normalize . normalize_range_arg . normalized_diff_ind . opaque.spct . oper_spectra . peaks . phenylalanine.spct . photobiology-package . photodiode.spct . photon_irradiance . photon_ratio . photons_energy_ratio . plus-.generic_spct . polyester.spct . pow-.generic_spct . print . print.solar_time . print.summary_generic_spct . print.tod_time . print.waveband . prod_spectra . pull_sample . q2e . q_fluence . q_fraction . q_irrad . q_ratio . q_response . qe_ratio . r4p_pkgs . range . rbindspct . reflectance . reflectance_spct . relative_AM . replace_bad_pixs . resp_spct . response . rgb_spct . rmDerivedMspct . rmDerivedSpct . round . rowwise . s_e_irrad2rgb . s_mean . s_mean_se . s_mean_se_band . s_median . s_prod . s_range . s_sd . s_se . s_sum . s_var . se.m . se . se.p . select_spct_attributes . setBSWFUsed . setFilterProperties . setGenericSpct . setHowMeasured . setIdFactor . setInstrDesc . setInstrSettings . setKType . setMultipleWl . setNormalized . setResponseType . setRfrType . setScaled . setSoluteProperties . setTfrType . setTimeUnit . setWhatMeasured . setWhenMeasured . setWhereMeasured . shared_member_class . sign . sinc . slash-.generic_spct . smooth_spct . solar_time . source_spct . spct_attr2tb . spct_classes . spct_metadata . spct_wide2long . spikes . split2mspct . split_bands . split_energy_irradiance . split_irradiance . split_photon_irradiance . stepsize . subset . subset2mspct . subt_spectra . sum_spectra . summary . summary_spct_classes . sun.daily.data . sun.daily.spct . sun.data . sun.spct . sun_angles . tag . thin_wl . times-.generic_spct . transmittance . transmittance_spct . trimInstrDesc . trimInstrSettings . trim_spct . trim_tails . trim_waveband . trim_wl . twilight2angle . two_irrads . two_reflectances . two_transmittances . tz_time_diff . uncollect2spct . untag . upgrade_spct . upgrade_spectra . using_Tfr . v_insert_hinges . v_replace_hinges . validate_geocode . valleys . verbose_as_default . w_length2rgb . w_length_range2rgb . water.spct . water_vp_sat . waveband . waveband_ratio . wb2rect_spct . wb2spct . wb2tagged_spct . wb_trim_as_default . white_body.spct . white_led.cps_spct . white_led.raw_spct . white_led.source_spct . wl2wavenumber . wls_at_target . yellow_gel.spct . 
Some associated R codes: NDxI.R . color.of.R . copy.attr.R . defunct.R . head-tail.R . join.mspct.R . leaf.data.R . led.data.R . mspct.methods.R . mspct.sample.R . na.rm.R . on-attach.R . photobio-utils.R . source-spct-fractions.R . source-spct-ratios.R . spct.absorbance.R . spct.absorptance.R . spct.conversion.R . spct.response.R . spct.spikes.R . water.vapour.R . wl-conversions.R . zmspct.classes.R .  Full photobiology package functions and examples
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