Package: photobiology 0.11.2

photobiology: Photobiological Calculations

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) <doi:10.19232/uv4pb.2015.1.14>.

Authors:Pedro J. Aphalo [aut, cre], Titta K. Kotilainen [ctb], Glenn Davis [ctb], Agnese Fazio [ctb]

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photobiology.pdf |photobiology.html
photobiology/json (API)
NEWS

# Install 'photobiology' in R:
install.packages('photobiology', repos = c('https://aphalo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/aphalo/photobiology/issues

Datasets:

On CRAN:

lightphotobiologyquantificationr4photobiology-suiteradiationspectrasun-position

453 exports 3 stars 3.03 score 29 dependencies 11 dependents 921 downloads

Last updated 4 months agofrom:81938f83a4

Exports:A_as_defaultA2Tabsorbanceabsorptanceadd_attr2tbaddress2tbAfr_as_defaultAfr2Tany2Aany2Afrany2Tas_energyas_quantumas_quantum_molas_todas.calibration_mspctas.calibration_spctas.chroma_mspctas.chroma_spctas.cps_mspctas.cps_spctas.filter_mspctas.filter_spctas.generic_mspctas.generic_spctas.object_mspctas.object_spctas.raw_mspctas.raw_spctas.reflector_mspctas.reflector_spctas.response_mspctas.response_spctas.solar_dateas.solute_mspctas.solute_spctas.source_mspctas.source_spctaverage_spctBSWF_used2tbcalc_filter_multiplierscalc_multiplierscalc_source_outputcalibration_mspctcalibration_spctcheck_spctcheck_spectrumcheckTimeUnitchroma_mspctchroma_spctclass_spctcleanclear_photobio.cacheclip_wlcollect2mspctcolorcolor_ofcolour_ofcomment2tbcompare_spctconvertTfrTypeconvertThicknessconvertTimeUnitconvolve_eachcopy_attributescps_mspctcps_spctcps2irradcps2Rfrcps2TfrD2_spectrumday_lengthday_nightdespikediffraction_double_slitdiffraction_single_slitdisable_check_spctdistance_to_sundiv_spectradrop_user_colse_fluencee_fractione_irrade_ratioe_responsee2qe2qmol_multiplierse2quantum_multipliersenable_check_spctenergy_as_defaultenergy_irradianceenergy_ratioenergy2wleq_ratioET_refET_ref_dayexpanseextend2extremesf_mspctfast_color_of_wbfast_color_of_wlfast_wb2rect_spctFEL_spectrumfilter_mspctfilter_propertiesfilter_properties<-filter_properties2tbfilter_spctfind_peaksfind_spikesfind_wlsfit_peaksfit_valleysfluenceformatted_rangefrequency2wlfscalefshiftgeneric_mspctgeneric_spctgeocode2tbget_attributesget_peaksget_valleysgetAfrTypegetBSWFUsedgetFilterPropertiesgetHowMeasuredgetIdFactorgetInstrDescgetInstrSettingsgetKTypegetMspctVersiongetMultipleWlgetNormalisationgetNormalisedgetNormalizationgetNormalizedgetResponseTypegetRfrTypegetScaledgetScalinggetSolutePropertiesgetSpctVersiongetTfrTypegetTimeUnitgetWhatMeasuredgetWhenMeasuredgetWhereMeasuredhead_tailhow_measuredhow_measured<-how_measured2tbilluminanceinsert_hingesinsert_spct_hingesinstr_desc2tbinstr_settings2tbintegrate_spctintegrate_xyinterpolate_mspctinterpolate_spctinterpolate_spectruminterpolate_wlirradirrad_extraterrestrialirradianceis_absorbance_basedis_absorptance_basedis_daytimeis_effectiveis_energy_basedis_mole_basedis_normalisedis_normalizedis_photon_basedis_scaledis_taggedis_transmittance_basedis_valid_geocodeis.any_mspctis.any_spctis.any_summary_spctis.calibration_mspctis.calibration_spctis.chroma_mspctis.chroma_spctis.cps_mspctis.cps_spctis.filter_mspctis.filter_spctis.generic_mspctis.generic_spctis.object_mspctis.object_spctis.old_spctis.raw_mspctis.raw_spctis.reflector_mspctis.reflector_spctis.response_mspctis.response_spctis.solar_dateis.solar_timeis.solute_mspctis.solute_spctis.source_mspctis.source_spctis.summary_chroma_spctis.summary_cps_spctis.summary_filter_spctis.summary_generic_spctis.summary_object_spctis.summary_raw_spctis.summary_reflector_spctis.summary_response_spctis.summary_solute_spctis.summary_source_spctis.wavebandisValidInstrDescisValidInstrSettingsjoin_mspctlat2tblength_geocodelon2tblonlat2tbmat2mspctmerge_attributesmerge2object_spctmidpointmsaplymsdplymslplymsmsplymspct_classesmspct2matmutate_mspctna_geocodeNDxInet_irradiancenew_wavebandnight_lengthnoon_timenormalisenormalised_diff_indnormalizationnormalizenormalize_range_argnormalized_diff_indnormalized2tbobject_mspctobject_spctoper_spectrapeaksphoton_as_defaultphoton_irradiancephoton_ratiophotons_energy_ratioprod_spectrapsychrometric_constantpull_sampleq_fluenceq_fractionq_irradq_ratioq_responseq2eqe_ratioquantum_as_defaultraw_mspctraw_spctrbindspctreflectancereflector_mspctreflector_spctrelative_AMreplace_bad_pixsresponseresponse_mspctresponse_spctRfr_fractionRfr_from_nRfr_normdiffRfr_p_from_nRfr_ratioRfr_s_from_nRfr_type2tbrgb_spctrmDerivedMspctrmDerivedSpctrowwise_responserowwise_sources_e_irrad2rgbs_means_mean_ses_mean_se_bands_medians_prods_ranges_sds_ses_sums_varsample_mspctsample_spctscaled2tbselect_spct_attributesset_check_spctsetAfrTypesetBSWFUsedsetCalibrationSpctsetChromaSpctsetCpsSpctsetFilterPropertiessetFilterSpctsetGenericSpctsetHowMeasuredsetIdFactorsetInstrDescsetInstrSettingssetKTypesetMultipleWlsetNormalisedsetNormalizedsetObjectSpctsetRawSpctsetReflectorSpctsetResponseSpctsetResponseTypesetRfrTypesetScaledsetSolutePropertiessetSoluteSpctsetSourceSpctsetTfrTypesetTimeUnitsetWhatMeasuredsetWhenMeasuredsetWhereMeasuredshared_member_classsmooth_spctsolar_timesolute_mspctsolute_propertiessolute_properties<-solute_spctsource_mspctsource_spctspct_attr2tbspct_attributesspct_classesspct_metadataspct_wide2longspikessplit_bandssplit_energy_irradiancesplit_irradiancesplit_photon_irradiancesplit2calibration_mspctsplit2cps_mspctsplit2filter_mspctsplit2mspctsplit2raw_mspctsplit2reflector_mspctsplit2response_mspctsplit2solute_mspctsplit2source_mspctspreadstepsizestrict_range_as_defaultsubset2mspctsubt_spectrasum_spectrasummary_spct_classessun_anglessun_azimuthsun_elevationsun_zenith_anglesunrise_timesunset_timeT2AT2AfrT2TtagTfr_as_defaultTfr_fractionTfr_normdiffTfr_ratioTfr_type2tbthin_wltime_unit2tbtransmittancetrim_mspcttrim_spcttrim_tailstrim_wavebandtrim_wltrim2overlaptrimInstrDesctrimInstrSettingstz_time_diffuncollect2spctunset_filter_qty_defaultunset_radiation_unit_defaultunset_user_defaultsuntagupgrade_spctupgrade_spectrause_cached_mult_as_defaultusing_Ausing_Afrusing_energyusing_photonusing_quantumusing_Tfrvalidate_geocodevalleysverbose_as_defaultw_length_range2rgbw_length2rgbwater_dpwater_fpwater_mvc2vpwater_RH2vpwater_vp_satwater_vp_sat_slopewater_vp2mvcwater_vp2RHwavebandwaveband_ratiowavenumber2wlwb_trim_as_defaultwb2rect_spctwb2spctwb2tagged_spctwhat_measuredwhat_measured<-what_measured2tbwhen_measuredwhen_measured<-when_measured2tbwhere_measuredwhere_measured<-wl_expansewl_maxwl_midpointwl_minwl_rangewl_stepsizewl2energywl2frequencywl2wavenumberwls_at_target

Dependencies:clicpp11dplyrfansigenericsgluelatticelifecyclelubridatemagrittrpillarpkgconfigplyrpolynompurrrR6Rcpprlangsplus2Rstringistringrtibbletidyrtidyselecttimechangeutf8vctrswithrzoo

User Guide: 0 The R for Photobiology Suite

Rendered fromuserguide-0-r4p-introduction.Rmdusingknitr::rmarkdownon Jun 29 2024.

Last update: 2023-04-02
Started: 2022-07-10

User Guide: 1 Radiation

Rendered fromuserguide-1-radiation.Rmdusingknitr::rmarkdownon Jun 29 2024.

Last update: 2024-02-21
Started: 2021-01-15

User Guide: 2 Astronomy and Atmosphere

Rendered fromuserguide-2-astronomy.Rmdusingknitr::rmarkdownon Jun 29 2024.

Last update: 2022-07-18
Started: 2021-01-15

Readme and manuals

Help Manual

Help pageTopics
photobiology: Photobiological Calculationsphotobiology-package photobiology
Arithmetic Operators^.generic_spct
CIE A illuminant dataA.illuminant.spct
Convert absorbance into transmittanceA2T A2T.default A2T.filter_mspct A2T.filter_spct A2T.numeric
Absorbanceabsorbance absorbance.default absorbance.filter_mspct absorbance.filter_spct absorbance.object_mspct absorbance.object_spct
Absorptanceabsorptance absorptance.default absorptance.filter_mspct absorptance.filter_spct absorptance.object_mspct absorptance.object_spct
Copy attributes from members of a generic_mspctaddress2tb add_attr2tb BSWF_used2tb comment2tb filter_properties2tb geocode2tb how_measured2tb instr_desc2tb instr_settings2tb lat2tb lon2tb lonlat2tb normalized2tb Rfr_type2tb scaled2tb Tfr_type2tb time_unit2tb what_measured2tb when_measured2tb
Convert transmittance into absorptance.Afr2T Afr2T.default Afr2T.filter_mspct Afr2T.filter_spct Afr2T.numeric Afr2T.object_mspct Afr2T.object_spct
Convert filter quantities.any2A any2Afr any2T
Convert spectral photon irradiance into spectral energy irradianceas_energy
Convert spectral energy irradiance into spectral photon irradianceas_quantum
Convert spectral energy irradiance into spectral photon irradianceas_quantum_mol
Convert datetime to time-of-dayas_tod
Coerce to a collection-of-spectraas.calibration_mspct as.calibration_mspct.calibration_spct as.calibration_mspct.data.frame as.calibration_mspct.default as.calibration_mspct.list as.calibration_mspct.matrix
Coerce to a spectrumas.calibration_spct as.calibration_spct.default
Coerce to a collection-of-spectraas.chroma_mspct as.chroma_mspct.chroma_spct as.chroma_mspct.data.frame as.chroma_mspct.default as.chroma_mspct.list
Coerce to a spectrumas.chroma_spct as.chroma_spct.default
Coerce to a collection-of-spectraas.cps_mspct as.cps_mspct.cps_spct as.cps_mspct.data.frame as.cps_mspct.default as.cps_mspct.list as.cps_mspct.matrix
Coerce to a spectrumas.cps_spct as.cps_spct.default
Coerce to a collection-of-spectraas.filter_mspct as.filter_mspct.data.frame as.filter_mspct.default as.filter_mspct.filter_spct as.filter_mspct.list as.filter_mspct.matrix
Coerce or convert into a filter spectrumas.filter_spct as.filter_spct.default as.filter_spct.solute_spct
Coerce to a collection-of-spectraas.generic_mspct as.generic_mspct.data.frame as.generic_mspct.default as.generic_mspct.generic_spct as.generic_mspct.list as.generic_mspct.matrix mat2mspct
Coerce to a spectrumas.generic_spct as.generic_spct.default
Coerce a collection of spectra into a matrixas.matrix-mspct as.matrix.generic_mspct mspct2mat
Coerce to a collection-of-spectraas.object_mspct as.object_mspct.data.frame as.object_mspct.default as.object_mspct.list as.object_mspct.object_spct
Coerce to a spectrumas.object_spct as.object_spct.default
Coerce to a collection-of-spectraas.raw_mspct as.raw_mspct.data.frame as.raw_mspct.default as.raw_mspct.list as.raw_mspct.matrix as.raw_mspct.raw_spct
Coerce to a spectrumas.raw_spct as.raw_spct.default
Coerce to a collection-of-spectraas.reflector_mspct as.reflector_mspct.data.frame as.reflector_mspct.default as.reflector_mspct.list as.reflector_mspct.matrix as.reflector_mspct.reflector_spct
Coerce to a spectrumas.reflector_spct as.reflector_spct.default
Coerce to a collection-of-spectraas.response_mspct as.response_mspct.data.frame as.response_mspct.default as.response_mspct.list as.response_mspct.matrix as.response_mspct.response_spct
Coerce to a spectrumas.response_spct as.response_spct.default
Convert a solar_time object into solar_date objectas.solar_date
Coerce to a collection-of-spectraas.solute_mspct as.solute_mspct.data.frame as.solute_mspct.default as.solute_mspct.list as.solute_mspct.matrix as.solute_mspct.solute_spct
Coerce to a solute spectrumas.solute_spct as.solute_spct.default as.solute_spct.filter_spct
Coerce to a collection-of-spectraas.source_mspct as.source_mspct.data.frame as.source_mspct.default as.source_mspct.list as.source_mspct.matrix as.source_mspct.source_spct
Coerce to a spectrumas.source_spct as.source_spct.default
Average spectral data.average_spct
Honeybee xyz chromaticity colour matching function databeesxyzCMF.spct
Theoretical optical bodiesblack_body.spct clear_body.spct white_body.spct
Combine collections of spectrac c.generic_mspct
Spectral weightscalc_multipliers
Scaled and/or interpolated light-source spectral outputcalc_source_output
Spectral response of a back-thinned CCD image sensor.ccd.spct
Check validity of spectral objectscheck_spct check_spct.calibration_spct check_spct.chroma_spct check_spct.cps_spct check_spct.default check_spct.filter_spct check_spct.generic_spct check_spct.object_spct check_spct.raw_spct check_spct.reflector_spct check_spct.response_spct check_spct.solute_spct check_spct.source_spct
Sanity check a spectrumcheck_spectrum
Sanity check of wavelengths (internal function).check_w.length
Check the "time.unit" attribute of an existing source_spct objectcheckTimeUnit
Linear energy CIE 2008 luminous efficiency function 10 deg dataciev10.spct
Linear energy CIE 2008 luminous efficiency function 2 deg dataciev2.spct
CIE xyz chromaticity coordinates (CC) 10 deg dataciexyzCC10.spct
CIE xyz chromaticity coordinates 2 deg dataciexyzCC2.spct
Linear energy CIE xyz colour matching function (CMF) 10 deg dataciexyzCMF10.spct
Linear energy CIE xyz colour matching function (CMF) 2 deg dataciexyzCMF2.spct
Query which is the class of a spectrumclass_spct
Clean (=replace) off-range values in a spectrumclean clean.cps_mspct clean.cps_spct clean.default clean.filter_mspct clean.filter_spct clean.generic_mspct clean.generic_spct clean.object_mspct clean.object_spct clean.raw_mspct clean.raw_spct clean.reflector_mspct clean.reflector_spct clean.response_mspct clean.response_spct clean.solute_mspct clean.solute_spct clean.source_mspct clean.source_spct
Theoretical spectrum of clear and apaque materialsclear.spct opaque.spct
Clip head and/or tail of a spectrumclip_wl clip_wl.default clip_wl.generic_mspct clip_wl.generic_spct clip_wl.list clip_wl.waveband
Form a new collectioncollect2mspct
Color of an objectcolor color_of color_of.default color_of.list color_of.numeric color_of.source_mspct color_of.source_spct color_of.waveband colour_of fast_color_of_wb fast_color_of_wl
Coarse-grained comparison of two spectracompare_spct
Ten-degree cone fundaamentalscone_fundamentals10.mspct cone_fundamentals10.spct
Convert the "Tfr.type" attributeconvertTfrType
Convert the "thickness" attribute of an existing filter_spct object.convertThickness
Convert the "time.unit" attribute of an existing source_spct objectconvertTimeUnit
Convolve function for collections of spectraconvolve_each
Copy attributescopy_attributes copy_attributes.default copy_attributes.generic_mspct copy_attributes.generic_spct copy_attributes.waveband
Conversion from counts per second to physical quantitiescps2irrad cps2Rfr cps2Tfr
Calculate deuterium lamp output spectrum from fitted constantsD2_spectrum
Data for typical calibration lampsD2.UV586 D2.UV653 D2.UV654 FEL.BN.9101.165
CIE D65 illuminant dataD65.illuminant.spct
Times for sun positionsday_length day_night day_night_fast is_daytime night_length noon_time sunrise_time sunset_time
Defunct functions and methodscalc_filter_multipliers defunct f_mspct getAfrType mutate_mspct sample_mspct sample_spct setAfrType T2T
Remove spikes from spectrumdespike despike.cps_mspct despike.cps_spct despike.data.frame despike.default despike.filter_mspct despike.filter_spct despike.generic_mspct despike.generic_spct despike.numeric despike.raw_mspct despike.raw_spct despike.reflector_mspct despike.reflector_spct despike.response_mspct despike.response_spct despike.solute_mspct despike.solute_spct despike.source_mspct despike.source_spct
Diffractiondiffraction_double_slit diffraction_single_slit
Dimensions of an Objectdim.generic_mspct dim<-.generic_mspct
Divide two spectra, even if the wavelengths values differdiv_spectra
Arithmetic Operators%/%.generic_spct div-.generic_spct
Drop user columnsdrop_user_cols drop_user_cols.calibration_spct drop_user_cols.chroma_spct drop_user_cols.cps_spct drop_user_cols.default drop_user_cols.filter_spct drop_user_cols.generic_mspct drop_user_cols.generic_spct drop_user_cols.object_spct drop_user_cols.raw_spct drop_user_cols.reflector_spct drop_user_cols.response_spct drop_user_cols.solute_spct drop_user_cols.source_spct
Energy fluencee_fluence e_fluence.default e_fluence.source_mspct e_fluence.source_spct
Energy:energy fractione_fraction e_fraction.default e_fraction.source_mspct e_fraction.source_spct
Energy irradiancee_irrad e_irrad.default e_irrad.source_mspct e_irrad.source_spct
Energy:energy ratioe_ratio e_ratio.default e_ratio.source_mspct e_ratio.source_spct
Energy-based photo-responsee_response e_response.default e_response.response_mspct e_response.response_spct
Convert energy-based quantities into photon-based quantities.e2q e2q.default e2q.response_mspct e2q.response_spct e2q.source_mspct e2q.source_spct
Calculate energy to quantum (mol) multiplierse2qmol_multipliers
Calculate energy to quantum multiplierse2quantum_multipliers
Enable or disable checksdisable_check_spct enable_check_spct set_check_spct
Set spectral-data optionsAfr_as_default A_as_default energy_as_default photon_as_default quantum_as_default Tfr_as_default unset_filter_qty_default unset_radiation_unit_default unset_user_defaults
Calculate (energy) irradiance from spectral irradianceenergy_irradiance
Energy:energy ratioenergy_ratio
Energy:photon ratioeq_ratio eq_ratio.default eq_ratio.source_mspct eq_ratio.source_spct
EvapotranspirationET_ref ET_ref_day
Extract or replace parts of a spectrum$<-.generic_spct Extract [.chroma_spct [.cps_spct [.filter_spct [.generic_spct [.object_spct [.raw_spct [.reflector_spct [.response_spct [.solute_spct [.source_spct [<-.generic_spct
Extract or replace members of a collection of spectra$<-.generic_mspct Extract_mspct [.generic_mspct [<-.generic_mspct [[<-.generic_mspct
Incandescent "FEL" lamp emission spectrumFEL_spectrum
Find peaks in a spectrumfind_peaks
Find spikesfind_spikes
Find wavelength values in a spectrumfind_wls
Find repeated w.length valuesfindMultipleWl
Refine position and value of extremes by fittingfit_peaks fit_valleys
Fluencefluence fluence.default fluence.source_mspct fluence.source_spct
Encode in a Common Formatformat.solar_time
Encode in a Common Formatformat.tod_time
Compute range and format itformatted_range
Rescale a spectrum using a summary functionfscale fscale.cps_mspct fscale.cps_spct fscale.default fscale.filter_mspct fscale.filter_spct fscale.generic_mspct fscale.generic_spct fscale.raw_mspct fscale.raw_spct fscale.reflector_mspct fscale.reflector_spct fscale.response_mspct fscale.response_spct fscale.solute_mspct fscale.solute_spct fscale.source_mspct fscale.source_spct
Shift the scale of a spectrum using a summary functionfshift fshift.cps_mspct fshift.cps_spct fshift.default fshift.filter_mspct fshift.filter_spct fshift.generic_mspct fshift.generic_spct fshift.raw_mspct fshift.raw_spct fshift.reflector_mspct fshift.reflector_spct fshift.response_mspct fshift.response_spct fshift.source_mspct fshift.source_spct
Collection-of-spectra constructorcalibration_mspct chroma_mspct cps_mspct filter_mspct generic_mspct object_mspct raw_mspct reflector_mspct response_mspct solute_mspct source_mspct
Get the metadata attributesget_attributes get_attributes.filter_spct get_attributes.generic_spct get_attributes.object_spct get_attributes.reflector_spct get_attributes.solute_spct get_attributes.source_spct get_attributes.waveband
Get peaks and valleys in a spectrumget_peaks get_valleys
Get the "filter.properties" attributefilter_properties getFilterProperties getFilterProperties.default getFilterProperties.filter_spct getFilterProperties.generic_mspct getFilterProperties.summary_filter_spct
Get the "how.measured" attributegetHowMeasured getHowMeasured.default getHowMeasured.generic_mspct getHowMeasured.generic_spct getHowMeasured.summary_generic_spct how_measured
Get the "idfactor" attributegetIdFactor
Get the "instr.desc" attributegetInstrDesc
Get the "instr.settings" attributegetInstrSettings
Get the "K.type" attributegetKType
Get the "mspct.version" attributegetMspctVersion
Get the "multiple.wl" attributegetMultipleWl
Query the "normalized" and "normalization" attributesgetNormalisation getNormalised getNormalization getNormalized
Get the "scaled" attributegetScaled getScaling
Get the "solute.properties" attributegetSoluteProperties getSoluteProperties.default getSoluteProperties.solute_mspct getSoluteProperties.solute_spct getSoluteProperties.summary_solute_spct solute_properties
Get the "spct.version" attributegetSpctVersion
Get the "time.unit" attribute of an existing source_spct objectgetTimeUnit
Get the "what.measured" attributegetWhatMeasured getWhatMeasured.default getWhatMeasured.generic_mspct getWhatMeasured.generic_spct getWhatMeasured.summary_generic_spct what_measured
Get the "when.measured" attributegetWhenMeasured getWhenMeasured.default getWhenMeasured.generic_mspct getWhenMeasured.generic_spct getWhenMeasured.summary_generic_spct when_measured
Get the "where.measured" attributegetWhereMeasured getWhereMeasured.default getWhereMeasured.generic_mspct getWhereMeasured.generic_spct getWhereMeasured.summary_generic_spct where_measured
Green birch leaf reflectance.green_leaf.spct
Return the First and Last Parts of an Objecthead_tail head_tail.data.frame head_tail.default head_tail.ftable head_tail.function head_tail.matrix head_tail.table
Irradianceilluminance illuminance.default illuminance.source_mspct illuminance.source_spct
Insert wavelength values into spectral data.insert_hinges
Insert new wavelength values into a spectruminsert_spct_hinges
Integrate spectral data.integrate_spct
Gives irradiance from spectral irradiance.integrate_xy
Map a spectrum to new wavelength values.interpolate_mspct interpolate_spct
Calculate spectral values at a different set of wavelengthsinterpolate_spectrum
Map spectra to new wavelength values.interpolate_wl interpolate_wl.default interpolate_wl.generic_mspct interpolate_wl.generic_spct
Irradianceirrad irrad.default irrad.source_mspct irrad.source_spct
Extraterrestrial irradianceirrad_extraterrestrial
Photon or energy irradiance from spectral energy or photon irradiance.irradiance
Query if a spectrum contains absorbance or transmittance datais_absorbance_based is_absorptance_based is_transmittance_based
Is an R object "effective"is_effective is_effective.default is_effective.generic_spct is_effective.source_spct is_effective.summary_generic_spct is_effective.summary_source_spct is_effective.waveband
Query if a spectrum contains mole or mass based datais_mass_based is_mole_based
Query whether a generic spectrum has been normalized.is_normalised is_normalized
Query if a spectrum contains photon- or energy-based data.is_energy_based is_photon_based
Query whether a generic spectrum has been scaledis_scaled
Query if a spectrum is taggedis_tagged
Query class of spectrum objectsis.any_mspct is.calibration_mspct is.chroma_mspct is.cps_mspct is.filter_mspct is.generic_mspct is.object_mspct is.raw_mspct is.reflector_mspct is.response_mspct is.solute_mspct is.source_mspct
Query class of spectrum objectsis.any_spct is.calibration_spct is.chroma_spct is.cps_spct is.filter_spct is.generic_spct is.object_spct is.raw_spct is.reflector_spct is.response_spct is.solute_spct is.source_spct
Query if an object has old class namesis.old_spct
Query classis.solar_date is.solar_time
Query class of spectrum summary objectsis.any_summary_spct is.summary_chroma_spct is.summary_cps_spct is.summary_filter_spct is.summary_generic_spct is.summary_object_spct is.summary_raw_spct is.summary_reflector_spct is.summary_response_spct is.summary_solute_spct is.summary_source_spct
Query if it is a wavebandis.waveband
Check the "instr.desc" attributeisValidInstrDesc
Check the "instr.settings" attributeisValidInstrSettings
Join all spectra in a collectionjoin_mspct join_mspct.default join_mspct.filter_mspct join_mspct.generic_mspct join_mspct.object_mspct join_mspct.reflector_mspct join_mspct.response_mspct join_mspct.solute_mspct join_mspct.source_mspct
Find labels from "waveband" objectlabels labels.generic_spct labels.waveband
Green Arabidopsis leaf reflectance and transmittance.Ler_leaf.spct Ler_leaf_rflt.spct Ler_leaf_trns.spct Ler_leaf_trns_i.spct
Logarithms and Exponentialsexp.generic_spct log log.generic_spct log10.generic_spct log2.generic_spct
Miscellaneous Mathematical Functionsabs.generic_spct MathFun sqrt.generic_spct
Merge and copy attributesmerge_attributes merge_attributes.default merge_attributes.generic_spct
Merge into object_spctmerge2object_spct
Arithmetic Operators-.generic_spct minus-.generic_spct
Arithmetic Operators%%.generic_spct mod-.generic_spct
Multi-spct transform methodsmsaply msdply mslply msmsply
Names of multi-spectra classesmspct_classes
Handle Missing Values in Objectsna.exclude.chroma_spct na.exclude.cps_spct na.exclude.filter_spct na.exclude.generic_mspct na.exclude.generic_spct na.exclude.object_spct na.exclude.raw_spct na.exclude.reflector_spct na.exclude.response_spct na.exclude.solute_spct na.exclude.source_spct na.omit na.omit.chroma_spct na.omit.cps_spct na.omit.filter_spct na.omit.generic_mspct na.omit.generic_spct na.omit.object_spct na.omit.raw_spct na.omit.reflector_spct na.omit.response_spct na.omit.solute_spct na.omit.source_spct
Net radiation fluxnet_irradiance
Normalization of an R objectnormalization normalization.default normalization.waveband
Normalize spectral datanormalise normalize normalize.cps_mspct normalize.cps_spct normalize.default normalize.filter_mspct normalize.filter_spct normalize.generic_mspct normalize.generic_spct normalize.raw_mspct normalize.raw_spct normalize.reflector_mspct normalize.reflector_spct normalize.response_mspct normalize.response_spct normalize.solute_mspct normalize.solute_spct normalize.source_mspct normalize.source_spct
Normalize a range argument into a true numeric rangenormalize_range_arg
Calculate a normalized difference.NDxI normalised_diff_ind normalized_diff_ind normalized_diff_ind.default normalized_diff_ind.generic_mspct normalized_diff_ind.generic_spct
Binary operation on two spectra, even if the wavelengths values differoper_spectra
Peaks or local maximapeaks peaks.cps_mspct peaks.cps_spct peaks.data.frame peaks.default peaks.filter_mspct peaks.filter_spct peaks.generic_mspct peaks.generic_spct peaks.numeric peaks.raw_mspct peaks.raw_spct peaks.reflector_mspct peaks.reflector_spct peaks.response_mspct peaks.response_spct peaks.solute_mspct peaks.solute_spct peaks.source_mspct peaks.source_spct
Molar spectral attenuation coefficient of phenylalaninephenylalanine.spct
Spectral response of a GaAsP photodiodephotodiode.spct
Photon irradiancephoton_irradiance
Photo:photon ratiophoton_ratio
Photon:energy ratiophotons_energy_ratio
Arithmetic Operators+.generic_spct plus-.generic_spct
Print spectral collection summaryprint print.generic_mspct print.generic_spct print.summary_generic_mspct
Print solar time and solar date objectsprint.solar_date print.solar_time
Print spectral summaryprint.summary_generic_spct
Print time-of-day objectsprint.tod_time
Print a "waveband" objectprint.waveband
Multiply two spectra, even if the wavelengths values differprod_spectra
Random sample of spectrapull_sample pull_sample.default pull_sample.generic_mspct pull_sample.generic_spct pull_sample.list
Photon fluenceq_fluence q_fluence.default q_fluence.source_mspct q_fluence.source_spct
Photon:photon fractionq_fraction q_fraction.default q_fraction.source_mspct q_fraction.source_spct
Photon irradianceq_irrad q_irrad.default q_irrad.source_mspct q_irrad.source_spct
Photon:photon ratioq_ratio q_ratio.default q_ratio.source_mspct q_ratio.source_spct
Photon-based photo-responseq_response q_response.default q_response.response_mspct q_response.response_spct
Convert photon-based quantities into energy-based quantitiesq2e q2e.default q2e.response_mspct q2e.response_spct q2e.source_mspct q2e.source_spct
Photon:energy ratioqe_ratio qe_ratio.default qe_ratio.source_mspct qe_ratio.source_spct
Packages in R for Photobiology suiter4p_pkgs
Row-bind spectrarbindspct
Reflectancereflectance reflectance.default reflectance.object_mspct reflectance.object_spct reflectance.reflector_mspct reflectance.reflector_spct
Relative Air Mass (AM)relative_AM
Replace bad pixels in a spectrumreplace_bad_pixs
Integrated responseresponse response.default response.response_mspct response.response_spct
reflectance:reflectance fractionRfr_fraction Rfr_fraction.default Rfr_fraction.reflector_mspct Rfr_fraction.reflector_spct
Reflectance at a planar boundaryRfr_from_n Rfr_p_from_n Rfr_s_from_n
reflectance:reflectance normalised differenceRfr_normdiff Rfr_normdiff.default Rfr_normdiff.reflector_mspct Rfr_normdiff.reflector_spct
reflectance:reflectance ratioRfr_ratio Rfr_ratio.default Rfr_ratio.reflector_mspct Rfr_ratio.reflector_spct
RGB color valuesrgb_spct
Remove "generic_mspct" and derived class attributes.rmDerivedMspct
Remove "generic_spct" and derived class attributes.rmDerivedSpct
Rounding of Numbersceiling.generic_spct floor.generic_spct round round.generic_spct signif.generic_spct trunc.generic_spct
Spectral irradiance to rgb color conversions_e_irrad2rgb
Mean from collection of spectras_mean s_mean.calibration_mspct s_mean.cps_mspct s_mean.default s_mean.filter_mspct s_mean.raw_mspct s_mean.reflector_mspct s_mean.response_mspct s_mean.source_mspct
Mean and standard error from collection of spectras_mean_se s_mean_se.calibration_mspct s_mean_se.cps_mspct s_mean_se.default s_mean_se.filter_mspct s_mean_se.raw_mspct s_mean_se.reflector_mspct s_mean_se.response_mspct s_mean_se.source_mspct
Mean plus and minus standard error from collection of spectras_mean_se_band s_mean_se_band.calibration_mspct s_mean_se_band.cps_mspct s_mean_se_band.default s_mean_se_band.filter_mspct s_mean_se_band.raw_mspct s_mean_se_band.reflector_mspct s_mean_se_band.response_mspct s_mean_se_band.source_mspct
Median of a collection of spectras_median s_median.calibration_mspct s_median.cps_mspct s_median.default s_median.filter_mspct s_median.raw_mspct s_median.reflector_mspct s_median.response_mspct s_median.source_mspct
Product from collection of spectras_prod s_prod.calibration_mspct s_prod.cps_mspct s_prod.default s_prod.filter_mspct s_prod.raw_mspct s_prod.reflector_mspct s_prod.response_mspct s_prod.source_mspct
Range of a collection of spectras_range s_range.calibration_mspct s_range.cps_mspct s_range.default s_range.filter_mspct s_range.raw_mspct s_range.reflector_mspct s_range.response_mspct s_range.source_mspct
Standard Deviation of a collection of spectras_sd s_sd.calibration_mspct s_sd.cps_mspct s_sd.default s_sd.filter_mspct s_sd.raw_mspct s_sd.reflector_mspct s_sd.response_mspct s_sd.source_mspct
Standard Error of a collection of spectras_se s_se.calibration_mspct s_se.cps_mspct s_se.default s_se.filter_mspct s_se.raw_mspct s_se.reflector_mspct s_se.response_mspct s_se.source_mspct
Sum from collection of spectras_sum s_sum.calibration_mspct s_sum.cps_mspct s_sum.default s_sum.filter_mspct s_sum.raw_mspct s_sum.reflector_mspct s_sum.response_mspct s_sum.source_mspct
Variance of a collection of spectras_var s_var.calibration_mspct s_var.cps_mspct s_var.default s_var.filter_mspct s_var.raw_mspct s_var.reflector_mspct s_var.response_mspct s_var.source_mspct
Merge user supplied attribute names with default onesselect_spct_attributes spct_attributes
The "bswf.used" attributegetBSWFUsed setBSWFUsed
Set the "filter.properties" attributefilter_properties<- setFilterProperties
Convert an R object into a spectrum object.setCalibrationSpct setChromaSpct setCpsSpct setFilterSpct setGenericSpct setObjectSpct setRawSpct setReflectorSpct setResponseSpct setSoluteSpct setSourceSpct
Set the "how.measured" attributehow_measured<- setHowMeasured
Set the "idfactor" attributesetIdFactor
Set the "instr.desc" attributesetInstrDesc
Set the "instr.settings" attributesetInstrSettings
Set the "K.type" attributesetKType
Set the "multiple.wl" attributesetMultipleWl
Set the "normalized" and "normalization" attributessetNormalised setNormalized
Set the "response.type" attributegetResponseType setResponseType
The "Rfr.type" attributegetRfrType setRfrType
Set the "scaled" attributesetScaled setScaled.default setScaled.generic_mspct setScaled.generic_spct setScaled.summary_generic_spct
Set the "solute.properties" attributesetSoluteProperties solute_properties<-
The "Tfr.type" attributegetTfrType setTfrType
Set the "time.unit" attribute of an existing source_spct objectsetTimeUnit
Set the "what.measured" attributesetWhatMeasured what_measured<-
Set the "when.measured" attributesetWhenMeasured setWhenMeasured.default setWhenMeasured.generic_mspct setWhenMeasured.generic_spct setWhenMeasured.summary_generic_spct when_measured<-
Set the "where.measured" attributesetWhereMeasured setWhereMeasured.default setWhereMeasured.generic_mspct setWhereMeasured.generic_spct setWhereMeasured.summary_generic_spct where_measured<-
Classes common to all collection members.shared_member_class
Signsign sign.generic_spct
Arithmetic Operators/.generic_spct slash-.generic_spct
Smooth a spectrumsmooth_spct smooth_spct.cps_spct smooth_spct.default smooth_spct.filter_spct smooth_spct.generic_mspct smooth_spct.reflector_spct smooth_spct.response_spct smooth_spct.solute_spct smooth_spct.source_spct
Local solar timesolar_time
Spectral-object constructorscalibration_spct chroma_spct cps_spct filter_spct generic_spct object_spct raw_spct reflector_spct response_spct solute_spct source_spct
Copy attributes into a tibblespct_attr2tb
Function returning a vector containing the names of spectra classes.spct_classes
Access metadataspct_metadata
Convert spectrum from wide to long formspct_wide2long
Spikesspikes spikes.cps_mspct spikes.cps_spct spikes.data.frame spikes.default spikes.filter_mspct spikes.filter_spct spikes.generic_mspct spikes.generic_spct spikes.numeric spikes.raw_mspct spikes.raw_spct spikes.reflector_mspct spikes.reflector_spct spikes.response_mspct spikes.response_spct spikes.solute_mspct spikes.solute_spct spikes.source_mspct spikes.source_spct
List-of-wavebands constructorsplit_bands
Energy irradiance for split spectrum regionssplit_energy_irradiance
Energy or photon irradiance for split spectrum regionssplit_irradiance
Photon irradiance for split spectrum regionssplit_photon_irradiance
Convert a 'wide' or untidy data frame into a collection of spectrasplit2calibration_mspct split2cps_mspct split2filter_mspct split2mspct split2raw_mspct split2reflector_mspct split2response_mspct split2solute_mspct split2source_mspct
Expanseexpanse expanse.default expanse.generic_mspct expanse.generic_spct expanse.numeric expanse.waveband spread wl_expanse
Subsetting spectraSubset subset.generic_spct
Convert 'long' or tidy spectral data into a collection of spectrasubset2mspct
Subtract two spectrasubt_spectra
Add two spectrasum_spectra
Summary of a collection of spectrasummary summary.generic_mspct summary.generic_spct
Function that returns a vector containing the names of spectral summary classes.summary_spct_classes
Solar anglesdistance_to_sun sun_angles sun_angles_fast sun_azimuth sun_elevation sun_zenith_angle
Daily solar spectral irradiance (simulated)sun.daily.data sun.daily.spct sun_daily.data sun_daily.spct
Time series of solar spectral irradiance (measured)sun_evening.mspct sun_evening.spct
Solar spectral irradiance (simulated)sun.data sun.spct
Convert transmittance into absorbance.T2A T2A.default T2A.filter_mspct T2A.filter_spct T2A.numeric
Convert transmittance into absorptance.T2Afr T2Afr.default T2Afr.filter_mspct T2Afr.filter_spct T2Afr.numeric T2Afr.object_mspct T2Afr.object_spct
Tag a spectrumtag tag.default tag.generic_mspct tag.generic_spct
transmittance:transmittance fractionTfr_fraction Tfr_fraction.default Tfr_fraction.filter_mspct Tfr_fraction.filter_spct
transmittance:transmittance normalised differenceTfr_normdiff Tfr_normdiff.default Tfr_normdiff.filter_mspct Tfr_normdiff.filter_spct
transmittance:transmittance ratioTfr_ratio Tfr_ratio.default Tfr_ratio.filter_mspct Tfr_ratio.filter_spct
Thin the density of wavelength valuesthin_wl thin_wl.calibration_mspct thin_wl.calibration_spct thin_wl.chroma_mspct thin_wl.chroma_spct thin_wl.cps_spct thin_wl.default thin_wl.filter_spct thin_wl.generic_mspct thin_wl.generic_spct thin_wl.object_spct thin_wl.raw_spct thin_wl.reflector_spct thin_wl.response_spct thin_wl.solute_spct thin_wl.source_spct
Arithmetic Operators*.generic_spct times-.generic_spct
Transmittancetransmittance transmittance.default transmittance.filter_mspct transmittance.filter_spct transmittance.object_mspct transmittance.object_spct
Trigonometric Functionsacos.generic_spct asin.generic_spct atan.generic_spct cos.generic_spct sin.generic_spct tan.generic_spct Trig
Trim (or expand) head and/or tail of a spectrumextend2extremes trim2overlap trim_mspct trim_spct
Trim (or expand) head and/or tailtrim_tails
Trim (or expand) head and/or tailtrim_waveband
Trim head and/or tail of a spectrumtrim_wl trim_wl.default trim_wl.generic_mspct trim_wl.generic_spct trim_wl.list trim_wl.waveband
Trim the "instr.desc" attributetrimInstrDesc
Trim the "instr.settings" attributetrimInstrSettings
Transmittance spectrum of plastic filmspolyester.spct two_filters.mspct two_filters.spct yellow_gel.spct
Time difference between two time zonestz_time_diff
Extract all members from a collectionuncollect2spct uncollect2spct.default uncollect2spct.generic_mspct
Remove tagsuntag untag.default untag.generic_mspct untag.generic_spct
Upgrade one spectral objectupgrade_spct
Upgrade one or more spectral objectsupgrade_spectra
Use photobiology optionsusing_A using_Afr using_energy using_photon using_quantum using_Tfr
Insert spectral data values at new wavelength values.v_insert_hinges
Overwrite spectral data values at existing wavelength values.v_replace_hinges
Validate a geocodeis_valid_geocode length_geocode na_geocode validate_geocode
Valleys or local minimavalleys valleys.cps_mspct valleys.cps_spct valleys.data.frame valleys.default valleys.filter_mspct valleys.filter_spct valleys.generic_mspct valleys.generic_spct valleys.numeric valleys.raw_mspct valleys.raw_spct valleys.reflector_mspct valleys.reflector_spct valleys.response_mspct valleys.response_spct valleys.solute_mspct valleys.solute_spct valleys.source_mspct valleys.source_spct
Set error reporting optionsstrict_range_as_default verbose_as_default
Wavelength range to rgb color conversionw_length_range2rgb
Wavelength to rgb color conversionw_length2rgb
Water vapour pressurepsychrometric_constant water_dp water_fp water_mvc2vp water_RH2vp water_vp2mvc water_vp2RH water_vp_sat water_vp_sat_slope
Molar spectral attenuation coefficient of waterwater.spct
Waveband constructor methodnew_waveband waveband
Photon or energy ratiowaveband_ratio
Set computation optionsuse_cached_mult_as_default wb_trim_as_default
Create tagged spectrum from wavebandsfast_wb2rect_spct wb2rect_spct
Create spectrum from wavebandswb2spct
Create tagged spectrum from wavebandswb2tagged_spct
White led bulb spectrumwhite_led.cps_spct white_led.raw_spct white_led.source_spct
Wavelength maximummax max.generic_mspct max.generic_spct max.waveband wl_max
Midpointmidpoint midpoint.default midpoint.generic_mspct midpoint.generic_spct midpoint.numeric midpoint.waveband wl_midpoint
Wavelength minimummin min.generic_mspct min.generic_spct min.waveband wl_min
Wavelength rangerange range.generic_mspct range.generic_spct range.waveband wl_range
Stepsizestepsize stepsize.default stepsize.generic_mspct stepsize.generic_spct stepsize.numeric wl_stepsize
Wavelength conversionsenergy2wl frequency2wl wavenumber2wl wl2energy wl2frequency wl2wavenumber
Find wavelengths values corresponding to a target spectral valuewls_at_target wls_at_target.cps_spct wls_at_target.data.frame wls_at_target.default wls_at_target.filter_spct wls_at_target.generic_mspct wls_at_target.generic_spct wls_at_target.raw_spct wls_at_target.reflector_spct wls_at_target.response_spct wls_at_target.solute_spct wls_at_target.source_spct