Package: photobiology 0.11.3.9000

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/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

463 exports 4 stars 9.40 score 29 dependencies 12 dependents 594 scripts 1.2k downloads

Last updated 7 days agofrom:b21bef0862. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 27 2024
R-4.5-winOKSep 27 2024
R-4.5-linuxOKSep 27 2024
R-4.4-winOKSep 27 2024
R-4.4-macOKSep 27 2024
R-4.3-winOKSep 27 2024
R-4.3-macOKSep 27 2024

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_measured2tbid_factorid_factor<-illuminanceinsert_hingesinsert_spct_hingesinstr_desc2tbinstr_descriptorinstr_descriptor<-instr_settingsinstr_settings<-instr_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_geocodelon2tblonlat2tbmake_var_labelsmat2mspctmerge_attributesmerge2object_spctmidpointmsaplymsdplymslplymsmsplymspct_classesmspct2matmultiple_wlmultiple_wl<-mutate_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_properties2tbsolute_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 Sep 27 2024.

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

User Guide: 1 Radiation

Rendered fromuserguide-1-radiation.Rmdusingknitr::rmarkdownon Sep 27 2024.

Last update: 2024-08-23
Started: 2021-01-15

User Guide: 2 Astronomy and Atmosphere

Rendered fromuserguide-2-astronomy.Rmdusingknitr::rmarkdownon Sep 27 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 solute_properties2tb 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.data.frame getHowMeasured.default getHowMeasured.generic_mspct getHowMeasured.generic_spct getHowMeasured.summary_generic_spct how_measured
Get the "idfactor" attributegetIdFactor id_factor
Get the "instr.desc" attributegetInstrDesc instr_descriptor
Get the "instr.settings" attributegetInstrSettings instr_settings
Get the "K.type" attributegetKType
Get the "mspct.version" attributegetMspctVersion
Get the "multiple.wl" attributegetMultipleWl multiple_wl
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.data.frame getWhatMeasured.default getWhatMeasured.generic_mspct getWhatMeasured.generic_spct getWhatMeasured.summary_generic_spct what_measured
Get the "when.measured" attributegetWhenMeasured getWhenMeasured.data.frame getWhenMeasured.default getWhenMeasured.generic_mspct getWhenMeasured.generic_spct getWhenMeasured.summary_generic_spct when_measured
Get the "where.measured" attributegetWhereMeasured getWhereMeasured.data.frame 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
Column or variable labelsmake_var_labels make_var_labels.calibration_spct make_var_labels.chroma_spct make_var_labels.cps_spct make_var_labels.default make_var_labels.filter_spct make_var_labels.object_spct make_var_labels.raw_spct make_var_labels.reflector_spct make_var_labels.response_spct make_var_labels.solute_spct make_var_labels.source_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 objectsprint.generic_mspct print.generic_spct
Print methods for metadata recordsprint.filter_properties print.instr_desc print.instr_settings print.metadata print.solute_properties
Print solar time and solar date objectsprint.solar_date print.solar_time
Print spectral summaryprint.summary_generic_mspct print.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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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.generic_spct 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" attributeid_factor<- setIdFactor
Set the "instr.desc" attributeinstr_descriptor<- setInstrDesc
Set the "instr.settings" attributeinstr_settings<- setInstrSettings
Set the "K.type" attributesetKType
Set the "multiple.wl" attributemultiple_wl<- setMultipleWl
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.data.frame setWhenMeasured.default setWhenMeasured.generic_mspct setWhenMeasured.generic_spct setWhenMeasured.summary_generic_spct when_measured<-
Set the "where.measured" attributesetWhereMeasured setWhereMeasured.data.frame 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
Function that returns a vector containing the names of spectral summary classes.summary_spct_classes
Summary of one or more spectrasummary.generic_mspct summary.generic_spct
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