Man pages for photobiology
Photobiological Calculations

A2TConvert absorbance into transmittance
absorbance_spctCalculate absorbance from spectral absorbance.
absorptance_spctCalculate absorptance from spectral absorptance.
adaptive_smoothingCustom smoothing
add_attr2tbCopy attributes from members of a generic_mspct
Afr2TConvert transmittance into absorptance.
A.illuminant.spctCIE A illuminant data
any2TConvert filter quantities.
as.calibration_mspctCoerce to a collection-of-spectra
as.calibration_spctCoerce to a spectrum
as.chroma_mspctCoerce to a collection-of-spectra
as.chroma_spctCoerce to a spectrum
as.cps_mspctCoerce to a collection-of-spectra
as.cps_spctCoerce to a spectrum
as_energyConvert spectral photon irradiance into spectral energy...
as.filter_mspctCoerce to a collection-of-spectra
as.filter_spctCoerce to a spectrum
as.generic_mspctCoerce to a collection-of-spectra
as.generic_spctCoerce to a spectrum
as.matrix-mspctCoerce a collection of spectra into a matrix
as.object_mspctCoerce to a collection-of-spectra
as.object_spctCoerce to a spectrum
as_quantumConvert spectral energy irradiance into spectral photon...
as_quantum_molConvert spectral energy irradiance into spectral photon...
as.raw_mspctCoerce to a collection-of-spectra
as.raw_spctCoerce to a spectrum
as.reflector_mspctCoerce to a collection-of-spectra
as.reflector_spctCoerce to a spectrum
as.response_mspctCoerce to a collection-of-spectra
as.response_spctCoerce to a spectrum
as.solar_dateConvert a solar_time object into solar_date object
as.source_mspctCoerce to a collection-of-spectra
as.source_spctCoerce to a spectrum
as_todConvert datetime to time-of-day
auto_hingesGuess whether insertion of hinges is needed or not
average_spctAverage spectral data.
beesxyzCMF.spctHoneybee xyz chromaticity colour matching function data
black_body.spctTheoretical black body
cCombine collections of spectra
calc_multipliersSpectral weights
calc_source_outputScaled and/or interpolated light-source spectral output
ccd.spctSpectral response of a back-thinned CCD image sensor.
checkMspctVersionCheck that the "mspct.version" attribute is set
check_spctCheck validity of spectral objects
checkSpctVersionCheck that the "spct.version" attribute is set
check_spectrumSanity check a spectrum
checkTimeUnitCheck the "time.unit" attribute of an existing source_spct...
check_w.lengthSanity check of wavelengths (internal function).
ciev10.spctLinear energy CIE 2008 luminous efficiency function 10 deg...
ciev2.spctLinear energy CIE 2008 luminous efficiency function 2 deg...
ciexyzCC10.spctCIE xyz chromaticity coordinates (CC) 10 deg data
ciexyzCC2.spctCIE xyz chromaticity coordinates 2 deg data
ciexyzCMF10.spctLinear energy CIE xyz colour matching function (CMF) 10 deg...
ciexyzCMF2.spctLinear energy CIE xyz colour matching function (CMF) 2 deg...
class_spctQuery which is the class of a spectrum
cleanClean (=replace) off-range values in a spectrum
clean_spctClean a spectrum
clear_body.spctTheoretical clear body
clear_photobio.cacheClear the spectral weights cache
clear.spctTheoretical spectrum of a clear material
clip_wlClip head and/or tail of a spectrum
collect2mspctForm a new collection
color_ofColor of an object
compare_spctCoarse-grained comparison of two spectra
cone_fundamentals10.spctTen-degree cone fundaamentals
convertTfrTypeConvert the "Tfr.type" attribute
convertThicknessConvert the "thickness" attribute of an existing filter_spct...
convertTimeUnitConvert the "time.unit" attribute of an existing source_spct...
convolve_eachConvolve function for collections of spectra
copy_attributesCopy attributes
cps2irradConversion from counts per second to physical quantities
D2_spectrumCalculate deuterium lamp output spectrum from fitted...
D2.UV586Data for typical calibration lamps
D2.UV653Data for typical calibration lamps
D2.UV654Data for typical calibration lamps
D65.illuminant.spctCIE D65 illuminant data
day_nightTimes for sun positions
defunctDefunct functions and methods
despikeRemove spikes from spectrum
dim.generic_mspctDimensions of an Object
div-.generic_spctArithmetic Operators
div_spectraDivide two spectra, even if the wavelengths values differ
drop_user_colsDrop user columns
e2qConvert energy-based quantities into photon-based quantities.
e2qmol_multipliersCalculate energy to quantum (mol) multipliers
e2quantum_multipliersCalculate energy to quantum multipliers
e_fluenceEnergy fluence
e_irradEnergy irradiance
enable_check_spctEnable or disable checks
energy_as_defaultSet spectral-data options
energy_irradianceCalculate (energy) irradiance from spectral irradiance
energy_ratioEnergy:energy ratio
eq_ratioEnergy:photon ratio
e_ratioEnergy:energy ratio
e_responseEnergy-based photo-response
extractExtract or replace parts of a spectrum
extract_mspctExtract or replace members of a collection of spectra
f_dispatcher_spctMath function dispatcher for spectra
FEL.BN.9101.165Data for typical calibration lamps
FEL_spectrumIncandescent "FEL" lamp emission spectrum
filter_cps.mspctCounts per second from a measurement of a plastic film
findMultipleWlFind repeated w.length values
find_peaksFind peaks in a spectrum
find_spikesFind spikes
find_wlsFind wavelength values in a spectrum
fit_peaksRefine position and value of extremes by fitting
format.solar_timeEncode in a Common Format
formatted_rangeCompute range and format it
format.tod_timeEncode in a Common Format
fscaleRescale a spectrum using a summary function
fscale_spctfscale a spectrum
fshiftShift the scale of a spectrum using a summary function
fshift_spctfshift a spectrum
generic_mspctCollection-of-spectra constructor
get_attributesGet the metadata attributes
getBSWFUsedGet the "bswf.used" attribute
getFilterPropertiesGet the "" attribute
getHowMeasuredGet the "how.measured" attribute
getIdFactorGet the "idfactor" attribute
getInstrDescGet the "instr.desc" attribute
getInstrSettingsGet the "instr.settings" attribute
getMspctVersionGet the "mspct.version" attribute
getMultipleWlGet the "multiple.wl" attribute
getNormalizedGet the "normalized" attribute
get_peaksGet peaks and valleys in a spectrum
getResponseTypeGet the "response.type" attribute
getRfrTypeGet the "Rfr.type" attribute
getScaledGet the "scaled" attribute
getSpctVersionGet the "spct.version" attribute
getTfrTypeGet the "Tfr.type" attribute
getTimeUnitGet the "time.unit" attribute of an existing source_spct...
getWhatMeasuredGet the "what.measured" attribute
getWhenMeasuredGet the "when.measured" attribute
getWhereMeasuredGet the "where.measured" attribute
green_leaf.spctGreen birch leaf reflectance.
head_tailReturn the First and Last Part of an Object
insert_hingesInsert wavelength values into spectral data.
insert_spct_hingesInsert new wavelength values into a spectrum
integrate_spctIntegrate spectral data.
integrate_xyGives irradiance from spectral irradiance.
interpolate_spctMap a spectrum to new wavelength values.
interpolate_spectrumCalculate spectral values at a different set of wavelengths
interpolate_wlMap spectra to new wavelength values.
irrad_extraterrestrialExtraterrestrial irradiance
irradiancePhoton or energy irradiance from spectral energy or photon...
is_absorbance_basedQuery if a spectrum contains absorbance or transmittance data
is_effectiveIs an R object "effective"
is.generic_mspctQuery class of spectrum objects
is.generic_spctQuery class of spectrum objects
is_normalizedQuery whether a generic spectrum has been normalized.
is.old_spctQuery if an object has old class names
is_photon_basedQuery if a spectrum contains photon- or energy-based data.
is_scaledQuery whether a generic spectrum has been scaled
is.solar_timeQuery class
is.summary_generic_spctQuery class of spectrum summary objects
is_taggedQuery if a spectrum is tagged
isValidInstrDescCheck the "instr.desc" attribute
isValidInstrSettingsCheck the "instr.settings" attribute
is.wavebandQuery if it is a waveband
join_mspctJoin all spectra in a collection
julian_daySolar astronomy using Meeus' algorithm
labelsFind labels from "waveband" object
Ler_leaf_rflt.spctGreen Arabidopsis leaf spectral reflectance.
Ler_leaf.spctGreen Arabidopsis leaf reflectance and transmittance.
Ler_leaf_trns_i.spctGreen Arabidopsis leaf spectral transmittance.
Ler_leaf_trns.spctGreen Arabidopsis leaf spectral transmittance.
l_insert_hingesInsert wavelength values into spectral data.
logLogarithms and Exponentials
MathFunMiscellaneous Mathematical Functions
maxWavelength maximum
merge2object_spctMerge into object_spct
merge_attributesMerge and copy attributes
minWavelength minimum
minus-.generic_spctArithmetic Operators
mod-.generic_spctArithmetic Operators
msmsplyMulti-spct transform methods
mspct_classesNames of multi-spectra classes
na.omitHandle Missing Values in Objects
net_irradianceNet radiation flux
normalizationNormalization of an R object
normalizeNormalize spectral data
normalized_diff_indCalculate a normalized index.
normalize_range_argNormalize a range argument into a true numeric range
opaque.spctTheoretical spectrum of an opaque material
oper_spectraBinary operation on two spectra, even if the wavelengths...
peaksPeaks or local maxima
photobiology-packagephotobiology: Photobiological Calculations
photodiode.spctSpectral response of a GaAsP photodiode
photon_irradiancePhoton irradiance
photon_ratioPhoto:photon ratio
photons_energy_ratioPhoton:energy ratio
plus-.generic_spctArithmetic Operators
polyester.spctTransmittance spectrum of clear polyester film
pow-.generic_spctArithmetic Operators
printPrint a spectral object
print.solar_timePrint solar time and solar date objects
print.summary_generic_spctPrint spectral summary
print.tod_timePrint time-of-day objects
print.wavebandPrint a "waveband" object
prod_spectraMultiply two spectra, even if the wavelengths values differ
q2eConvert photon-based quantities into energy-based quantities
qe_ratioPhoton:energy ratio
q_fluencePhoton fluence
q_irradPhoton irradiance
q_ratioPhoton:photon ratio
q_responsePhoton-based photo-response
r4p_pkgsPackages in R for Photobiology suite
rangeWavelength range
rbindspctRow-bind spectra
reflectance_spctCalculate reflectance from spectral reflectance
relative_AMRelative Air Mass (AM)
replace_bad_pixsReplace bad pixels in a spectrum
responseIntegrated response
resp_spctCalculate response from spectral response
Rfr_from_nReflectance at a planar boundary
rgb_spctRGB color values
rmDerivedMspctRemove "generic_mspct" and derived class attributes.
rmDerivedSpctRemove "generic_spct" and derived class attributes.
roundRounding of Numbers
rowwiserowwise functions for collections of spectra
seStandard error of the mean
s_e_irrad2rgbSpectral irradiance to rgb color conversion
select_spct_attributesMerge user supplied attribute names with default ones
setBSWFUsedSet the "bswf.used" attribute
setFilterPropertiesSet the "" attribute
setGenericSpctConvert an R object into a spectrum object.
setHowMeasuredSet the "how.measured" attribute
setIdFactorSet the "idfactor" attribute
setInstrDescSet the "instr.desc" attribute
setInstrSettingsSet the "instr.settings" attribute
setMultipleWlSet the "multiple.wl" attribute
setNormalizedSet the "normalized" and "normalization" attributes
setResponseTypeSet the "response.type" attribute
setRfrTypeSet the "Rfr.type" attribute
setScaledSet the "scaled" attribute
setTfrTypeSet the "Tfr.type" attribute
setTimeUnitSet the "time.unit" attribute of an existing source_spct...
setWhatMeasuredSet the "what.measured" attribute
setWhenMeasuredSet the "when.measured" attribute
setWhereMeasuredSet the "where.measured" attribute
shared_member_classClasses common to all collection members.
slash-.generic_spctArithmetic Operators
s_meanMean from collection of spectra
s_mean_seMean and standard error from collection of spectra
s_medianMedian of a collection of spectra
smooth_spctSmooth a spectrum
solar_timeLocal solar time
source_spctSpectral-object constructor
spct_attr2tbCopy attributes into a tibble
spct_classesFunction that returns a vector containing the names of...
spct_metadataAccess metadata
split2mspctConvert a 'wide' or untidy data frame into a collection of...
split_bandsList-of-wavebands constructor
split_energy_irradianceEnergy irradiance for split spectrum regions
split_irradianceEnergy or photon irradiance for split spectrum regions
split_photon_irradiancePhoton irradiance for split spectrum regions
s_prodProduct from collection of spectra
s_rangeRange of a collection of spectra
s_sdStandard Deviation of a collection of spectra
s_seStandard Error of a collection of spectra
s_sumSum from collection of spectra
subsetSubsetting spectra
subset2mspctConvert 'long' or tidy spectral data into a collection of...
subt_spectraSubtract two spectra
summarySummary of a spectral object
summary_spct_classesFunction that returns a vector containing the names of...
sum_spectraAdd two spectra
sun_anglesSolar angles
sun.daily.dataDaily solar spectral irradiance (simulated)
sun.daily.spctDaily solar spectral irradiance (simulated)
sun.dataSolar spectral irradiance (simulated)
sun.spctSolar spectral irradiance (simulated)
s_varVariance of a collection of spectra
T2AConvert transmittance into absorbance.
T2AfrConvert transmittance into absorptance.
tagTag a spectrum
thin_wlThin the density of wavelength values
times-.generic_spctArithmetic Operators
transmittance_spctCalculate transmittance from spectral transmittance.
TrigTrigonometric Functions
trimInstrDescTrim the "instr.desc" attribute
trimInstrSettingsTrim the "instr.settings" attribute
trim_spctTrim (or expand) head and/or tail of a spectrum
trim_tailsTrim (or expand) head and/or tail
trim_wavebandTrim (or expand) head and/or tail
trim_wlTrim head and/or tail of a spectrum
twilight2angletwilight argument check and conversion
tz_time_diffTime difference between two time zones
uncollect2spctExtract all members from a collection
untagRemove tags
upgrade_spctUpgrade one spectral object
upgrade_spectraUpgrade one or more spectral objects
using_TfrUse photobiology options
validate_geocodeValidate a geocode
valleysValleys or local minima
verbose_as_defaultSet error reporting options
v_insert_hingesInsert spectral data values at new wavelength values.
v_replace_hingesOverwrite spectral data values at existing wavelength values.
water_vp_satWater vapour pressure
wavebandWaveband constructor method
waveband_ratioPhoton or energy ratio
wb2rect_spctCreate tagged spectrum from wavebands
wb2spctCreate spectrum from wavebands
wb2tagged_spctCreate tagged spectrum from wavebands
wb_trim_as_defaultSet computation options
white_body.spctTheoretical white body
white_led.cps_spctWhite led bulb spectrum
white_led.raw_spctWhite led bulb spectrum
white_led.source_spctWhite led bulb spectrum
w_length2rgbWavelength to rgb color conversion
w_length_range2rgbWavelength range to rgb color conversion
wls_at_targetFind wavelengths values corresponding to a target spectral...
yellow_gel.spctTransmittance spectrum of yellow theatrical gel.
photobiology documentation built on March 26, 2022, 1:08 a.m.