R: Photobiological Calculations

# Photobiological Calculations

## Documentation for package ‘photobiology’ version 0.9.21

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P Q R S T U V W Y misc

photobiology-package | photobiology: Photobiological Calculations

## -- A --

A.illuminant.spct | CIE A illuminant data
A2T | Convert absorbance into transmittance
A2T.default | Convert absorbance into transmittance
A2T.filter_mspct | Convert absorbance into transmittance
A2T.filter_spct | Convert absorbance into transmittance
abs.generic_spct | Miscellaneous Mathematical Functions
absorbance | Absorbance
absorbance.default | Absorbance
absorbance.filter_mspct | Absorbance
absorbance.filter_spct | Absorbance
absorbance.object_mspct | Absorbance
absorbance.object_spct | Absorbance
absorptance | Absorptance
absorptance.default | Absorptance
absorptance.filter_mspct | Absorptance
absorptance.filter_spct | Absorptance
absorptance.object_mspct | Absorptance
absorptance.object_spct | Absorptance
acos.generic_spct | Trigonometric Functions
add_attr2tb | Copy attributes from members of a generic_mspct
Afr_as_default | Set spectral-data options
as.calibration_mspct | Coerce to a collection-of-spectra
as.calibration_mspct.calibration_spct | Coerce to a collection-of-spectra
as.calibration_mspct.data.frame | Coerce to a collection-of-spectra
as.calibration_mspct.default | Coerce to a collection-of-spectra
as.calibration_mspct.list | Coerce to a collection-of-spectra
as.calibration_mspct.matrix | Coerce to a collection-of-spectra
as.calibration_spct | Coerce to a spectrum
as.calibration_spct.default | Coerce to a spectrum
as.chroma_mspct | Coerce to a collection-of-spectra
as.chroma_mspct.chroma_spct | Coerce to a collection-of-spectra
as.chroma_mspct.data.frame | Coerce to a collection-of-spectra
as.chroma_mspct.default | Coerce to a collection-of-spectra
as.chroma_mspct.list | Coerce to a collection-of-spectra
as.chroma_spct | Coerce to a spectrum
as.chroma_spct.default | Coerce to a spectrum
as.cps_mspct | Coerce to a collection-of-spectra
as.cps_mspct.cps_spct | Coerce to a collection-of-spectra
as.cps_mspct.data.frame | Coerce to a collection-of-spectra
as.cps_mspct.default | Coerce to a collection-of-spectra
as.cps_mspct.list | Coerce to a collection-of-spectra
as.cps_mspct.matrix | Coerce to a collection-of-spectra
as.cps_spct | Coerce to a spectrum
as.cps_spct.default | Coerce to a spectrum
as.filter_mspct | Coerce to a collection-of-spectra
as.filter_mspct.data.frame | Coerce to a collection-of-spectra
as.filter_mspct.default | Coerce to a collection-of-spectra
as.filter_mspct.filter_spct | Coerce to a collection-of-spectra
as.filter_mspct.list | Coerce to a collection-of-spectra
as.filter_mspct.matrix | Coerce to a collection-of-spectra
as.filter_spct | Coerce to a spectrum
as.filter_spct.default | Coerce to a spectrum
as.generic_mspct | Coerce to a collection-of-spectra
as.generic_mspct.data.frame | Coerce to a collection-of-spectra
as.generic_mspct.default | Coerce to a collection-of-spectra
as.generic_mspct.generic_spct | Coerce to a collection-of-spectra
as.generic_mspct.list | Coerce to a collection-of-spectra
as.generic_mspct.matrix | Coerce to a collection-of-spectra
as.generic_spct | Coerce to a spectrum
as.generic_spct.default | Coerce to a spectrum
as.matrix-mspct | Coerce a collection of spectra into a matrix
as.matrix.generic_mspct | Coerce a collection of spectra into a matrix
as.object_mspct | Coerce to a collection-of-spectra
as.object_mspct.data.frame | Coerce to a collection-of-spectra
as.object_mspct.default | Coerce to a collection-of-spectra
as.object_mspct.list | Coerce to a collection-of-spectra
as.object_mspct.object_spct | Coerce to a collection-of-spectra
as.object_spct | Coerce to a spectrum
as.object_spct.default | Coerce to a spectrum
as.raw_mspct | Coerce to a collection-of-spectra
as.raw_mspct.data.frame | Coerce to a collection-of-spectra
as.raw_mspct.default | Coerce to a collection-of-spectra
as.raw_mspct.list | Coerce to a collection-of-spectra
as.raw_mspct.matrix | Coerce to a collection-of-spectra
as.raw_mspct.raw_spct | Coerce to a collection-of-spectra
as.raw_spct | Coerce to a spectrum
as.raw_spct.default | Coerce to a spectrum
as.reflector_mspct | Coerce to a collection-of-spectra
as.reflector_mspct.data.frame | Coerce to a collection-of-spectra
as.reflector_mspct.default | Coerce to a collection-of-spectra
as.reflector_mspct.list | Coerce to a collection-of-spectra
as.reflector_mspct.matrix | Coerce to a collection-of-spectra
as.reflector_mspct.reflector_spct | Coerce to a collection-of-spectra
as.reflector_spct | Coerce to a spectrum
as.reflector_spct.default | Coerce to a spectrum
as.response_mspct | Coerce to a collection-of-spectra
as.response_mspct.data.frame | Coerce to a collection-of-spectra
as.response_mspct.default | Coerce to a collection-of-spectra
as.response_mspct.list | Coerce to a collection-of-spectra
as.response_mspct.matrix | Coerce to a collection-of-spectra
as.response_mspct.response_spct | Coerce to a collection-of-spectra
as.response_spct | Coerce to a spectrum
as.response_spct.default | Coerce to a spectrum
as.solar_date | Convert a solar_time object into solar_date object
as.source_mspct | Coerce to a collection-of-spectra
as.source_mspct.data.frame | Coerce to a collection-of-spectra
as.source_mspct.default | Coerce to a collection-of-spectra
as.source_mspct.list | Coerce to a collection-of-spectra
as.source_mspct.matrix | Coerce to a collection-of-spectra
as.source_mspct.source_spct | Coerce to a collection-of-spectra
as.source_spct | Coerce to a spectrum
as.source_spct.default | Coerce to a spectrum
asin.generic_spct | Trigonometric Functions
as_energy | Convert spectral photon irradiance into spectral energy irradiance
as_quantum | Convert spectral energy irradiance into spectral photon irradiance
as_quantum_mol | Convert spectral energy irradiance into spectral photon irradiance
as_tod | Convert date to time-of-day in hours, minutes or seconds
atan.generic_spct | Trigonometric Functions
average_spct | Average spectral data.
A_as_default | Set spectral-data options

## -- B --

beesxyzCMF.spct | Honeybee xyz chromaticity colour matching function data
black_body.spct | Theoretical black body

## -- C --

c.generic_mspct | Combine collections of spectra
calc_filter_multipliers | Defunct functions and methods
calc_multipliers | Spectral weights
calc_source_output | Scaled and/or interpolated light-source spectral output
calibration_mspct | Collection-of-spectra constructor
calibration_spct | Spectral-object constructor
ccd.spct | Spectral response of a back-thinned CCD image sensor.
ceiling.generic_spct | Rounding of Numbers
checkTimeUnit | Check the "time.unit" attribute of an existing source_spct object
check_spct | Check validity of spectral objects
check_spct.calibration_spct | Check validity of spectral objects
check_spct.chroma_spct | Check validity of spectral objects
check_spct.cps_spct | Check validity of spectral objects
check_spct.default | Check validity of spectral objects
check_spct.filter_spct | Check validity of spectral objects
check_spct.generic_spct | Check validity of spectral objects
check_spct.object_spct | Check validity of spectral objects
check_spct.raw_spct | Check validity of spectral objects
check_spct.reflector_spct | Check validity of spectral objects
check_spct.response_spct | Check validity of spectral objects
check_spct.source_spct | Check validity of spectral objects
check_spectrum | Sanity check a spectrum
check_w.length | Sanity check of wavelengths (internal function).
chroma_mspct | Collection-of-spectra constructor
chroma_spct | Spectral-object constructor
ciev10.spct | Linear energy CIE 2008 luminous efficiency function 10 deg data
ciev2.spct | Linear energy CIE 2008 luminous efficiency function 2 deg data
ciexyzCC10.spct | CIE xyz chromaticity coordinates (CC) 10 deg data
ciexyzCC2.spct | CIE xyz chromaticity coordinates 2 deg data
ciexyzCMF10.spct | Linear energy CIE xyz colour matching function (CMF) 10 deg data
ciexyzCMF2.spct | Linear energy CIE xyz colour matching function (CMF) 2 deg data
class_spct | Query which is the class of an spectrum
clean | Clean (=replace) off-range values in a spectrum
clean.cps_mspct | Clean (=replace) off-range values in a spectrum
clean.cps_spct | Clean (=replace) off-range values in a spectrum
clean.default | Clean (=replace) off-range values in a spectrum
clean.filter_mspct | Clean (=replace) off-range values in a spectrum
clean.filter_spct | Clean (=replace) off-range values in a spectrum
clean.generic_mspct | Clean (=replace) off-range values in a spectrum
clean.generic_spct | Clean (=replace) off-range values in a spectrum
clean.raw_mspct | Clean (=replace) off-range values in a spectrum
clean.raw_spct | Clean (=replace) off-range values in a spectrum
clean.reflector_mspct | Clean (=replace) off-range values in a spectrum
clean.reflector_spct | Clean (=replace) off-range values in a spectrum
clean.response_mspct | Clean (=replace) off-range values in a spectrum
clean.response_spct | Clean (=replace) off-range values in a spectrum
clean.source_mspct | Clean (=replace) off-range values in a spectrum
clean.source_spct | Clean (=replace) off-range values in a spectrum
clear.spct | Theoretical spectrum of a clear material
clear_body.spct | Theoretical clear body
clip_wl | Clip head and/or tail of a spectrum
clip_wl.default | Clip head and/or tail of a spectrum
clip_wl.generic_mspct | Clip head and/or tail of a spectrum
clip_wl.generic_spct | Clip head and/or tail of a spectrum
clip_wl.list | Clip head and/or tail of a spectrum
clip_wl.waveband | Clip head and/or tail of a spectrum
color | Color of an object
color_of | Color of an object
color_of.default | Color of an object
color_of.list | Color of an object
color_of.numeric | Color of an object
color_of.source_mspct | Color of an object
color_of.source_spct | Color of an object
color_of.waveband | Color of an object
colour_of | Color of an object
convertTimeUnit | Convert the "time.unit" attribute of an existing source_spct object
convolve_each | Convolve function for collections of spectra
copy_attributes | Copy attributes
copy_attributes.default | Copy attributes
copy_attributes.generic_spct | Copy attributes
copy_attributes.waveband | Copy attributes
cos.generic_spct | Trigonometric Functions
cospi.generic_spct | Trigonometric Functions
cps2irrad | Conversion from counts per second to physical quantities
cps2Rfr | Conversion from counts per second to physical quantities
cps2Tfr | Conversion from counts per second to physical quantities
cps_mspct | Collection-of-spectra constructor
cps_spct | Spectral-object constructor

## -- D --

D2.UV586 | Data for typical calibration lamps
D2.UV653 | Data for typical calibration lamps
D2.UV654 | Data for typical calibration lamps
D2_spectrum | Calculate deuterium lamp output spectrum from fitted constants
D65.illuminant.spct | CIE D65 illuminant data
day_length | Times for sun positions
day_night | Times for sun positions
day_night_fast | Times for sun positions
defunct | Defunct functions and methods
dim.generic_mspct | Dimensions of an Object
dim<-.generic_mspct | Dimensions of an Object
div-.generic_spct | Arithmetic Operators
div_spectra | Divide two spectra, even if the wavelengths values differ

## -- E --

e2q | Convert energy-based quantities into photon-based quantities.
e2q.default | Convert energy-based quantities into photon-based quantities.
e2q.response_mspct | Convert energy-based quantities into photon-based quantities.
e2q.response_spct | Convert energy-based quantities into photon-based quantities.
e2q.source_mspct | Convert energy-based quantities into photon-based quantities.
e2q.source_spct | Convert energy-based quantities into photon-based quantities.
e2qmol_multipliers | Calculate energy to quantum (mol) multipliers
e2quantum_multipliers | Calculate energy to quantum multipliers
energy_as_default | Set spectral-data options
energy_irradiance | Calculate (energy) irradiance from spectral irradiance
energy_ratio | Energy:energy ratio
eq_ratio | Energy:photon ratio
eq_ratio.default | Energy:photon ratio
eq_ratio.source_mspct | Energy:photon ratio
eq_ratio.source_spct | Energy:photon ratio
exp.generic_spct | Logarithms and Exponentials
expanse | Expanse
expanse.default | Expanse
expanse.generic_mspct | Expanse
expanse.generic_spct | Expanse
expanse.numeric | Expanse
expanse.waveband | Expanse
extend2extremes | Trim (or expand) head and/or tail of a spectrum
Extract | Extract or replace parts of a spectrum
Extract_mspct | Extract or replace members of a collection of spectra
e_fluence | Energy fluence
e_fluence.default | Energy fluence
e_fluence.source_mspct | Energy fluence
e_fluence.source_spct | Energy fluence
e_irrad | Energy irradiance
e_irrad.default | Energy irradiance
e_irrad.source_mspct | Energy irradiance
e_irrad.source_spct | Energy irradiance
e_ratio | Energy:energy ratio
e_ratio.default | Energy:energy ratio
e_ratio.source_mspct | Energy:energy ratio
e_ratio.source_spct | Energy:energy ratio
e_response | Energy-based photo-response
e_response.default | Energy-based photo-response
e_response.response_mspct | Energy-based photo-response
e_response.response_spct | Energy-based photo-response

## -- F --

FEL.BN.9101.165 | Data for typical calibration lamps
FEL_spectrum | Incandescent "FEL" lamp emission spectrum
filter_mspct | Collection-of-spectra constructor
filter_spct | Spectral-object constructor
findMultipleWl | Find repeated w.length values
find_peaks | Find peaks in a spectrum
floor.generic_spct | Rounding of Numbers
fluence | Fluence
fluence.default | Fluence
fluence.source_mspct | Fluence
fluence.source_spct | Fluence
format.solar_time | Encode in a Common Format
formatted_range | Compute range and format it
fscale | Rescale a spectrum using a summary function
fscale.cps_mspct | Rescale a spectrum using a summary function
fscale.cps_spct | Rescale a spectrum using a summary function
fscale.default | Rescale a spectrum using a summary function
fscale.filter_mspct | Rescale a spectrum using a summary function
fscale.filter_spct | Rescale a spectrum using a summary function
fscale.generic_mspct | Rescale a spectrum using a summary function
fscale.generic_spct | Rescale a spectrum using a summary function
fscale.raw_mspct | Rescale a spectrum using a summary function
fscale.raw_spct | Rescale a spectrum using a summary function
fscale.reflector_mspct | Rescale a spectrum using a summary function
fscale.reflector_spct | Rescale a spectrum using a summary function
fscale.response_mspct | Rescale a spectrum using a summary function
fscale.response_spct | Rescale a spectrum using a summary function
fscale.source_mspct | Rescale a spectrum using a summary function
fscale.source_spct | Rescale a spectrum using a summary function
fshift | Shift the scale of a spectrum using a summary function
fshift.cps_mspct | Shift the scale of a spectrum using a summary function
fshift.cps_spct | Shift the scale of a spectrum using a summary function
fshift.default | Rescale a spectrum using a summary function
fshift.filter_mspct | Shift the scale of a spectrum using a summary function
fshift.filter_spct | Shift the scale of a spectrum using a summary function
fshift.generic_mspct | Shift the scale of a spectrum using a summary function
fshift.generic_spct | Shift the scale of a spectrum using a summary function
fshift.raw_mspct | Shift the scale of a spectrum using a summary function
fshift.raw_spct | Shift the scale of a spectrum using a summary function
fshift.reflector_mspct | Shift the scale of a spectrum using a summary function
fshift.reflector_spct | Shift the scale of a spectrum using a summary function
fshift.response_mspct | Shift the scale of a spectrum using a summary function
fshift.response_spct | Shift the scale of a spectrum using a summary function
fshift.source_mspct | Shift the scale of a spectrum using a summary function
fshift.source_spct | Shift the scale of a spectrum using a summary function
f_mspct | Defunct functions and methods

## -- G --

generic_mspct | Collection-of-spectra constructor
generic_spct | Spectral-object constructor
geocode2tb | Copy attributes from members of a generic_mspct
getAfrType | Get the "Afr.type" attribute
getBSWFUsed | Get the "bswf.used" attribute
getIdFactor | Get the "idfactor" attribute
getInstrDesc | Get the "instr.desc" attribute
getInstrSettings | Get the "instr.settings" attribute
getMspctVersion | Get the "mspct.version" attribute
getMultipleWl | Get the "multiple.wl" attribute
getNormalized | Get the "normalized" attribute
getRfrType | Get the "Rfr.type" attribute
getScaled | Get the "scaled" attribute
getSpctVersion | Get the "spct.version" attribute
getTfrType | Get the "Tfr.type" attribute
getTimeUnit | Get the "time.unit" attribute of an existing source_spct object
getWhatMeasured | Get the "what.measured" attribute
getWhenMeasured | Get the "when.measured" attribute
getWhenMeasured.default | Get the "when.measured" attribute
getWhenMeasured.generic_mspct | Get the "when.measured" attribute
getWhenMeasured.generic_spct | Get the "when.measured" attribute
getWhenMeasured.summary_generic_spct | Get the "when.measured" attribute
getWhereMeasured | Get the "where.measured" attribute
getWhereMeasured.default | Get the "where.measured" attribute
getWhereMeasured.generic_mspct | Get the "where.measured" attribute
getWhereMeasured.generic_spct | Get the "where.measured" attribute
getWhereMeasured.summary_generic_spct | Get the "where.measured" attribute
get_attributes | Get the metadata attributes
get_attributes.filter_spct | Get the metadata attributes
get_attributes.generic_spct | Get the metadata attributes
get_attributes.object_spct | Get the metadata attributes
get_attributes.reflector_spct | Get the metadata attributes
get_attributes.source_spct | Get the metadata attributes
get_attributes.waveband | Get the metadata attributes
get_peaks | Get peaks and valleys in a spectrum
get_valleys | Get peaks and valleys in a spectrum
green_leaf.spct | Green birch leaf reflectance.

## -- H --

head_tail | Return the First and Last Part of an Object
head_tail.data.frame | Return the First and Last Part of an Object
head_tail.default | Return the First and Last Part of an Object
head_tail.ftable | Return the First and Last Part of an Object
head_tail.function | Return the First and Last Part of an Object
head_tail.matrix | Return the First and Last Part of an Object
head_tail.table | Return the First and Last Part of an Object

## -- I --

insert_hinges | Insert wavelength values into spectral data.
insert_spct_hinges | Insert new wavelength values into a spectrum
integrate_spct | Integrate spectral data.
integrate_xy | Gives irradiance from spectral irradiance.
interpolate_mspct | Map a spectrum to new wavelength values.
interpolate_spct | Map a spectrum to new wavelength values.
interpolate_spectrum | Calculate spectral values at a different set of wavelengths
interpolate_wl | Map spectra to new wavelength values.
interpolate_wl.default | Map spectra to new wavelength values.
interpolate_wl.generic_mspct | Map spectra to new wavelength values.
interpolate_wl.generic_spct | Map spectra to new wavelength values.
irrad | Irradiance
irrad.default | Irradiance
irrad.source_mspct | Irradiance
irrad.source_spct | Irradiance
irradiance | Photon or energy irradiance from spectral energy or photon irradiance.
is.any_mspct | Query class of spectrum objects
is.any_spct | Query class of spectrum objects
is.any_summary_spct | Query class of spectrum summary objects
is.calibration_mspct | Query class of spectrum objects
is.calibration_spct | Query class of spectrum objects
is.chroma_mspct | Query class of spectrum objects
is.chroma_spct | Query class of spectrum objects
is.cps_mspct | Query class of spectrum objects
is.cps_spct | Query class of spectrum objects
is.filter_mspct | Query class of spectrum objects
is.filter_spct | Query class of spectrum objects
is.generic_mspct | Query class of spectrum objects
is.generic_spct | Query class of spectrum objects
is.object_mspct | Query class of spectrum objects
is.object_spct | Query class of spectrum objects
is.old_spct | Query if an object has old class names
is.raw_mspct | Query class of spectrum objects
is.raw_spct | Query class of spectrum objects
is.reflector_mspct | Query class of spectrum objects
is.reflector_spct | Query class of spectrum objects
is.response_mspct | Query class of spectrum objects
is.response_spct | Query class of spectrum objects
is.solar_date | Query class
is.solar_time | Query class
is.source_mspct | Query class of spectrum objects
is.source_spct | Query class of spectrum objects
is.summary_chroma_spct | Query class of spectrum summary objects
is.summary_cps_spct | Query class of spectrum summary objects
is.summary_filter_spct | Query class of spectrum summary objects
is.summary_generic_spct | Query class of spectrum summary objects
is.summary_object_spct | Query class of spectrum summary objects
is.summary_raw_spct | Query class of spectrum summary objects
is.summary_reflector_spct | Query class of spectrum summary objects
is.summary_response_spct | Query class of spectrum summary objects
is.summary_source_spct | Query class of spectrum summary objects
is.waveband | Query if it is a waveband
isValidInstrDesc | Check the "instr.desc" attribute
isValidInstrSettings | Check the "instr.settings" attribute
is_absorbance_based | Query if a spectrum contains absorbance or transmittance data
is_effective | Is an R object "effective"
is_effective.default | Is an R object "effective"
is_effective.generic_spct | Is an R object "effective"
is_effective.source_spct | Is an R object "effective"
is_effective.summary_generic_spct | Is an R object "effective"
is_effective.summary_source_spct | Is an R object "effective"
is_effective.waveband | Is an R object "effective"
is_energy_based | Query if a spectrum contains photon- or energy-based data.
is_normalized | Query whether a generic spectrum has been normalized.
is_photon_based | Query if a spectrum contains photon- or energy-based data.
is_scaled | Query whether a generic spectrum has been scaled
is_tagged | Query if it is an spectrum is tagged
is_transmittance_based | Query if a spectrum contains absorbance or transmittance data

## -- J --

join_mspct | Join all spectra in a collection
join_mspct.default | Join all spectra in a collection
join_mspct.filter_mspct | Join all spectra in a collection
join_mspct.generic_mspct | Join all spectra in a collection
join_mspct.object_mspct | Join all spectra in a collection
join_mspct.reflector_mspct | Join all spectra in a collection
join_mspct.response_mspct | Join all spectra in a collection
join_mspct.source_mspct | Join all spectra in a collection

## -- L --

labels | Find labels from "waveband" object
labels.generic_spct | Find labels from "waveband" object
labels.waveband | Find labels from "waveband" object
lat2tb | Copy attributes from members of a generic_mspct
Ler_leaf.spct | Green Arabidopsis leaf reflectance and transmittance.
Ler_leaf_rflt.spct | Green Arabidopsis leaf spectral reflectance.
Ler_leaf_trns.spct | Green Arabidopsis leaf spectral transmittance.
Ler_leaf_trns_i.spct | Green Arabidopsis leaf spectral transmittance.
log | Logarithms and Exponentials
log.generic_spct | Logarithms and Exponentials
log10.generic_spct | Logarithms and Exponentials
log2.generic_spct | Logarithms and Exponentials
lon2tb | Copy attributes from members of a generic_mspct

## -- M --

mat2mspct | Coerce to a collection-of-spectra
MathFun | Miscellaneous Mathematical Functions
max | Wavelength maximum
max.generic_mspct | Wavelength maximum
max.generic_spct | Wavelength maximum
max.waveband | Wavelength maximum
merge2object_spct | Merge into object_spct
merge_attributes | Merge and copy attributes
merge_attributes.default | Merge and copy attributes
merge_attributes.generic_spct | Merge and copy attributes
midpoint | Midpoint
midpoint.default | Midpoint
midpoint.generic_mspct | Midpoint
midpoint.generic_spct | Midpoint
midpoint.numeric | Midpoint
midpoint.waveband | Midpoint
min | Wavelength minimum
min.generic_mspct | Wavelength minimum
min.generic_spct | Wavelength minimum
min.waveband | Wavelength minimum
minus-.generic_spct | Arithmetic Operators
mod-.generic_spct | Arithmetic Operators
msaply | Multi-spct transform methods
msdply | Multi-spct transform methods
mslply | Multi-spct transform methods
msmsply | Multi-spct transform methods
mspct2mat | Coerce a collection of spectra into a matrix
mspct_classes | Names of multi-spectra classes
mutate_mspct | Defunct functions and methods

## -- N --

na.exclude.generic_spct | Handle Missing Values in Objects
na.omit.chroma_spct | Handle Missing Values in Objects
na.omit.cps_spct | Handle Missing Values in Objects
na.omit.filter_spct | Handle Missing Values in Objects
na.omit.raw_spct | Handle Missing Values in Objects
na.omit.reflector_spct | Handle Missing Values in Objects
na.omit.response_spct | Handle Missing Values in Objects
na.omit.source_spct | Handle Missing Values in Objects
new_waveband | Waveband constructor method
night_length | Times for sun positions
noon_time | Times for sun positions
normalization | Normalization of an R object
normalization.default | Normalization of an R object
normalization.waveband | Normalization of an R object
normalize | Normalize spectral data
normalize.cps_mspct | Normalize spectral data
normalize.cps_spct | Normalize spectral data
normalize.default | Normalize spectral data
normalize.filter_mspct | Normalize spectral data
normalize.filter_spct | Normalize spectral data
normalize.generic_spct | Normalize spectral data
normalize.raw_mspct | Normalize spectral data
normalize.raw_spct | Normalize spectral data
normalize.reflector_mspct | Normalize spectral data
normalize.reflector_spct | Normalize spectral data
normalize.response_mspct | Normalize spectral data
normalize.response_spct | Normalize spectral data
normalize.source_mspct | Normalize spectral data
normalize.source_spct | Normalize spectral data
normalized_diff_ind | Calculate a normalized index.
normalize_range_arg | Normalize a range argument into a true numeric range

## -- O --

object_mspct | Collection-of-spectra constructor
object_spct | Spectral-object constructor
opaque.spct | Theoretical spectrum of an opaque material
oper_spectra | Binary operation on two spectra, even if the wavelengths values differ

## -- P --

peaks | Peaks or local maxima
peaks.cps_spct | Peaks or local maxima
peaks.data.frame | Peaks or local maxima
peaks.default | Peaks or local maxima
peaks.filter_spct | Peaks or local maxima
peaks.generic_mspct | Peaks or local maxima
peaks.generic_spct | Peaks or local maxima
peaks.numeric | Peaks or local maxima
peaks.reflector_spct | Peaks or local maxima
peaks.response_spct | Peaks or local maxima
peaks.source_spct | Peaks or local maxima
photobiology | photobiology: Photobiological Calculations
photodiode.spct | Spectral response of a GaAsP photodiode
photons_energy_ratio | Photon:energy ratio
photon_as_default | Set spectral-data options
photon_irradiance | Photon irradiance
photon_ratio | Photo:photon ratio
plus-.generic_spct | Arithmetic Operators
polyester.spct | Transmittance spectrum of clear polyester film
print | Print a spectral object
print.generic_mspct | Print a spectral object
print.generic_spct | Print a spectral object
print.solar_date | Print solar time and solar date objects
print.solar_time | Print solar time and solar date objects
print.summary_generic_spct | Print spectral summary
print.waveband | Print a "waveband" object
prod_spectra | Multiply two spectra, even if the wavelengths values differ

## -- Q --

q2e | Convert photon-based quantities into energy-based quantities
q2e.default | Convert photon-based quantities into energy-based quantities
q2e.response_mspct | Convert photon-based quantities into energy-based quantities
q2e.response_spct | Convert photon-based quantities into energy-based quantities
q2e.source_mspct | Convert photon-based quantities into energy-based quantities
q2e.source_spct | Convert photon-based quantities into energy-based quantities
qe_ratio | Photon:energy ratio
qe_ratio.default | Photon:energy ratio
qe_ratio.source_mspct | Photon:energy ratio
qe_ratio.source_spct | Photon:energy ratio
quantum_as_default | Set spectral-data options
q_fluence | Photon fluence
q_fluence.default | Photon fluence
q_fluence.source_mspct | Photon fluence
q_fluence.source_spct | Photon fluence
q_irrad | Photon irradiance
q_irrad.default | Photon irradiance
q_irrad.source_mspct | Photon irradiance
q_irrad.source_spct | Photon irradiance
q_ratio | Photon:photon ratio
q_ratio.default | Photon:photon ratio
q_ratio.source_mspct | Photon:photon ratio
q_ratio.source_spct | Photon:photon ratio
q_response | Photon-based photo-response
q_response.default | Photon-based photo-response
q_response.response_mspct | Photon-based photo-response
q_response.response_spct | Photon-based photo-response

## -- R --

range | Wavelength range
range.generic_mspct | Wavelength range
range.generic_spct | Wavelength range
range.waveband | Wavelength range
raw_mspct | Collection-of-spectra constructor
raw_spct | Spectral-object constructor
rbindspct | Row-bind spectra
reflectance | Reflectance
reflectance.default | Reflectance
reflectance.object_mspct | Reflectance
reflectance.object_spct | Reflectance
reflectance.reflector_mspct | Reflectance
reflectance.reflector_spct | Reflectance
reflector_mspct | Collection-of-spectra constructor
reflector_spct | Spectral-object constructor
relative_AM | Relative Air Mass (AM)
response | Integrated response
response.default | Integrated response
response.response_mspct | Integrated response
response.response_spct | Integrated response
response_mspct | Collection-of-spectra constructor
response_spct | Spectral-object constructor
rgb_spct | RGB color values
rmDerivedMspct | Remove "generic_mspct" and derived class attributes.
rmDerivedSpct | Remove "generic_spct" and derived class attributes.
round | Rounding of Numbers
round.generic_spct | Rounding of Numbers

## -- S --

setAfrType | Set the "Afr.type" attribute
setBSWFUsed | Set the "bswf.used" attribute
setCalibrationSpct | Convert an R object into a spectrum object.
setChromaSpct | Convert an R object into a spectrum object.
setCpsSpct | Convert an R object into a spectrum object.
setFilterSpct | Convert an R object into a spectrum object.
setGenericSpct | Convert an R object into a spectrum object.
setIdFactor | Set the "idfactor" attribute
setInstrDesc | Set the "instr.desc" attribute
setInstrSettings | Set the "instr.settings" attribute
setMultipleWl | Set the "multiple.wl" attribute
setNormalized | Set the "normalized" attribute
setObjectSpct | Convert an R object into a spectrum object.
setRawSpct | Convert an R object into a spectrum object.
setReflectorSpct | Convert an R object into a spectrum object.
setResponseSpct | Convert an R object into a spectrum object.
setRfrType | Set the "Rfr.type" attribute
setScaled | Set the "scaled" attribute
setSourceSpct | Convert an R object into a spectrum object.
setTfrType | Set the "Tfr.type" attribute
setTimeUnit | Set the "time.unit" attribute of an existing source_spct object
setWhatMeasured | Set the "what.measured" attribute
setWhenMeasured | Set the "when.measured" attribute
setWhenMeasured.default | Set the "when.measured" attribute
setWhenMeasured.generic_mspct | Set the "when.measured" attribute
setWhenMeasured.generic_spct | Set the "when.measured" attribute
setWhenMeasured.summary_generic_spct | Set the "when.measured" attribute
setWhereMeasured | Set the "where.measured" attribute
setWhereMeasured.default | Set the "where.measured" attribute
setWhereMeasured.generic_mspct | Set the "where.measured" attribute
setWhereMeasured.generic_spct | Set the "where.measured" attribute
setWhereMeasured.summary_generic_spct | Set the "where.measured" attribute
shared_member_class | Classes common to all collection members.
sign | Sign
sign.generic_spct | Sign
signif.generic_spct | Rounding of Numbers
sin.generic_spct | Trigonometric Functions
sinpi.generic_spct | Trigonometric Functions
slash-.generic_spct | Arithmetic Operators
smooth_spct | Smooth a spectrum
smooth_spct.default | Smooth a spectrum
smooth_spct.filter_spct | Smooth a spectrum
smooth_spct.reflector_spct | Smooth a spectrum
smooth_spct.response_spct | Smooth a spectrum
smooth_spct.source_spct | Smooth a spectrum
solar_time | Local solar time
source_mspct | Collection-of-spectra constructor
source_spct | Spectral-object constructor
spct_classes | Function that returns a vector containing the names of spectra classes.
split2calibration_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2cps_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2filter_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2raw_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2reflector_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2response_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split2source_mspct | Convert a 'wide' or untidy data frame into a collection of spectra
split_bands | List-of-wavebands constructor
split_energy_irradiance | Energy irradiance for split spectrum regions
split_irradiance | Energy or photon irradiance for split spectrum regions
split_photon_irradiance | Photon irradiance for split spectrum regions
spread | Expanse
sqrt.generic_spct | Miscellaneous Mathematical Functions
stepsize | Stepsize
stepsize.default | Stepsize
stepsize.generic_mspct | Stepsize
stepsize.generic_spct | Stepsize
stepsize.numeric | Stepsize
strict_range_as_default | Set error reporting options
subset2mspct | Convert 'long' or tidy spectral data into a collection of spectra
subt_spectra | Subtract two spectra
summary | Summary of a spectral object
summary.generic_spct | Summary of a spectral object
summary_spct_classes | Function that returns a vector containing the names of spectral summary classes.
sum_spectra | Add two spectra
sun.daily.data | Daily solar spectral irradiance (simulated)
sun.daily.spct | Daily solar spectral irradiance (simulated)
sun.data | Solar spectral irradiance (simulated)
sun.spct | Solar spectral irradiance (simulated)
sunrise_time | Times for sun positions
sunset_time | Times for sun positions
sun_angles | Solar angles
sun_angles_fast | Solar angles
sun_azimuth | Solar angles
sun_elevation | Solar angles
sun_zenith_angle | Solar angles
s_e_irrad2rgb | Spectral irradiance to rgb color conversion

## -- T --

T2A | Convert transmittance into absorbance.
T2A.default | Convert transmittance into absorbance.
T2A.filter_mspct | Convert transmittance into absorbance.
T2A.filter_spct | Convert transmittance into absorbance.
T2Afr | Convert transmittance into absorptance.
T2Afr.default | Convert transmittance into absorptance.
T2Afr.filter_mspct | Convert transmittance into absorptance.
T2Afr.filter_spct | Convert transmittance into absorptance.
T2Afr.object_mspct | Convert transmittance into absorptance.
T2Afr.object_spct | Convert transmittance into absorptance.
T2T | Convert transmittance type.
T2T.default | Convert transmittance type.
T2T.filter_mspct | Convert transmittance type.
T2T.filter_spct | Convert transmittance type.
T2T.object_mspct | Convert transmittance type.
T2T.object_spct | Convert transmittance type.
tag | Tag a spectrum
tag.default | Tag a spectrum
tag.generic_mspct | Tag a spectrum
tag.generic_spct | Tag a spectrum
tan.generic_spct | Trigonometric Functions
tanpi.generic_spct | Trigonometric Functions
Tfr_as_default | Set spectral-data options
times-.generic_spct | Arithmetic Operators
transmittance | Transmittance
transmittance.default | Transmittance
transmittance.filter_mspct | Transmittance
transmittance.filter_spct | Transmittance
transmittance.object_mspct | Transmittance
transmittance.object_spct | Transmittance
Trig | Trigonometric Functions
trim2overlap | Trim (or expand) head and/or tail of a spectrum
trimInstrDesc | Trim the "instr.desc" attribute
trimInstrSettings | Trim the "instr.settings" attribute
trim_mspct | Trim (or expand) head and/or tail of a spectrum
trim_spct | Trim (or expand) head and/or tail of a spectrum
trim_tails | Trim (or expand) head and/or tail
trim_waveband | Trim (or expand) head and/or tail
trim_wl | Trim head and/or tail of a spectrum
trim_wl.default | Trim head and/or tail of a spectrum
trim_wl.generic_mspct | Trim head and/or tail of a spectrum
trim_wl.generic_spct | Trim head and/or tail of a spectrum
trim_wl.list | Trim head and/or tail of a spectrum
trim_wl.waveband | Trim head and/or tail of a spectrum
trunc.generic_spct | Rounding of Numbers
tz_time_diff | Time difference between two time zones

## -- U --

unset_filter_qty_default | Set spectral-data options
unset_radiation_unit_default | Set spectral-data options
unset_user_defaults | Set spectral-data options
untag | Remove tags
untag.default | Remove tags
untag.generic_mspct | Remove tags
untag.generic_spct | Remove tags
upgrade_spct | Upgrade one spectral object
upgrade_spectra | Upgrade one or more spectral objects
use_cached_mult_as_default | Set computation options
using_A | Use photobiology options
using_Afr | Use photobiology options
using_energy | Use photobiology options
using_photon | Use photobiology options
using_quantum | Use photobiology options
using_Tfr | Use photobiology options

## -- V --

valleys | Valleys or local minima
valleys.cps_spct | Valleys or local minima
valleys.data.frame | Valleys or local minima
valleys.default | Valleys or local minima
valleys.filter_spct | Valleys or local minima
valleys.generic_mspct | Valleys or local minima
valleys.generic_spct | Valleys or local minima
valleys.numeric | Valleys or local minima
valleys.reflector_spct | Valleys or local minima
valleys.response_spct | Valleys or local minima
valleys.source_spct | Valleys or local minima
verbose_as_default | Set error reporting options
v_insert_hinges | Insert wavelength values into spectral data.

## -- W --

water_dp | Water vapour pressure
water_mvc2vp | Water vapour pressure
water_vp2mvc | Water vapour pressure
water_vp_sat | Water vapour pressure
waveband | Waveband constructor method
waveband_ratio | Photon or energy ratio
wb2rect_spct | Create tagged spectrum from wavebands
wb2spct | Create spectrum from wavebands
wb2tagged_spct | Create tagged spectrum from wavebands
wb_trim_as_default | Set computation options
what_measured2tb | Copy attributes from members of a generic_mspct
when_measured2tb | Copy attributes from members of a generic_mspct
white_body.spct | Theoretical white body
white_led.cps_spct | White led bulb spectrum
white_led.raw_spct | White led bulb spectrum
white_led.source_spct | White led bulb spectrum
wl_expanse | Expanse
wl_max | Wavelength maximum
wl_midpoint | Midpoint
wl_min | Wavelength minimum
wl_range | Wavelength range
wl_stepsize | Stepsize
w_length2rgb | Wavelength to rgb color conversion
w_length_range2rgb | Wavelength range to rgb color conversion

## -- Y --

yellow_gel.spct | Transmittance spectrum of yellow theatrical gel.

## -- misc --

$<-.generic_mspct | Extract or replace members of a collection of spectra
$<-.generic_spct | Extract or replace parts of a spectrum
%%.generic_spct | Arithmetic Operators
%/%.generic_spct | Arithmetic Operators
*.generic_spct | Arithmetic Operators
+.generic_spct | Arithmetic Operators
-.generic_spct | Arithmetic Operators
/.generic_spct | Arithmetic Operators
[.chroma_spct | Extract or replace parts of a spectrum
[.cps_spct | Extract or replace parts of a spectrum
[.filter_spct | Extract or replace parts of a spectrum
[.generic_mspct | Extract or replace members of a collection of spectra
[.generic_spct | Extract or replace parts of a spectrum
[.object_spct | Extract or replace parts of a spectrum
[.raw_spct | Extract or replace parts of a spectrum
[.reflector_spct | Extract or replace parts of a spectrum
[.response_spct | Extract or replace parts of a spectrum
[.source_spct | Extract or replace parts of a spectrum
[<-.generic_mspct | Extract or replace members of a collection of spectra
[<-.generic_spct | Extract or replace parts of a spectrum
[[<-.generic_mspct | Extract or replace members of a collection of spectra
^.generic_spct | Arithmetic Operators