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photobiology

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Version

Install

install.packages('photobiology')

Monthly Downloads

649

Version

0.9.16

License

GPL (>= 2)

Maintainer

Pedro Aphalo

Last Published

June 25th, 2017

Functions in photobiology (0.9.16)

D2.UV586

Data for typical calibration lamps
D2.UV653

Data for typical calibration lamps
A.illuminant.spct

CIE A illuminant data
A2T

Convert absorbance into transmittance
absorbance

Absorbance
absorbance_spct

Calculate absorbance from spectral absorbance.
D65.illuminant.spct

CIE D65 illuminant data
FEL.BN.9101.165

Data for typical calibration lamps
as.solar_date

Convert a solar_time object into solar_date object
as_energy

Convert spectral photon irradiance into spectral energy irradiance
calc_source_output

Light-source spectral output
ccd.spct

Spectral response of a back-thinned CCD image sensor.
ciev10.spct

Linear energy CIE 2008 luminous efficiency function 10 deg data
ciev2.spct

Linear energy CIE 2008 luminous efficiency function 2 deg data
T2A

Convert transmittance into absorbance.
Trig

Trigonometric Functions
beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data
black_body.spct

Theoretical black body
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
copy_attributes

Copy attributes from one R object to another
cps2irrad

Conversion from counts per second to physical quantities
e_ratio

Energy:energy ratio
e_response

Energy-based photo-response
fluence

Fluence
format.solar_time

Encode in a Common Format
getInstrDesc

Get the "instr.desc" attribute
getInstrSettings

Get the "instr.settings" attribute
getTfrType

Get the "Tfr.type" attribute
FEL_spectrum

Incandescent "FEL" lamp emission spectrum
MathFun

Miscellaneous Mathematical Functions
absorptance

Absorptance
absorptance_spct

Calculate absorptance from spectral absorptance.
getTimeUnit

Get the "time.unit" attribute of an existing source_spct object
integrate_spct

Integrate spectral data.
integrate_xy

Gives irradiance from spectral irradiance.
isValidInstrSettings

Check the "instr.settings" attribute
ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data
ciexyzCC2.spct

CIE xyz chromaticity coordinates 2 deg data
clean_spct

Clean a spectrum
clear.spct

Theoretical spectrum of a clear clear material
D2.UV654

Data for typical calibration lamps
D2_spectrum

Calculate deuterim lamp output spectrum from fitted constants
as.generic_spct

Spectral-object copy constructor
as_tod

Convert date to time-of-day in hours, minutes or seconds
average_spct

Average spectral data.
check_spectrum

Sanity check of a spectrum.
check_w.length

Sanity check of wavelengths (internal function).
is_absorbance_based

Query if a spectrum contains absorbance or transmittance data
min

Wavelength minimum
minus-.generic_spct

Arithmetic Operators
normalization

Normalization of an R object
as.generic_mspct

Collection-of-spectra copy-constructor
normalize

Normalize spectral data
photodiode.spct

Spectral response of a GaAsP photodiode
photon_irradiance

Photon irradiance
q_irrad

Photon irradiance
c.generic_mspct

Combine collections of spectra
calc_multipliers

Spectral weights
checkMspctVersion

Check that the "mspct.version" attribute is set
checkSpctVersion

Check that the "spct.version" attribute is set
as_quantum

Convert spectral energy irradiance into spectral photon irradiance
as_quantum_mol

Convert spectral energy irradiance into spectral photon irradiance
checkTimeUnit

Check the "time.unit" attribute of an existing source_spct object
check_spct

Check validity of spectral objects
clear_body.spct

Theoretical clear body
clear_photobio.cache

clear the spectral weights cache
div_spectra

Divide two spectra, even if the wavelengths values differ
q_ratio

Photon:photon ratio
range

Wavelength range
rbindspct

Row-bind spectra
setGenericSpct

Convert an R object into a spectrum object.
setInstrDesc

Set the "instr.desc" attribute
e2q

Convert energy-based quantities into photon-based quantities.
energy_irradiance

Calculate (energy) irradiance from spectral irradiance
energy_ratio

Energy:energy ratio
filter_cps.mspct

Counts per second from a measurement of a plastic film
class_spct

Query which is the class of an spectrum
clean

Clean (=replace) off-range values in a spectrum
dim.generic_mspct

Dimensions of an Object
day_night

Times for sun positions
defunct

Defunct functions and methods
e_fluence

Energy fluence
find_peaks

Find peaks in a spectrum
getNormalized

Get the "normalized" attribute
getRfrType

Get the "Rfr.type" attribute
green_leaf.spct

Green birch leaf reflectance.
head_tail

Return the First and Last Part of an Object
clip_wl

Clip head and/or tail of a spectrum
color_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
interpolate_wl

Map spectra to new wavelength values.
irrad

Irradiance
is.solar_time

Query class
is.summary_generic_spct

Query class of spectrum summary objects
div-.generic_spct

Arithmetic Operators
e2qmol_multipliers

Calculate energy to quantum (mol) multipliers
e2quantum_multipliers

Calculate energy to quantum multipliers
fshift

Shift the scale of a spectrum using a summary function
fshift_spct

fshift a spectrum
getScaled

Get the "scaled" attribute
getSpctVersion

Get the "spct.version" attribute
getWhatMeasured

Get the "what.measured" attribute
eq_ratio

Energy:photon ratio
Extract

Extract or replace parts of a spectrum
fscale

Rescale a spectrum using a summary function
l_insert_hinges

Insert wavelength values into spectral data.
labels

Find labels from "waveband" object
normalize_range_arg

Normalize a range argument into a true numeric range
normalized_diff_ind

Calculate a normalized index.
fscale_spct

fscale a spectrum
generic_mspct

Collection-of-spectra constructor
getBSWFUsed

Get the "bswf.used" attribute
insert_hinges

Insert wavelength values into spectral data.
e_irrad

Energy irradiance
Extract_mspct

Extract or replace members of a collection of spectra
f_dispatcher_spct

Math function dispatcher for spectra
getMspctVersion

Get the "mspct.version" attribute
insert_spct_hinges

Insert new wavelength values into a spectrum
irradiance

Photon (quantum) irradiance from spectral (energy) irradiance.
is.generic_mspct

Query class of spectrum objects
plus-.generic_spct

Arithmetic Operators
polyester.spct

Transmittance spectrum of clear polyester film
print.solar_time

Print solar time and solar date objects
print.summary_generic_spct

Print spectral summary
reflectance

Reflectance
reflectance_spct

Calculate reflectance from spectral reflectance
s_e_irrad2rgb

Spectrum to rgb color conversion
setBSWFUsed

Set the "bswf.used" attribute
getWhenMeasured

Get the "when.measured" attribute
is.generic_spct

Query class of spectrum objects
is.old_spct

Query if an object has old class names
is_photon_based

Query if a spectrum contains photon- or energy-based data.
solar_time

Local solar time
source_spct

Spectral-object constructor
spct_classes

Function that returns a vector containing the names of spectra classes.
split2mspct

Convert a 'wide' or untidy data frame into a collection of spectra
is.waveband

Query if it is a waveband
isValidInstrDesc

Check the "instr.desc" attribute
is_tagged

Query if it is an spectrum is tagged
julian_day

Solar astronomy using Meeus' algorithm
sun.daily.spct

Daily solar spectral irradiance (simulated)
trimInstrDesc

Trim the "instr.desc" attribute
trimInstrSettings

Trim the "instr.settings" attribute
w_length_range2rgb

Wavelength range to rgb color conversion
waveband

Waveband constructor method
white_body.spct

Theoretical white body
white_led.cps_spct

White led bulb spectrum
sun.data

Solar spectral irradiance (simulated)
opaque.spct

Theoretical spectrum of an opaque material
oper_spectra

Binary operation on two spectra, even if the wavelengths values differ
peaks

Peaks or local maxima
photobiology-package

photobiology: Photobiological Calculations
is_scaled

Query whether a generic spectrum has been scaled
merge.generic_spct

Merge two generic_spct objects
midpoint

Central wavelength value
mspct_classes

Names of multi-spectra classes
na.omit.source_spct

Handle Missing Values in Objects
photon_ratio

Photo:photon ratio
photons_energy_ratio

Photon:energy ratio
print.waveband

Print a "waveband" object
setTimeUnit

Set the "time.unit" attribute of an existing source_spct object
setWhatMeasured

Set the "what.measured" attribute
spread

Length of object in wavelength units
stepsize

Stepsize
getMultipleWl

Get the "multiple.wl" attribute
getWhereMeasured

Get the "where.measured" attribute
get_peaks

Get peaks and valleys in a spectrum
sum_spectra

Add two spectra
summary

Summary of a spectral object
transmittance

Transmittance
transmittance_spct

Calculate transmittance from spectral transmittance.
interpolate_spct

Map a spectrum to new wavelength values.
interpolate_spectrum

Calculate spectral values at a different set of wavelengths
is_effective

Is an R object "effective"
is_normalized

Query whether a generic spectrum has been normalized.
log

Logarithms and Exponentials
max

Wavelength maximum
mod-.generic_spct

Arithmetic Operators
msmsply

Multi-spct transform methods
prod_spectra

Multiply two spectra, even if the wavelengths values differ
resp_spct

Calculate response from spectral response
response

Integrated response
setNormalized

Set the "normalized" attribute
q2e

Convert photon-based quantities into energy-based quantities
q_fluence

Photon fluence
rmDerivedSpct

Remove "generic_spct" and derived class attributes.
round

Rounding of Numbers
^.generic_spct

Arithmetic Operators
print

Print a spectral object
q_response

Photon-based photo-response
qe_ratio

Photon:energy ratio
rgb_spct

RGB color values
setInstrSettings

Set the "instr.settings" attribute
setMultipleWl

Set the "multiple.wl" attribute
setWhenMeasured

Set the "when.measured" attribute
setWhereMeasured

Set the "where.measured" attribute
rmDerivedMspct

Remove "generic_mspct" and derived class attributes.
setScaled

Set the "scaled" attribute
setTfrType

Set the "Tfr.type" attribute
shared_member_class

Classes common to all collection members.
split_bands

List-of-wavebands constructor
split_energy_irradiance

Energy irradiance for split spectrum regions
sun.spct

Solar spectral irradiance (simulated)
sun_angles

Solar angles
untag

Remove tags
upgrade_spct

Upgrade one spectral object
white_led.raw_spct

White led bulb spectrum
white_led.source_spct

White led bulb spectrum
sign

Sign
split_irradiance

Energy or photon irradiance for split spectrum regions
split_photon_irradiance

Photon irradiance for split spectrum regions
setRfrType

Set the "Rfr.type" attribute
slash-.generic_spct

Arithmetic Operators
smooth_spct

Smooth a spectrum
subset2mspct

Convert 'long' or tidy spectral data into a collection of spectra
subt_spectra

Subtract two spectra
tag

Tag a spectrum
times-.generic_spct

Arithmetic Operators
twilight2angle

twilight argument check and conversion
trim_waveband

Trim (or expand) head and/or tail
trim_wl

Trim head and/or tail of a spectrum
waveband_ratio

Photon or energy ratio
tz_time_diff

Time difference between two time zones
valleys

Valleys or local minima
w_length2rgb

Wavelength to rgb color conversion
yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.
wb2rect_spct

Create tagged spectrum from wavebands
wb2spct

Create spectrum from wavebands
wb2tagged_spct

Create tagged spectrum from wavebands
summary_spct_classes

Function that returns a vector containing the names of spectral summary classes.
sun.daily.data

Daily solar spectral irradiance (simulated)
trim_tails

Trim (or expand) head and/or tail
upgrade_spectra

Upgrade one or more spectral objects
v_insert_hinges

Insert wavelength values into spectral data.
trim_spct

Trim (or expand) head and/or tail