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photobiology (version 0.9.4)

Photobiological Calculations

Description

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. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision.

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Install

install.packages('photobiology')

Monthly Downloads

1,001

Version

0.9.4

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

February 1st, 2016

Functions in photobiology (0.9.4)

function to be numerically minimized

absorbance_spct

Calculate absorbance from spectral absorbance.

Sanity check of wavelengths (internal function).

Linear energy CIE 2008 luminous efficiency function 2 deg data

ciexyzCMF10.spct

Linear energy CIE xyz colour matching function (CMF) 10 deg data

Incandescent "FEL" lamp emission spectrum

Average spectral data.

checkSpctVersion

Check that the "spct.version" attribute is set

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

e_irrad.source_mspct

Energy irradiance

Color of an object

is.generic_spct

Query class of spectrum objects

Peaks or local maxima

plus-.generic_spct

Arithmetic Operators

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

date argument check and conversion

clear_photobio.cache

clear the spectral weights cache

Integrate spectral data.

Extract or replace parts of a spectrum

as.generic_spct

Spectral-object copy constructor

Miscellaneous Mathematical Functions

Theoretical spectrum of a clear clear material

e_ratio.source_mspct

Energy:energy ratio

Names of multi-spectra classes

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

max.generic_mspct

Maximun wavelength

Clip head and/or tail of a spectrum

Wavelength range

setWhenMeasured.generic_mspct

Set the "when.measured" attribute

Photo:photon ratio

Convert transmittance into absorbance.

range.generic_mspct

Range of wavelength

Remove "generic_mspct" and derived class attributes.

Convert spectral energy irradiance into spectral photon irradiance

color.source_mspct

w_length_range2rgb

Wavelength range to rgb color conversion

Calculate response from spectral response

labels.generic_spct

Find labels from spectral object

checkMspctVersion

Check that the "mspct.version" attribute is set

ciexyzCMF2.spct

Linear energy CIE xyz colour matching function (CMF) 2 deg data

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

calc_multipliers

Spectral weights

Query which is the class of an spectrum

Convolve function for collections of spectra

Get peaks and valleys in a spectrum

Get the "Rfr.type" attribute

e2quantum_multipliers

Calculate energy to quantum multipliers

Times for sun positions

eq_ratio.source_mspct

Energy:photon ratio

Spectrum to rgb color conversion

irrad.source_mspct

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

Get the "spct.version" attribute

midpoint.generic_mspct

Central wavelength value

print.generic_mspct

Print a spectral collection object

print.summary_generic_spct

Print spectral summary

Set the "scaled" attribute

Check validity of spectral objects

setWhereMeasured.generic_mspct

Set the "where.measured" attribute

Get the "scaled" attribute

D65.illuminant.spct

CIE D65 illuminant data

photons_energy_ratio

Photon:energy ratio

Multiply two spectra, even if the wavelengths values differ

shared_member_class

Classes common to all collection members.

fshift a spectrum

q_ratio.source_mspct

Photon:photon ratio

absorbance.filter_mspct

transmittance.filter_mspct

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

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

is.generic_mspct

Query class of spectrum objects

absorptance.filter_mspct

calc_source_output

Light-source spectral output

reflectance_spct

Calculate reflectance from spectral reflectance

is.summary_generic_spct

Query class of spectrum summary objects

Rescale a spectrum using a summary function

getWhereMeasured.generic_mspct

Get the "where.measured" attribute

Query whether a generic spectrum has been normalized.

slash-.generic_spct

Arithmetic Operators

Query whether a generic spectrum has been scaled

Logarithms and Exponentials

stepsize.generic_mspct

c.generic_mspct

Combine collections of spectra

Create tagged spectrum from wavebands

Set the "multiple.wl" attribute

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

Calculate deuterim lamp output spectrum from fitted constants

Wavelength to rgb color conversion

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Spectral-object constructor

Collection-of-spectra constructor

is_effective.summary_generic_spct

Is an R object "effective"

labels.waveband

Find labels from "waveband" object

normalized_diff_ind

Calculate a normalized index.

convertTimeUnit

Convert the "time.unit" attribute of an existing source_spct object

Convert spectral photon irradiance into spectral energy irradiance

Query if it is a waveband

CIE xyz chromaticity coordinates 2 deg data

min.generic_mspct

Minimum wavelength

Waveband constructor method

is_photon_based

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

Transmittance spectrum of clear polyester film

mod-.generic_spct

Arithmetic Operators

Add two spectra

black_body.spct

Theoretical black body

q_irrad.source_mspct

Photon irradiance

Row-bind spectra

Convert spectral energy irradiance into spectral photon irradiance

insert_spct_hinges

Insert new wavelength values into a spectrum

clear_body.spct

Theoretical clear body

Set the "Tfr.type" attribute

div-.generic_spct

Arithmetic Operators

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

Print a "waveband" object

dim.generic_mspct

Dimensions of an Object

Solar spectral irradiance (simulated)

Spectral response of a back-thinned CCD image sensor.

Energy:energy ratio

getInstrSettings

Get the "instr.settings" attribute

Solar spectral irradiance (simulated)

Get the "normalized" attribute

Multi-spct transform methods

Valleys or local minima

Gives irradiance from spectral irradiance.

qe_ratio.source_mspct

Photon:energy ratio

Insert wavelength values into spectral data.

merge.generic_spct

Merge two generic_spct objects

Set the "instr.desc" attribute

Set the "Rfr.type" attribute

Linear energy CIE 2008 luminous efficiency function 10 deg data

Normalize spectral data

Smooth a spectrum

Subtract two spectra

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

fluence.source_mspct

Divide two spectra, even if the wavelengths values differ

Trim head and/or tail of a spectrum

Arithmetic Operators

Photon or energy ratio

Insert interpolated spectral irradiance values.

absorptance_spct

Calculate absorptance from spectral absorptance.

photodiode.spct

Spectral response of a GaAsP photodiode

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

RGB color values

Get the "instr.desc" attribute

q_response.response_mspct

Photon-based photo-response

getWhenMeasured.generic_mspct

Get the "when.measured" attribute

photobiology-package

Photobiological Calculations

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

q_fluence.source_mspct

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

Get the "multiple.wl" attribute

minus-.generic_spct

Arithmetic Operators

Theoretical spectrum of an opaque material

upgrade_spectra

Upgrade one or more spectral objects

print.generic_spct

Print a spectral object

split_energy_irradiance

Energy irradiance for split spectrum regions

normalize_range_arg

Normalize a range argument into a true numeric range

transmittance_spct

Calculate transmittance from spectral transmittance.

e_response.response_mspct

Energy-based photo-response

Rounding of Numbers

twilight argument check and conversion

Find peaks in a spectrum

summary.generic_spct

Summary of a spectral object

Convert an R object into a spectrum object.

split_irradiance

Energy or photon irradiance for split spectrum regions

response.response_mspct

Integrated response

Extract or replace members of a collection of spectra

time argument check and conversion

Get the "Tfr.type" attribute

Wavelength maximum

Convert photon-based quantities into energy-based quantities

setInstrSettings

Set the "instr.settings" attribute

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

Trim (or expand) head and/or tail

white_body.spct

Theoretical white body

times-.generic_spct

Arithmetic Operators

Daily solar spectral irradiance (simulated)

List-of-wavebands constructor

Trim (or expand) head and/or tail

Create tagged spectrum from wavebands

Remove "generic_spct" and derived class attributes.

Trim (or expand) head and/or tail

summary_spct_classes

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

A.illuminant.spct

CIE A illuminant data

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

Convert energy-based quantities into photon-based quantities.

e_fluence.source_mspct

fscale a spectrum

Shift the scale of a spectrum using a summary function

Get the "bswf.used" attribute

Wavelength minimum

Map spectra to new wavelength values.

reflectance.reflector_mspct

Set the "bswf.used" attribute

Set the "normalized" attribute

split_photon_irradiance

Photon irradiance for split spectrum regions

spread.generic_mspct

Length of object in wavelength units

Normalization of an R object

photon_irradiance

Photon irradiance

Upgrade one spectral object

Create spectrum from wavebands

Convert absorbance into transmittance

Trigonometric Functions

as.generic_mspct

Collection-of-spectra copy-constructor

Sanity check of a spectrum.

Defunct functions and methods

Convert date to time-of-day in hours

f_dispatcher_spct

Math function dispatcher for spectra

getMspctVersion

Get the "mspct.version" attribute

Query if it is an spectrum is tagged

Query if an object has old class names

interpolate_spct

Map a spectrum to new wavelength values.

Daily solar spectral irradiance (simulated)