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photobiology (version 0.9.5)

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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Version

Install

install.packages('photobiology')

Monthly Downloads

1,001

Version

0.9.5

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

February 3rd, 2016

Functions in photobiology (0.9.5)

calc_source_output

Light-source spectral output

e_ratio.source_mspct

Energy:energy ratio

convertTimeUnit

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

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

fshift a spectrum

q_ratio.source_mspct

Photon:photon ratio

Energy:energy ratio

midpoint.generic_mspct

Central wavelength value

Linear energy CIE 2008 luminous efficiency function 2 deg data

range.generic_mspct

Range of wavelength

A.illuminant.spct

CIE A illuminant data

RGB color values

Collection-of-spectra constructor

getInstrSettings

Get the "instr.settings" attribute

photons_energy_ratio

Photon:energy ratio

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

transmittance.filter_mspct

getWhereMeasured.generic_mspct

Get the "where.measured" attribute

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

absorptance.filter_mspct

Sanity check of wavelengths (internal function).

Query which is the class of an spectrum

Set the "bswf.used" attribute

Add two spectra

Get the "spct.version" attribute

as.generic_mspct

Collection-of-spectra copy-constructor

Set the "scaled" attribute

as.generic_spct

Spectral-object copy constructor

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

Create tagged spectrum from wavebands

clear_body.spct

Theoretical clear body

color.source_mspct

eq_ratio.source_mspct

Energy:photon ratio

absorptance_spct

Calculate absorptance from spectral absorptance.

Query whether a generic spectrum has been normalized.

Convert an R object into a spectrum object.

Wavelength minimum

Defunct functions and methods

Average spectral data.

is.summary_generic_spct

Query class of spectrum summary objects

q_fluence.source_mspct

Valleys or local minima

photobiology-package

Photobiological Calculations

max.generic_mspct

Maximun wavelength

photon_irradiance

Photon irradiance

Get the "instr.desc" attribute

clear_photobio.cache

clear the spectral weights cache

is_effective.summary_generic_spct

Is an R object "effective"

Get the "scaled" attribute

absorbance_spct

Calculate absorbance from spectral absorbance.

Query whether a generic spectrum has been scaled

Divide two spectra, even if the wavelengths values differ

black_body.spct

Theoretical black body

mod-.generic_spct

Arithmetic Operators

q_response.response_mspct

Photon-based photo-response

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

Logarithms and Exponentials

e_response.response_mspct

Energy-based photo-response

Solar spectral irradiance (simulated)

e2quantum_multipliers

Calculate energy to quantum multipliers

Rounding of Numbers

absorbance.filter_mspct

reflectance.reflector_mspct

split_energy_irradiance

Energy irradiance for split spectrum regions

Gives irradiance from spectral irradiance.

fluence.source_mspct

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

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

fscale a spectrum

Set the "Rfr.type" attribute

Get peaks and valleys in a spectrum

Query if an object has old class names

plus-.generic_spct

Arithmetic Operators

Integrate spectral data.

getMspctVersion

Get the "mspct.version" attribute

Trigonometric Functions

c.generic_mspct

Combine collections of spectra

labels.generic_spct

Find labels from spectral object

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Remove "generic_mspct" and derived class attributes.

Print a "waveband" object

qe_ratio.source_mspct

Photon:energy ratio

CIE xyz chromaticity coordinates 2 deg data

ciexyzCMF2.spct

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

Arithmetic Operators

checkSpctVersion

Check that the "spct.version" attribute is set

Set the "multiple.wl" attribute

ciexyzCMF10.spct

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

Theoretical spectrum of a clear clear material

Daily solar spectral irradiance (simulated)

Convolve function for collections of spectra

setWhereMeasured.generic_mspct

Set the "where.measured" attribute

Query if it is an spectrum is tagged

Convert spectral energy irradiance into spectral photon irradiance

merge.generic_spct

Merge two generic_spct objects

Set the "instr.desc" attribute

Remove "generic_spct" and derived class attributes.

minus-.generic_spct

Arithmetic Operators

response.response_mspct

Integrated response

Convert energy-based quantities into photon-based quantities.

insert_spct_hinges

Insert new wavelength values into a spectrum

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

Photo:photon ratio

Convert absorbance into transmittance

split_irradiance

Energy or photon irradiance for split spectrum regions

e_irrad.source_mspct

Energy irradiance

Convert transmittance into absorbance.

Spectral-object constructor

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

print.generic_spct

Print a spectral object

function to be numerically minimized

Wavelength to rgb color conversion

white_body.spct

Theoretical white body

Upgrade one spectral object

split_photon_irradiance

Photon irradiance for split spectrum regions

shared_member_class

Classes common to all collection members.

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Solar spectral irradiance (simulated)

e_fluence.source_mspct

Convert spectral energy irradiance into spectral photon irradiance

time argument check and conversion

summary.generic_spct

Summary of a spectral object

calc_multipliers

Spectral weights

Wavelength range

Trim (or expand) head and/or tail

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

irrad.source_mspct

Peaks or local maxima

w_length_range2rgb

Wavelength range to rgb color conversion

reflectance_spct

Calculate reflectance from spectral reflectance

Shift the scale of a spectrum using a summary function

min.generic_mspct

Minimum wavelength

setInstrSettings

Set the "instr.settings" attribute

div-.generic_spct

Arithmetic Operators

Convert date to time-of-day in hours

Normalize spectral data

Normalization of an R object

Times for sun positions

twilight argument check and conversion

Extract or replace members of a collection of spectra

Multiply two spectra, even if the wavelengths values differ

date argument check and conversion

Get the "multiple.wl" attribute

stepsize.generic_mspct

Query if it is a waveband

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

photodiode.spct

Spectral response of a GaAsP photodiode

Waveband constructor method

Create spectrum from wavebands

setWhenMeasured.generic_mspct

Set the "when.measured" attribute

dim.generic_mspct

Dimensions of an Object

Get the "bswf.used" attribute

Get the "normalized" attribute

Daily solar spectral irradiance (simulated)

getWhenMeasured.generic_mspct

Get the "when.measured" attribute

slash-.generic_spct

Arithmetic Operators

Trim head and/or tail of a spectrum

Wavelength maximum

Names of multi-spectra classes

Multi-spct transform methods

Trim (or expand) head and/or tail

Photon or energy ratio

Subtract two spectra

Get the "Tfr.type" attribute

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

Convert photon-based quantities into energy-based quantities

q_irrad.source_mspct

Photon irradiance

spread.generic_mspct

Length of object in wavelength units

Spectrum to rgb color conversion

Calculate deuterim lamp output spectrum from fitted constants

Trim (or expand) head and/or tail

Calculate response from spectral response

upgrade_spectra

Upgrade one or more spectral objects

summary_spct_classes

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

Row-bind spectra

Insert wavelength values into spectral data.

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

Smooth a spectrum

normalized_diff_ind

Calculate a normalized index.

times-.generic_spct

Arithmetic Operators

Clip head and/or tail of a spectrum

D65.illuminant.spct

CIE D65 illuminant data

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

Incandescent "FEL" lamp emission spectrum

Spectral response of a back-thinned CCD image sensor.

Sanity check of a spectrum.

Linear energy CIE 2008 luminous efficiency function 10 deg data

Extract or replace parts of a spectrum

is.generic_spct

Query class of spectrum objects

Map spectra to new wavelength values.

labels.waveband

Find labels from "waveband" object

Theoretical spectrum of an opaque material

normalize_range_arg

Normalize a range argument into a true numeric range

Get the "Rfr.type" attribute

print.summary_generic_spct

Print spectral summary

is_photon_based

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

Miscellaneous Mathematical Functions

checkMspctVersion

Check that the "mspct.version" attribute is set

Check validity of spectral objects

Color of an object

Rescale a spectrum using a summary function

f_dispatcher_spct

Math function dispatcher for spectra

Find peaks in a spectrum

Convert spectral photon irradiance into spectral energy irradiance

is.generic_mspct

Query class of spectrum objects

print.generic_mspct

Print a spectral collection object

Set the "normalized" attribute

transmittance_spct

Calculate transmittance from spectral transmittance.

Set the "Tfr.type" attribute

Create tagged spectrum from wavebands

List-of-wavebands constructor

Transmittance spectrum of clear polyester film

interpolate_spct

Map a spectrum to new wavelength values.