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photobiology (version 0.9.6)

'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

649

Version

0.9.6

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

April 2nd, 2016

Functions in photobiology (0.9.6)

Incandescent "FEL" lamp emission spectrum

as.generic_mspct

Collection-of-spectra copy-constructor

Check validity of spectral objects

clear_body.spct

Theoretical clear body

CIE xyz chromaticity coordinates 2 deg data

black_body.spct

Theoretical black body

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

dim.generic_mspct

Dimensions of an Object

copy_attributes

Copy attributes

Convert energy-based quantities into photon-based quantities.

Extract or replace members of a collection of spectra

Get the "scaled" attribute

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

Query whether a generic spectrum has been normalized.

getWhereMeasured

Get the "where.measured" attribute

Is an R object "effective"

Wavelength minimum

Logarithms and Exponentials

print.summary_generic_spct

Print spectral summary

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Integrated response

Row-bind spectra

Spectrum to rgb color conversion

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

Length of object in wavelength units

A.illuminant.spct

CIE A illuminant data

Set the "instr.desc" attribute

Calculate deuterim lamp output spectrum from fitted constants

Set the "scaled" attribute

Trigonometric Functions

Peaks or local maxima

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

D65.illuminant.spct

CIE D65 illuminant data

Conversion from counts per second to physical quantities

Summary of a spectral object

Times for sun positions

Defunct functions and methods

Convert spectral energy irradiance into spectral photon irradiance

calc_source_output

Light-source spectral output

div-.generic_spct

Arithmetic Operators

Rescale a spectrum using a summary function

Query if an object has old class names

l_insert_hinges

Insert wavelength values into spectral data.

Map spectra to new wavelength values.

Query which is the class of an spectrum

Collection-of-spectra constructor

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

time argument check and conversion

checkSpctVersion

Check that the "spct.version" attribute is set

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Linear energy CIE 2008 luminous efficiency function 2 deg data

is.summary_generic_spct

Query class of spectrum summary objects

Convert absorbance into transmittance

normalize_range_arg

Normalize a range argument into a true numeric range

Multiply two spectra, even if the wavelengths values differ

getInstrSettings

Get the "instr.settings" attribute

Get the "instr.desc" attribute

convertTimeUnit

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

Photon:energy ratio

Transmittance spectrum of clear polyester film

Spectral response of a back-thinned CCD image sensor.

Gives irradiance from spectral irradiance.

Set the "normalized" attribute

photons_energy_ratio

Photon:energy ratio

Convert date to time-of-day in hours

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

Solar spectral irradiance (simulated)

setWhereMeasured

Set the "where.measured" attribute

ciexyzCMF2.spct

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

Clean a spectrum

checkMspctVersion

Check that the "mspct.version" attribute is set

Clip head and/or tail of a spectrum

Find labels from "waveband" object

Energy:energy ratio

Photon or energy ratio

Energy:photon ratio

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

Insert wavelength values into spectral data.

Get peaks and valleys in a spectrum

Arithmetic Operators

split_photon_irradiance

Photon irradiance for split spectrum regions

Convert an R object into a spectrum object.

Subtract two spectra

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

Query if it is a waveband

Energy:energy ratio

Trim (or expand) head and/or tail

Convert photon-based quantities into energy-based quantities

Photon-based photo-response

Get the "spct.version" attribute

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

e2quantum_multipliers

Calculate energy to quantum multipliers

fscale a spectrum

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

merge.generic_spct

Merge two generic_spct objects

getWhenMeasured

Get the "when.measured" attribute

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Sanity check of wavelengths (internal function).

photobiology-package

'Photobiological' Calculations

Miscellaneous Mathematical Functions

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

setInstrSettings

Set the "instr.settings" attribute

normalized_diff_ind

Calculate a normalized index.

Remove "generic_mspct" and derived class attributes.

Wavelength range

RGB color values

plus-.generic_spct

Arithmetic Operators

calc_multipliers

Spectral weights

Rounding of Numbers

as.generic_spct

Spectral-object copy constructor

absorbance_spct

Calculate absorbance from spectral absorbance.

Set the "bswf.used" attribute

setWhenMeasured

Set the "when.measured" attribute

c.generic_mspct

Combine collections of spectra

List-of-wavebands constructor

split_irradiance

Energy or photon irradiance for split spectrum regions

shared_member_class

Classes common to all collection members.

Daily solar spectral irradiance (simulated)

summary_spct_classes

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

Daily solar spectral irradiance (simulated)

is_photon_based

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

Extract or replace parts of a spectrum

Waveband constructor method

Set the "Tfr.type" attribute

Trim head and/or tail of a spectrum

Convolve function for collections of spectra

Convert transmittance into absorbance.

upgrade_spectra

Upgrade one or more spectral objects

function to be numerically minimized

v_insert_hinges

Insert wavelength values into spectral data.

Normalize spectral data

Multi-spct transform methods

Theoretical spectrum of an opaque material

Valleys or local minima

Find peaks in a spectrum

Convert spectral energy irradiance into spectral photon irradiance

Photon:photon ratio

Energy irradiance

Convert spectral photon irradiance into spectral energy irradiance

Add two spectra

Create tagged spectrum from wavebands

Central wavelength value

Get the "bswf.used" attribute

is.generic_spct

Query class of spectrum objects

Get the "multiple.wl" attribute

ciexyzCMF10.spct

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

Names of multi-spectra classes

transmittance_spct

Calculate transmittance from spectral transmittance.

Integrate spectral data.

twilight argument check and conversion

clear_photobio.cache

clear the spectral weights cache

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

photodiode.spct

Spectral response of a GaAsP photodiode

Normalization of an R object

slash-.generic_spct

Arithmetic Operators

Create spectrum from wavebands

Spectral-object constructor

Color of an object

f_dispatcher_spct

Math function dispatcher for spectra

setWhatMeasured

Set the "what.measured" attribute

white_body.spct

Theoretical white body

Trim (or expand) head and/or tail

Linear energy CIE 2008 luminous efficiency function 10 deg data

Get the "Tfr.type" attribute

reflectance_spct

Calculate reflectance from spectral reflectance

Query if it is an spectrum is tagged

Theoretical spectrum of a clear clear material

photon_irradiance

Photon irradiance

mod-.generic_spct

Arithmetic Operators

Print a "waveband" object

Calculate response from spectral response

Smooth a spectrum

split_energy_irradiance

Energy irradiance for split spectrum regions

Set the "Rfr.type" attribute

times-.generic_spct

Arithmetic Operators

Wavelength to rgb color conversion

Upgrade one spectral object

Trim (or expand) head and/or tail

Average spectral data.

date argument check and conversion

filter_cps.mspct

Counts per second from a measurement of a plastic film

Shift the scale of a spectrum using a summary function

Get the "normalized" attribute

Get the "Rfr.type" attribute

getWhatMeasured

Get the "what.measured" attribute

getMspctVersion

Get the "mspct.version" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

interpolate_spct

Map a spectrum to new wavelength values.

Query whether a generic spectrum has been scaled

Wavelength maximum

minus-.generic_spct

Arithmetic Operators

Print a spectral object

Photon irradiance

Remove "generic_spct" and derived class attributes.

w_length_range2rgb

Wavelength range to rgb color conversion

absorptance_spct

Calculate absorptance from spectral absorptance.

Sanity check of a spectrum.

Energy-based photo-response

Divide two spectra, even if the wavelengths values differ

fshift a spectrum

is.generic_mspct

Query class of spectrum objects

Photo:photon ratio

Set the "multiple.wl" attribute

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

Solar spectral irradiance (simulated)

Create tagged spectrum from wavebands