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photobiology (version 0.9.7)

'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

0.9.7

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

April 6th, 2016

Functions in photobiology (0.9.7)

Miscellaneous Mathematical Functions

Color of an object

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

Defunct functions and methods

Energy irradiance

f_dispatcher_spct

Math function dispatcher for spectra

dim.generic_mspct

Dimensions of an Object

Check validity of spectral objects

Logarithms and Exponentials

Shift the scale of a spectrum using a summary function

Integrate spectral data.

l_insert_hinges

Insert wavelength values into spectral data.

merge.generic_spct

Merge two generic_spct objects

photons_energy_ratio

Photon:energy ratio

plus-.generic_spct

Arithmetic Operators

mod-.generic_spct

Arithmetic Operators

Print a "waveband" object

Set the "Rfr.type" attribute

Row-bind spectra

Photo:photon ratio

setWhatMeasured

Set the "what.measured" attribute

Spectral-object constructor

Calculate deuterim lamp output spectrum from fitted constants

Photon:photon ratio

transmittance_spct

Calculate transmittance from spectral transmittance.

D65.illuminant.spct

CIE D65 illuminant data

Incandescent "FEL" lamp emission spectrum

Daily solar spectral irradiance (simulated)

as.generic_mspct

Collection-of-spectra copy-constructor

filter_cps.mspct

Counts per second from a measurement of a plastic film

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

Convert absorbance into transmittance

A.illuminant.spct

CIE A illuminant data

Clean a spectrum

ciexyzCMF10.spct

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

Get the "multiple.wl" attribute

Trim head and/or tail of a spectrum

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Map spectra to new wavelength values.

convertTimeUnit

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

clear_photobio.cache

clear the spectral weights cache

Convert spectral energy irradiance into spectral photon irradiance

copy_attributes

Copy attributes

Conversion from counts per second to physical quantities

Spectral response of a back-thinned CCD image sensor.

checkSpctVersion

Check that the "spct.version" attribute is set

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

is_photon_based

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

Theoretical spectrum of a clear clear material

Multi-spct transform methods

Extract or replace members of a collection of spectra

Normalize spectral data

Get the "normalized" attribute

Collection-of-spectra constructor

Find peaks in a spectrum

as.generic_spct

Spectral-object copy constructor

e2quantum_multipliers

Calculate energy to quantum multipliers

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

Get the "scaled" attribute

c.generic_mspct

Combine collections of spectra

setInstrSettings

Set the "instr.settings" attribute

getWhatMeasured

Get the "what.measured" attribute

Get the "Rfr.type" attribute

Extract or replace parts of a spectrum

photodiode.spct

Spectral response of a GaAsP photodiode

Convert transmittance into absorbance.

checkMspctVersion

Check that the "mspct.version" attribute is set

Convert spectral energy irradiance into spectral photon irradiance

Convert photon-based quantities into energy-based quantities

Rescale a spectrum using a summary function

Convert energy-based quantities into photon-based quantities.

Remove "generic_spct" and derived class attributes.

Linear energy CIE 2008 luminous efficiency function 2 deg data

fscale a spectrum

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

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

Get the "Tfr.type" attribute

Create tagged spectrum from wavebands

split_energy_irradiance

Energy irradiance for split spectrum regions

Get peaks and valleys in a spectrum

function to be numerically minimized

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Names of multi-spectra classes

Normalization of an R object

List-of-wavebands constructor

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

absorptance_spct

Calculate absorptance from spectral absorptance.

Central wavelength value

calc_multipliers

Spectral weights

Linear energy CIE 2008 luminous efficiency function 10 deg data

print.summary_generic_spct

Print spectral summary

Add two spectra

Photon-based photo-response

Multiply two spectra, even if the wavelengths values differ

Set the "Tfr.type" attribute

Energy:energy ratio

Energy:photon ratio

div-.generic_spct

Arithmetic Operators

clear_body.spct

Theoretical clear body

Energy:energy ratio

Set the "instr.desc" attribute

Trim (or expand) head and/or tail

Solar spectral irradiance (simulated)

Theoretical spectrum of an opaque material

date argument check and conversion

time argument check and conversion

Smooth a spectrum

minus-.generic_spct

Arithmetic Operators

Query which is the class of an spectrum

Subtract two spectra

photon_irradiance

Photon irradiance

Photon:energy ratio

Get the "instr.desc" attribute

Times for sun positions

Set the "multiple.wl" attribute

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

getMspctVersion

Get the "mspct.version" attribute

Print a spectral object

RGB color values

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

Arithmetic Operators

Photon or energy ratio

getWhereMeasured

Get the "where.measured" attribute

Wavelength minimum

Create tagged spectrum from wavebands

Gives irradiance from spectral irradiance.

Insert wavelength values into spectral data.

is.generic_mspct

Query class of spectrum objects

Query if it is a waveband

Transmittance spectrum of clear polyester film

Convert an R object into a spectrum object.

slash-.generic_spct

Arithmetic Operators

Trim (or expand) head and/or tail

Wavelength maximum

Wavelength to rgb color conversion

black_body.spct

Theoretical black body

w_length_range2rgb

Wavelength range to rgb color conversion

Remove "generic_mspct" and derived class attributes.

Wavelength range

Find labels from "waveband" object

Summary of a spectral object

Solar spectral irradiance (simulated)

Set the "bswf.used" attribute

Query if it is an spectrum is tagged

absorbance_spct

Calculate absorbance from spectral absorbance.

Sanity check of a spectrum.

Sanity check of wavelengths (internal function).

Rounding of Numbers

reflectance_spct

Calculate reflectance from spectral reflectance

Convolve function for collections of spectra

upgrade_spectra

Upgrade one or more spectral objects

Set the "normalized" attribute

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

Calculate response from spectral response

Set the "scaled" attribute

setWhereMeasured

Set the "where.measured" attribute

Convert date to time-of-day in hours

split_irradiance

Energy or photon irradiance for split spectrum regions

setWhenMeasured

Set the "when.measured" attribute

Divide two spectra, even if the wavelengths values differ

Create spectrum from wavebands

shared_member_class

Classes common to all collection members.

twilight argument check and conversion

Energy-based photo-response

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

fshift a spectrum

Valleys or local minima

is.generic_spct

Query class of spectrum objects

Waveband constructor method

is.summary_generic_spct

Query class of spectrum summary objects

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

Query whether a generic spectrum has been scaled

Photon irradiance

Daily solar spectral irradiance (simulated)

Convert spectral photon irradiance into spectral energy irradiance

Average spectral data.

ciexyzCMF2.spct

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

calc_source_output

Light-source spectral output

Get the "bswf.used" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

Query if an object has old class names

Get the "spct.version" attribute

Peaks or local maxima

normalized_diff_ind

Calculate a normalized index.

normalize_range_arg

Normalize a range argument into a true numeric range

Integrated response

v_insert_hinges

Insert wavelength values into spectral data.

white_body.spct

Theoretical white body

Trigonometric Functions

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

CIE xyz chromaticity coordinates 2 deg data

getInstrSettings

Get the "instr.settings" attribute

interpolate_spct

Map a spectrum to new wavelength values.

getWhenMeasured

Get the "when.measured" attribute

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

Clip head and/or tail of a spectrum

Is an R object "effective"

Query whether a generic spectrum has been normalized.

photobiology-package

'Photobiological' Calculations

Spectrum to rgb color conversion

Length of object in wavelength units

summary_spct_classes

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

times-.generic_spct

Arithmetic Operators

Upgrade one spectral object

Trim (or expand) head and/or tail

split_photon_irradiance

Photon irradiance for split spectrum regions