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photobiology

Package 'photobiology' defines a system of classes for storing spectral data and accompanying metadata. For each of these classes specialised summary methods, maths operators and functions are provided. In addition, classes for storing collections of objects of the classes for individual spectra are defined as well as 'apply' functions. Extraction and replacement operators are also implemented.

This package is the core of a suite of R packages for photobiological calculations described at the r4photobiology web site.

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Version

Install

install.packages('photobiology')

Monthly Downloads

649

Version

0.9.11

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

September 11th, 2016

Functions in photobiology (0.9.11)

function to be numerically minimized

A.illuminant.spct

CIE A illuminant data

absorptance_spct

Calculate absorptance from spectral absorptance.

Convert spectral energy irradiance into spectral photon irradiance

Convert absorbance into transmittance

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral photon irradiance into spectral energy irradiance

absorbance_spct

Calculate absorbance from spectral absorbance.

as.generic_spct

Spectral-object copy constructor

Check validity of spectral objects

Spectral response of a back-thinned CCD image sensor.

calc_multipliers

Spectral weights

calc_source_output

Light-source spectral output

black_body.spct

Theoretical black body

c.generic_mspct

Combine collections of spectra

as.generic_mspct

Collection-of-spectra copy-constructor

Average spectral data.

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

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

Linear energy CIE 2008 luminous efficiency function 10 deg data

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

Sanity check of a spectrum.

Linear energy CIE 2008 luminous efficiency function 2 deg data

ciexyzCMF10.spct

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

CIE xyz chromaticity coordinates 2 deg data

checkMspctVersion

Check that the "mspct.version" attribute is set

checkSpctVersion

Check that the "spct.version" attribute is set

Sanity check of wavelengths (internal function).

Query which is the class of an spectrum

Color of an object

Theoretical spectrum of a clear clear material

ciexyzCMF2.spct

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

Clip head and/or tail of a spectrum

clear_body.spct

Theoretical clear body

clear_photobio.cache

clear the spectral weights cache

convertTimeUnit

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

Clean a spectrum

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

Conversion from counts per second to physical quantities

Calculate deuterim lamp output spectrum from fitted constants

Times for sun positions

Convert date to time-of-day in hours

Defunct functions and methods

Convolve function for collections of spectra

dim.generic_mspct

Dimensions of an Object

copy_attributes

Copy attributes

D65.illuminant.spct

CIE D65 illuminant data

date argument check and conversion

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

e2quantum_multipliers

Calculate energy to quantum multipliers

Extract or replace parts of a spectrum

Extract or replace members of a collection of spectra

Convert energy-based quantities into photon-based quantities.

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

Rescale a spectrum using a summary function

fscale a spectrum

fshift a spectrum

Get the "scaled" attribute

Get the "spct.version" attribute

Query if it is an spectrum is tagged

Query whether a generic spectrum has been scaled

Energy irradiance

Energy:energy ratio

Energy:photon ratio

Shift the scale of a spectrum using a summary function

Collection-of-spectra constructor

Get the "normalized" attribute

Map spectra to new wavelength values.

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Get the "Rfr.type" attribute

Query if it is a waveband

l_insert_hinges

Insert wavelength values into spectral data.

Wavelength minimum

minus-.generic_spct

Arithmetic Operators

Names of multi-spectra classes

Normalization of an R object

Transmittance spectrum of clear polyester film

getMspctVersion

Get the "mspct.version" attribute

Convert photon-based quantities into energy-based quantities

Arithmetic Operators

Photon:energy ratio

getWhatMeasured

Get the "what.measured" attribute

Get the "multiple.wl" attribute

getWhenMeasured

Get the "when.measured" attribute

Gives irradiance from spectral irradiance.

interpolate_spct

Map a spectrum to new wavelength values.

Query whether a generic spectrum has been normalized.

is_photon_based

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

Divide two spectra, even if the wavelengths values differ

Miscellaneous Mathematical Functions

Wavelength maximum

div-.generic_spct

Arithmetic Operators

filter_cps.mspct

Counts per second from a measurement of a plastic film

getWhereMeasured

Get the "where.measured" attribute

Find peaks in a spectrum

Insert wavelength values into spectral data.

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Is an R object "effective"

normalize_range_arg

Normalize a range argument into a true numeric range

Find labels from "waveband" object

Normalize spectral data

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

Logarithms and Exponentials

Peaks or local maxima

Print a spectral object

print.summary_generic_spct

Print spectral summary

Wavelength range

Row-bind spectra

Get peaks and valleys in a spectrum

Calculate response from spectral response

Integrated response

Get the "bswf.used" attribute

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

is.generic_mspct

Query class of spectrum objects

is.generic_spct

Query class of spectrum objects

Central wavelength value

merge.generic_spct

Merge two generic_spct objects

Photo:photon ratio

photon_irradiance

Photon irradiance

photobiology-package

Photobiological Calculations

Photon irradiance

RGB color values

Remove "generic_mspct" and derived class attributes.

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

setWhatMeasured

Set the "what.measured" attribute

shared_member_class

Classes common to all collection members.

times-.generic_spct

Arithmetic Operators

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

Length of object in wavelength units

v_insert_hinges

Insert wavelength values into spectral data.

transmittance_spct

Calculate transmittance from spectral transmittance.

Valleys or local minima

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

setWhenMeasured

Set the "when.measured" attribute

setWhereMeasured

Set the "where.measured" attribute

Solar spectral irradiance (simulated)

Daily solar spectral irradiance (simulated)

Convert transmittance into absorbance.

Upgrade one spectral object

upgrade_spectra

Upgrade one or more spectral objects

Create tagged spectrum from wavebands

white_body.spct

Theoretical white body

photons_energy_ratio

Photon:energy ratio

photodiode.spct

Spectral response of a GaAsP photodiode

Photon:photon ratio

plus-.generic_spct

Arithmetic Operators

Set the "scaled" attribute

Convert an R object into a spectrum object.

Set the "instr.desc" attribute

Photon-based photo-response

Set the "Tfr.type" attribute

slash-.generic_spct

Arithmetic Operators

Energy-based photo-response

Energy:energy ratio

Incandescent "FEL" lamp emission spectrum

f_dispatcher_spct

Math function dispatcher for spectra

Get the "instr.desc" attribute

Get the "Tfr.type" attribute

getInstrSettings

Get the "instr.settings" attribute

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

insert_spct_hinges

Insert new wavelength values into a spectrum

Integrate spectral data.

Query if an object has old class names

is.summary_generic_spct

Query class of spectrum summary objects

mod-.generic_spct

Arithmetic Operators

normalized_diff_ind

Calculate a normalized index.

Multi-spct transform methods

Theoretical spectrum of an opaque material

Print a "waveband" object

Multiply two spectra, even if the wavelengths values differ

Spectrum to rgb color conversion

Set the "bswf.used" attribute

summary_spct_classes

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

Smooth a spectrum

Trigonometric Functions

Summary of a spectral object

Set the "normalized" attribute

Set the "Rfr.type" attribute

split_irradiance

Energy or photon irradiance for split spectrum regions

split_photon_irradiance

Photon irradiance for split spectrum regions

Trim (or expand) head and/or tail

Trim head and/or tail of a spectrum

Create tagged spectrum from wavebands

Create spectrum from wavebands

Spectral-object constructor

reflectance_spct

Calculate reflectance from spectral reflectance

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

Subtract two spectra

Add two spectra

Daily solar spectral irradiance (simulated)

Solar spectral irradiance (simulated)

twilight argument check and conversion

Photon or energy ratio

Waveband constructor method

Rounding of Numbers

Remove "generic_spct" and derived class attributes.

setInstrSettings

Set the "instr.settings" attribute

Set the "multiple.wl" attribute

List-of-wavebands constructor

split_energy_irradiance

Energy irradiance for split spectrum regions

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

time argument check and conversion

Trim (or expand) head and/or tail

w_length_range2rgb

Wavelength range to rgb color conversion

Trim (or expand) head and/or tail

Wavelength to rgb color conversion