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photobiolgy

Package 'photobiolgy' defines a system of classes for storing spectral data and accompanying metdata. 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

0.9.9

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

August 1st, 2016

Functions in photobiology (0.9.9)

Convert absorbance into transmittance

absorptance_spct

Calculate absorptance from spectral absorptance.

absorbance_spct

Calculate absorbance from spectral absorbance.

Convert spectral energy irradiance into spectral photon irradiance

A.illuminant.spct

CIE A illuminant data

function to be numerically minimized

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral photon irradiance into spectral energy irradiance

calc_multipliers

Spectral weights

Check validity of spectral objects

c.generic_mspct

Combine collections of spectra

calc_source_output

Light-source spectral output

black_body.spct

Theoretical black body

as.generic_spct

Spectral-object copy constructor

Average spectral data.

Spectral response of a back-thinned CCD image sensor.

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

as.generic_mspct

Collection-of-spectra copy-constructor

Sanity check of a spectrum.

CIE xyz chromaticity coordinates 2 deg data

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

Sanity check of wavelengths (internal function).

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

Linear energy CIE 2008 luminous efficiency function 2 deg data

Linear energy CIE 2008 luminous efficiency function 10 deg data

checkMspctVersion

Check that the "mspct.version" attribute is set

ciexyzCMF10.spct

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

checkSpctVersion

Check that the "spct.version" attribute is set

clear_photobio.cache

clear the spectral weights cache

Clean a spectrum

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

Color of an object

convertTimeUnit

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

Theoretical spectrum of a clear clear material

clear_body.spct

Theoretical clear body

Clip head and/or tail of a spectrum

ciexyzCMF2.spct

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

Query which is the class of an spectrum

Convert date to time-of-day in hours

Times for sun positions

Defunct functions and methods

dim.generic_mspct

Dimensions of an Object

Conversion from counts per second to physical quantities

Divide two spectra, even if the wavelengths values differ

Calculate deuterim lamp output spectrum from fitted constants

Convert energy-based quantities into photon-based quantities.

div-.generic_spct

Arithmetic Operators

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

f_dispatcher_spct

Math function dispatcher for spectra

Incandescent "FEL" lamp emission spectrum

Get peaks and valleys in a spectrum

Get the "bswf.used" attribute

Energy:energy ratio

Rescale a spectrum using a summary function

Energy:photon ratio

fshift a spectrum

Get the "Tfr.type" attribute

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

e2quantum_multipliers

Calculate energy to quantum multipliers

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

fscale a spectrum

getWhereMeasured

Get the "where.measured" attribute

Insert wavelength values into spectral data.

insert_spct_hinges

Insert new wavelength values into a spectrum

Query if it is a waveband

Integrate spectral data.

l_insert_hinges

Insert wavelength values into spectral data.

merge.generic_spct

Merge two generic_spct objects

Central wavelength value

Print a "waveband" object

Multiply two spectra, even if the wavelengths values differ

date argument check and conversion

D65.illuminant.spct

CIE D65 illuminant data

Energy:energy ratio

Extract or replace parts of a spectrum

Extract or replace members of a collection of spectra

Energy-based photo-response

getMspctVersion

Get the "mspct.version" attribute

getWhatMeasured

Get the "what.measured" attribute

Get the "multiple.wl" attribute

reflectance_spct

Calculate reflectance from spectral reflectance

getWhenMeasured

Get the "when.measured" attribute

Remove "generic_spct" and derived class attributes.

setWhenMeasured

Set the "when.measured" attribute

Rounding of Numbers

setWhereMeasured

Set the "where.measured" attribute

times-.generic_spct

Arithmetic Operators

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

Trim (or expand) head and/or tail

transmittance_spct

Calculate transmittance from spectral transmittance.

Convolve function for collections of spectra

Trim (or expand) head and/or tail

copy_attributes

Copy attributes

Energy irradiance

filter_cps.mspct

Counts per second from a measurement of a plastic film

Find peaks in a spectrum

Shift the scale of a spectrum using a summary function

Collection-of-spectra constructor

Get the "scaled" attribute

interpolate_spct

Map a spectrum to new wavelength values.

Gives irradiance from spectral irradiance.

Get the "spct.version" attribute

is.summary_generic_spct

Query class of spectrum summary objects

Query if an object has old class names

Find labels from "waveband" object

Logarithms and Exponentials

Normalization of an R object

Names of multi-spectra classes

Wavelength range

Row-bind spectra

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Map spectra to new wavelength values.

is.generic_mspct

Query class of spectrum objects

is.generic_spct

Query class of spectrum objects

Wavelength maximum

Miscellaneous Mathematical Functions

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

Peaks or local maxima

Arithmetic Operators

Transmittance spectrum of clear polyester film

Photon:photon ratio

Photon-based photo-response

Set the "Tfr.type" attribute

Set the "scaled" attribute

Spectral-object constructor

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

Daily solar spectral irradiance (simulated)

Trigonometric Functions

Upgrade one spectral object

Photon or energy ratio

Waveband constructor method

upgrade_spectra

Upgrade one or more spectral objects

Get the "normalized" attribute

Get the "Rfr.type" attribute

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

mod-.generic_spct

Arithmetic Operators

Multi-spct transform methods

photobiology-package

'Photobiological' Calculations

photodiode.spct

Spectral response of a GaAsP photodiode

photon_irradiance

Photon irradiance

Photo:photon ratio

Convert an R object into a spectrum object.

Set the "instr.desc" attribute

split_irradiance

Energy or photon irradiance for split spectrum regions

setWhatMeasured

Set the "what.measured" attribute

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

split_photon_irradiance

Photon irradiance for split spectrum regions

Subtract two spectra

Add two spectra

Daily solar spectral irradiance (simulated)

Solar spectral irradiance (simulated)

Photon irradiance

Remove "generic_mspct" and derived class attributes.

RGB color values

List-of-wavebands constructor

split_energy_irradiance

Energy irradiance for split spectrum regions

Create tagged spectrum from wavebands

time argument check and conversion

white_body.spct

Theoretical white body

getInstrSettings

Get the "instr.settings" attribute

Get the "instr.desc" attribute

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Is an R object "effective"

Query whether a generic spectrum has been scaled

Query if it is an spectrum is tagged

normalized_diff_ind

Calculate a normalized index.

Theoretical spectrum of an opaque material

photons_energy_ratio

Photon:energy ratio

plus-.generic_spct

Arithmetic Operators

Trim (or expand) head and/or tail

Trim head and/or tail of a spectrum

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

Wavelength minimum

is_photon_based

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

Query whether a generic spectrum has been normalized.

minus-.generic_spct

Arithmetic Operators

Normalize spectral data

normalize_range_arg

Normalize a range argument into a true numeric range

Print a spectral object

print.summary_generic_spct

Print spectral summary

Calculate response from spectral response

Set the "normalized" attribute

Set the "Rfr.type" attribute

Integrated response

slash-.generic_spct

Arithmetic Operators

Smooth a spectrum

summary_spct_classes

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

Summary of a spectral object

Solar spectral irradiance (simulated)

Convert transmittance into absorbance.

v_insert_hinges

Insert wavelength values into spectral data.

Spectrum to rgb color conversion

Set the "bswf.used" attribute

Photon:energy ratio

Convert photon-based quantities into energy-based quantities

Set the "multiple.wl" attribute

setInstrSettings

Set the "instr.settings" attribute

shared_member_class

Classes common to all collection members.

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

Length of object in wavelength units

Create tagged spectrum from wavebands

Valleys or local minima

Create spectrum from wavebands

twilight argument check and conversion

w_length_range2rgb

Wavelength range to rgb color conversion

Wavelength to rgb color conversion