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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

0.9.13

License

GPL (>= 2)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

December 18th, 2016

Functions in photobiology (0.9.13)

Convert date to time-of-day in hours, minutes or seconds

absorptance_spct

Calculate absorptance from spectral absorptance.

A.illuminant.spct

CIE A illuminant data

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral photon irradiance into spectral energy irradiance

Convert spectral energy irradiance into spectral photon irradiance

Convert absorbance into transmittance

absorbance_spct

Calculate absorbance from spectral absorbance.

calc_source_output

Light-source spectral output

Spectral response of a back-thinned CCD image sensor.

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

black_body.spct

Theoretical black body

as.generic_spct

Spectral-object copy constructor

as.generic_mspct

Collection-of-spectra copy-constructor

calc_multipliers

Spectral weights

c.generic_mspct

Combine collections of spectra

Average spectral data.

Convert a solar_time object into solar_date object

checkSpctVersion

Check that the "spct.version" attribute is set

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

CIE xyz chromaticity coordinates 2 deg data

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

Sanity check of wavelengths (internal function).

checkMspctVersion

Check that the "mspct.version" attribute is set

Query which is the class of an spectrum

Clean a spectrum

Sanity check of a spectrum.

Check validity of spectral objects

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

clear_body.spct

Theoretical clear body

convertTimeUnit

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

Conversion from counts per second to physical quantities

copy_attributes

Copy attributes from one R object to another

Convolve function for collections of spectra

div-.generic_spct

Arithmetic Operators

Divide two spectra, even if the wavelengths values differ

f_dispatcher_spct

Math function dispatcher for spectra

Incandescent "FEL" lamp emission spectrum

Convert energy-based quantities into photon-based quantities.

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

Extract or replace parts of a spectrum

Extract or replace members of a collection of spectra

ciexyzCMF2.spct

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

ciexyzCMF10.spct

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

Calculate deuterim lamp output spectrum from fitted constants

Data for typical calibration lamps

Defunct functions and methods

dim.generic_mspct

Dimensions of an Object

Collection-of-spectra constructor

FEL.BN.9101.165

Data for typical calibration lamps

Shift the scale of a spectrum using a summary function

filter_cps.mspct

Counts per second from a measurement of a plastic film

Find peaks in a spectrum

Clip head and/or tail of a spectrum

Color of an object

Data for typical calibration lamps

Data for typical calibration lamps

Rescale a spectrum using a summary function

Get the "Rfr.type" attribute

Get the "normalized" attribute

fshift a spectrum

getWhereMeasured

Get the "where.measured" attribute

D65.illuminant.spct

CIE D65 illuminant data

Insert wavelength values into spectral data.

Times for sun positions

Energy:energy ratio

Energy-based photo-response

Energy:photon ratio

Energy:energy ratio

format.solar_time

Encode in a Common Format

fscale a spectrum

getMspctVersion

Get the "mspct.version" attribute

Get the "multiple.wl" attribute

Is an R object "effective"

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Find labels from "waveband" object

Logarithms and Exponentials

Arithmetic Operators

normalized_diff_ind

Calculate a normalized index.

Linear energy CIE 2008 luminous efficiency function 2 deg data

Theoretical spectrum of an opaque material

Linear energy CIE 2008 luminous efficiency function 10 deg data

Transmittance spectrum of clear polyester film

clear_photobio.cache

clear the spectral weights cache

Theoretical spectrum of a clear clear material

Energy irradiance

e2quantum_multipliers

Calculate energy to quantum multipliers

getInstrSettings

Get the "instr.settings" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

Get the "instr.desc" attribute

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Query whether a generic spectrum has been normalized.

Integrate spectral data.

is_photon_based

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

Miscellaneous Mathematical Functions

Wavelength maximum

Normalize spectral data

normalize_range_arg

Normalize a range argument into a true numeric range

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

Normalization of an R object

Names of multi-spectra classes

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

photon_irradiance

Photon irradiance

Photo:photon ratio

Photon-based photo-response

Set the "bswf.used" attribute

Convert photon-based quantities into energy-based quantities

Get the "scaled" attribute

Map spectra to new wavelength values.

Get the "bswf.used" attribute

Convert an R object into a spectrum object.

Get peaks and valleys in a spectrum

Get the "spct.version" attribute

is.generic_mspct

Query class of spectrum objects

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

is.generic_spct

Query class of spectrum objects

Calculate response from spectral response

Query if an object has old class names

Set the "normalized" attribute

Set the "multiple.wl" attribute

split_irradiance

Energy or photon irradiance for split spectrum regions

setWhenMeasured

Set the "when.measured" attribute

setWhatMeasured

Set the "what.measured" attribute

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

split_photon_irradiance

Photon irradiance for split spectrum regions

Print a "waveband" object

Peaks or local maxima

print.summary_generic_spct

Print spectral summary

Row-bind spectra

reflectance_spct

Calculate reflectance from spectral reflectance

setWhereMeasured

Set the "where.measured" attribute

shared_member_class

Classes common to all collection members.

Spectral-object constructor

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

Query whether a generic spectrum has been scaled

Query if it is an spectrum is tagged

Query if it is a waveband

interpolate_spct

Map a spectrum to new wavelength values.

Gives irradiance from spectral irradiance.

Wavelength minimum

is.summary_generic_spct

Query class of spectrum summary objects

minus-.generic_spct

Arithmetic Operators

photobiology-package

Photobiological Calculations

photodiode.spct

Spectral response of a GaAsP photodiode

Solar spectral irradiance (simulated)

Daily solar spectral irradiance (simulated)

Valleys or local minima

Convert transmittance into absorbance.

v_insert_hinges

Insert wavelength values into spectral data.

Trim (or expand) head and/or tail

Trigonometric Functions

Trim head and/or tail of a spectrum

twilight argument check and conversion

RGB color values

Integrated response

print.solar_time

Print solar time and solar date objects

Print a spectral object

Remove "generic_mspct" and derived class attributes.

Remove "generic_spct" and derived class attributes.

slash-.generic_spct

Arithmetic Operators

split_energy_irradiance

Energy irradiance for split spectrum regions

List-of-wavebands constructor

Summary of a spectral object

summary_spct_classes

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

transmittance_spct

Calculate transmittance from spectral transmittance.

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

merge.generic_spct

Merge two generic_spct objects

Time difference between two time zones

Photon irradiance

Central wavelength value

Photon:photon ratio

Set the "instr.desc" attribute

Set the "Rfr.type" attribute

setInstrSettings

Set the "instr.settings" attribute

Local solar time

Smooth a spectrum

Set the "scaled" attribute

Get the "Tfr.type" attribute

getWhenMeasured

Get the "when.measured" attribute

getWhatMeasured

Get the "what.measured" attribute

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

Multi-spct transform methods

mod-.generic_spct

Arithmetic Operators

l_insert_hinges

Insert wavelength values into spectral data.

Solar astronomy using Meeus' algorithm

Multiply two spectra, even if the wavelengths values differ

plus-.generic_spct

Arithmetic Operators

photons_energy_ratio

Photon:energy ratio

Photon:energy ratio

Wavelength range

Spectrum to rgb color conversion

Subtract two spectra

Rounding of Numbers

Add two spectra

times-.generic_spct

Arithmetic Operators

Daily solar spectral irradiance (simulated)

Create tagged spectrum from wavebands

Solar spectral irradiance (simulated)

upgrade_spectra

Upgrade one or more spectral objects

Upgrade one spectral object

white_body.spct

Theoretical white body

Photon or energy ratio

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

Set the "Tfr.type" attribute

Waveband constructor method

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

Length of object in wavelength units

Trim (or expand) head and/or tail

Trim (or expand) head and/or tail

Wavelength to rgb color conversion

w_length_range2rgb

Wavelength range to rgb color conversion

Create tagged spectrum from wavebands

Create spectrum from wavebands