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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

0.9.15

License

GPL (>= 2)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

April 29th, 2017

Functions in photobiology (0.9.15)

A.illuminant.spct

CIE A illuminant data

Convert absorbance into transmittance

D65.illuminant.spct

CIE D65 illuminant data

FEL.BN.9101.165

Data for typical calibration lamps

Data for typical calibration lamps

Data for typical calibration lamps

Data for typical calibration lamps

Calculate deuterim lamp output spectrum from fitted constants

Incandescent "FEL" lamp emission spectrum

Miscellaneous Mathematical Functions

absorptance_spct

Calculate absorptance from spectral absorptance.

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

black_body.spct

Theoretical black body

absorbance_spct

Calculate absorbance from spectral absorbance.

calc_source_output

Light-source spectral output

Spectral response of a back-thinned CCD image sensor.

Convert transmittance into absorbance.

Trigonometric Functions

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral energy irradiance into spectral photon irradiance

Convert a solar_time object into solar_date object

Convert spectral photon irradiance into spectral energy irradiance

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

Average spectral data.

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

checkMspctVersion

Check that the "mspct.version" attribute is set

checkSpctVersion

Check that the "spct.version" attribute is set

Clip head and/or tail of a spectrum

Color of an object

Linear energy CIE 2008 luminous efficiency function 10 deg data

Linear energy CIE 2008 luminous efficiency function 2 deg data

Query which is the class of an spectrum

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

calc_multipliers

Spectral weights

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

as.generic_mspct

Collection-of-spectra copy-constructor

as.generic_spct

Spectral-object copy constructor

Sanity check of a spectrum.

Sanity check of wavelengths (internal function).

c.generic_mspct

Combine collections of spectra

Check validity of spectral objects

ciexyzCMF10.spct

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

ciexyzCMF2.spct

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

Divide two spectra, even if the wavelengths values differ

Convert energy-based quantities into photon-based quantities.

CIE xyz chromaticity coordinates 2 deg data

dim.generic_mspct

Dimensions of an Object

div-.generic_spct

Arithmetic Operators

copy_attributes

Copy attributes from one R object to another

Conversion from counts per second to physical quantities

Energy:energy ratio

Energy-based photo-response

Rescale a spectrum using a summary function

fscale a spectrum

Collection-of-spectra constructor

Get the "bswf.used" attribute

getWhatMeasured

Get the "what.measured" attribute

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Energy:energy ratio

getWhereMeasured

Get the "where.measured" attribute

Get peaks and valleys in a spectrum

filter_cps.mspct

Counts per second from a measurement of a plastic film

Find peaks in a spectrum

Get the "scaled" attribute

Get the "spct.version" attribute

green_leaf.spct

Green birch leaf reflectance.

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

Convolve function for collections of spectra

Insert wavelength values into spectral data.

Gives irradiance from spectral irradiance.

interpolate_spct

Map a spectrum to new wavelength values.

Query whether a generic spectrum has been scaled

Query if it is an spectrum is tagged

is.summary_generic_spct

Query class of spectrum summary objects

Query if it is a waveband

Solar astronomy using Meeus' algorithm

l_insert_hinges

Insert wavelength values into spectral data.

normalized_diff_ind

Calculate a normalized index.

Theoretical spectrum of an opaque material

photon_irradiance

Photon irradiance

Photo:photon ratio

print.summary_generic_spct

Print spectral summary

Clean a spectrum

Theoretical spectrum of a clear clear material

Times for sun positions

Defunct functions and methods

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

e2quantum_multipliers

Calculate energy to quantum multipliers

format.solar_time

Encode in a Common Format

Energy:photon ratio

Extract or replace parts of a spectrum

Extract or replace members of a collection of spectra

Find labels from "waveband" object

Logarithms and Exponentials

Multi-spct transform methods

Names of multi-spectra classes

f_dispatcher_spct

Math function dispatcher for spectra

Get the "instr.desc" attribute

getInstrSettings

Get the "instr.settings" attribute

Get the "Tfr.type" attribute

getWhenMeasured

Get the "when.measured" attribute

Query if an object has old class names

Energy irradiance

Shift the scale of a spectrum using a summary function

fshift a spectrum

Multiply two spectra, even if the wavelengths values differ

Convert photon-based quantities into energy-based quantities

Set the "multiple.wl" attribute

getMspctVersion

Get the "mspct.version" attribute

Get the "multiple.wl" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

Integrate spectral data.

Get the "normalized" attribute

Get the "Rfr.type" attribute

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Set the "normalized" attribute

setWhereMeasured

Set the "where.measured" attribute

shared_member_class

Classes common to all collection members.

is.generic_mspct

Query class of spectrum objects

is.generic_spct

Query class of spectrum objects

Central wavelength value

Wavelength minimum

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Is an R object "effective"

na.omit.source_spct

Handle Missing Values in Objects

Normalization of an R object

plus-.generic_spct

Arithmetic Operators

Photon:photon ratio

Photon-based photo-response

Remove "generic_mspct" and derived class attributes.

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

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

isValidInstrDesc

Check the "instr.desc" attribute

isValidInstrSettings

Check the "instr.settings" attribute

photons_energy_ratio

Photon:energy ratio

Trim (or expand) head and/or tail

Trim (or expand) head and/or tail

v_insert_hinges

Insert wavelength values into spectral data.

Valleys or local minima

Print a "waveband" object

Integrated response

RGB color values

Set the "Tfr.type" attribute

Map spectra 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.

Wavelength maximum

merge.generic_spct

Merge two generic_spct objects

Transmittance spectrum of clear polyester film

Arithmetic Operators

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

Peaks or local maxima

Print a spectral object

minus-.generic_spct

Arithmetic Operators

mod-.generic_spct

Arithmetic Operators

Normalize spectral data

normalize_range_arg

Normalize a range argument into a true numeric range

Remove "generic_spct" and derived class attributes.

Set the "Rfr.type" attribute

Set the "scaled" attribute

Spectral-object constructor

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

print.solar_time

Print solar time and solar date objects

Photon irradiance

Rounding of Numbers

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

List-of-wavebands constructor

Daily solar spectral irradiance (simulated)

Daily solar spectral irradiance (simulated)

Trim head and/or tail of a spectrum

photobiology-package

photobiology: Photobiological Calculations

photodiode.spct

Spectral response of a GaAsP photodiode

Row-bind spectra

Photon:energy ratio

Wavelength range

reflectance_spct

Calculate reflectance from spectral reflectance

Calculate response from spectral response

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

Smooth a spectrum

Local solar time

setWhatMeasured

Set the "what.measured" attribute

setWhenMeasured

Set the "when.measured" attribute

split_photon_irradiance

Photon irradiance for split spectrum regions

white_led.source_spct

White led bulb spectrum

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

Set the "instr.desc" attribute

setInstrSettings

Set the "instr.settings" attribute

slash-.generic_spct

Arithmetic Operators

Length of object in wavelength units

Solar spectral irradiance (simulated)

Solar spectral irradiance (simulated)

Upgrade one spectral object

upgrade_spectra

Upgrade one or more spectral objects

Subtract two spectra

Add two spectra

transmittance_spct

Calculate transmittance from spectral transmittance.

Trim the "instr.desc" attribute

Create tagged spectrum from wavebands

Create spectrum from wavebands

Spectrum to rgb color conversion

Set the "bswf.used" attribute

Convert an R object into a spectrum object.

split_energy_irradiance

Energy irradiance for split spectrum regions

split_irradiance

Energy or photon irradiance for split spectrum regions

times-.generic_spct

Arithmetic Operators

trimInstrSettings

Trim the "instr.settings" attribute

Trim (or expand) head and/or tail

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

Summary of a spectral object

summary_spct_classes

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

Time difference between two time zones

Wavelength to rgb color conversion

w_length_range2rgb

Wavelength range to rgb color conversion

white_led.cps_spct

White led bulb spectrum

white_led.raw_spct

White led bulb spectrum

twilight argument check and conversion

Waveband constructor method

Photon or energy ratio

Create tagged spectrum from wavebands

white_body.spct

Theoretical white body