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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

1,284

Version

0.9.14

License

GPL (>= 2)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro J. Aphalo

Last Published

March 20th, 2017

Functions in photobiology (0.9.14)

as.generic_mspct

Collection-of-spectra copy-constructor

Rescale a spectrum using a summary function

fscale a spectrum

isValidInstrSettings

Check the "instr.settings" attribute

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

isValidInstrDesc

Check the "instr.desc" attribute

Find labels from "waveband" object

Logarithms and Exponentials

Peaks or local maxima

photobiology-package

photobiology: Photobiological Calculations

Arithmetic Operators

Remove "generic_mspct" and derived class attributes.

times-.generic_spct

Arithmetic Operators

calc_multipliers

Spectral weights

Create tagged spectrum from wavebands

white_led.source_spct

White led bulb spectrum

white_led.raw_spct

White led bulb spectrum

Convert photon-based quantities into energy-based quantities

RGB color values

Length of object in wavelength units

Photon or energy ratio

as.generic_spct

Spectral-object copy constructor

Map spectra to new wavelength values.

absorbance_spct

Calculate absorbance from spectral absorbance.

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

Average spectral data.

checkSpctVersion

Check that the "spct.version" attribute is set

clear_body.spct

Theoretical clear body

dim.generic_mspct

Dimensions of an Object

clear_photobio.cache

clear the spectral weights cache

checkMspctVersion

Check that the "mspct.version" attribute is set

div-.generic_spct

Arithmetic Operators

Energy irradiance

Get the "normalized" attribute

Get the "Rfr.type" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

Integrate spectral data.

D65.illuminant.spct

CIE D65 illuminant data

Solar spectral irradiance (simulated)

slash-.generic_spct

Arithmetic Operators

FEL.BN.9101.165

Data for typical calibration lamps

w_length_range2rgb

Wavelength range to rgb color conversion

Trim (or expand) head and/or tail

white_led.cps_spct

White led bulb spectrum

white_body.spct

Theoretical white body

is.summary_generic_spct

Query class of spectrum summary objects

Query if it is a waveband

Wavelength maximum

merge.generic_spct

Merge two generic_spct objects

Theoretical spectrum of an opaque material

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

photodiode.spct

Spectral response of a GaAsP photodiode

photon_irradiance

Photon irradiance

Photon-based photo-response

reflectance_spct

Calculate reflectance from spectral reflectance

Set the "instr.desc" attribute

Data for typical calibration lamps

split_photon_irradiance

Photon irradiance for split spectrum regions

Local solar time

Data for typical calibration lamps

Convert transmittance into absorbance.

Trigonometric Functions

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

black_body.spct

Theoretical black body

Sanity check of a spectrum.

Sanity check of wavelengths (internal function).

Query which is the class of an spectrum

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

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Divide two spectra, even if the wavelengths values differ

Convert energy-based quantities into photon-based quantities.

Energy:energy ratio

Shift the scale of a spectrum using a summary function

fshift a spectrum

photons_energy_ratio

Photon:energy ratio

Multiply two spectra, even if the wavelengths values differ

Print a "waveband" object

Trim head and/or tail of a spectrum

Convert an R object into a spectrum object.

Trim (or expand) head and/or tail

Spectral-object constructor

split_irradiance

Energy or photon irradiance for split spectrum regions

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

transmittance_spct

Calculate transmittance from spectral transmittance.

upgrade_spectra

Upgrade one or more spectral objects

v_insert_hinges

Insert wavelength values into spectral data.

setWhereMeasured

Set the "where.measured" attribute

Daily solar spectral irradiance (simulated)

Add two 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

Times for sun positions

Defunct functions and methods

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

e2quantum_multipliers

Calculate energy to quantum multipliers

Extract or replace members of a collection of spectra

f_dispatcher_spct

Math function dispatcher for spectra

getMspctVersion

Get the "mspct.version" attribute

Trim the "instr.desc" attribute

A.illuminant.spct

CIE A illuminant data

Convert absorbance into transmittance

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral energy irradiance into spectral photon irradiance

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

Get the "multiple.wl" attribute

getWhatMeasured

Get the "what.measured" attribute

getWhenMeasured

Get the "when.measured" attribute

Gives irradiance from spectral irradiance.

interpolate_spct

Map a spectrum to new wavelength values.

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

Is an R object "effective"

Multi-spct transform methods

Names of multi-spectra classes

plus-.generic_spct

Arithmetic Operators

Transmittance spectrum of clear polyester film

Calculate response from spectral response

Integrated response

Set the "normalized" attribute

setWhenMeasured

Set the "when.measured" attribute

Set the "Rfr.type" attribute

Create tagged spectrum from wavebands

split_energy_irradiance

Energy irradiance for split spectrum regions

Wavelength to rgb color conversion

Upgrade one spectral object

Daily solar spectral irradiance (simulated)

Subtract two spectra

Convert a solar_time object into solar_date object

Linear energy CIE 2008 luminous efficiency function 10 deg data

Color of an object

copy_attributes

Copy attributes from one R object to another

Conversion from counts per second to physical quantities

Extract or replace parts of a spectrum

Energy:photon ratio

Spectrum to rgb color conversion

Set the "bswf.used" attribute

List-of-wavebands constructor

setWhatMeasured

Set the "what.measured" attribute

absorptance_spct

Calculate absorptance from spectral absorptance.

Get the "scaled" attribute

Data for typical calibration lamps

format.solar_time

Encode in a Common Format

Get the "bswf.used" attribute

Collection-of-spectra constructor

green_leaf.spct

Green birch leaf reflectance.

Insert wavelength values into spectral data.

is.generic_mspct

Query class of spectrum objects

is.generic_spct

Query class of spectrum objects

Solar astronomy using Meeus' algorithm

l_insert_hinges

Insert wavelength values into spectral data.

Normalization of an R object

Normalize spectral data

print.summary_generic_spct

Print spectral summary

print.solar_time

Print solar time and solar date objects

Row-bind spectra

Wavelength range

Remove "generic_spct" and derived class attributes.

Find peaks in a spectrum

filter_cps.mspct

Counts per second from a measurement of a plastic film

Get the "spct.version" attribute

setInstrSettings

Set the "instr.settings" attribute

Set the "multiple.wl" attribute

shared_member_class

Classes common to all collection members.

Time difference between two time zones

Solar spectral irradiance (simulated)

twilight argument check and conversion

summary_spct_classes

Function that returns a vector containing the names of spectral summary

Summary of a spectral object

trimInstrSettings

Trim the "instr.settings" attribute

Create spectrum from wavebands

getInstrSettings

Get the "instr.settings" attribute

Photo:photon ratio

Get the "instr.desc" attribute

Get peaks and valleys in a spectrum

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

minus-.generic_spct

Arithmetic Operators

mod-.generic_spct

Arithmetic Operators

Energy:energy ratio

Convolve function for collections of spectra

convertTimeUnit

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

Query if an object has old class names

normalized_diff_ind

Calculate a normalized index.

Query whether a generic spectrum has been scaled

Query if it is an spectrum is tagged

Central wavelength value

Wavelength minimum

Photon:photon ratio

Photon irradiance

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

Energy-based photo-response

Trim (or expand) head and/or tail

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

Linear energy CIE 2008 luminous efficiency function 2 deg data

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

Clip head and/or tail of a spectrum

Valleys or local minima

Smooth a spectrum

c.generic_mspct

Combine collections of spectra

Print a spectral object

normalize_range_arg

Normalize a range argument into a true numeric range

calc_source_output

Light-source spectral output

Spectral response of a back-thinned CCD image sensor.

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

CIE xyz chromaticity coordinates 2 deg data

Waveband constructor method

Query whether a generic spectrum has been normalized.

is_photon_based

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

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

Set the "scaled" attribute