photobiology package - RDocumentation

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Package photobiology is a set of tools designed to facilitate photobiology-related data analysis and simulation. It is the core a suite of packages with additional packages providing support for plotting spectra with pacakge 'ggplot2', example data sets and definitions that are specific to certain subject areas.

We have attempted to keep a good balance between fast computation, easy to maintain code, and a clear interface. The package has in addition to user-friendly methods and objects, also functions optimized for raw performance.

This suite of R packages started as a rewrite of the package UVcalc that was developed as a companion to a handbook of methods in plant UV photobiology writen within the COST Action FA0906 UV4growth.

The programming has been done until now by Pedro J. Aphalo, but the information used was collected, discussed and evaluated in many cases by other contributors to the handbook and by researchers in academy and industry.

Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., & Rosenqvist, E. (Eds.) (2012) Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). PDF file available from http://hdl.handle.net/10138/37558

Please, see the web site R4Photobiology for details on other packages available as part of the suite, and on how to install them.

The current release of photobiology is available through CRAN for R (>= 3.2.0).

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Version

Install

install.packages('photobiology')

Monthly Downloads

649

Version

0.9.8

License

GPL (>= 3)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

May 19th, 2016

Functions in photobiology (0.9.8)

Miscellaneous Mathematical Functions

Times for sun positions

ciexyzCMF10.spct

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

Extract or replace parts of a spectrum

plus-.generic_spct

Arithmetic Operators

reflectance_spct

Calculate reflectance from spectral reflectance

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

RGB color values

Conversion from counts per second to physical quantities

Solar spectral irradiance (simulated)

Energy irradiance

Convert spectral energy irradiance into spectral photon irradiance

Check validity of spectral objects

Photo:photon ratio

Trim head and/or tail of a spectrum

Logarithms and Exponentials

interpolate_spct

Map a spectrum to new wavelength values.

Print a "waveband" object

checkMspctVersion

Check that the "mspct.version" attribute is set

Clip head and/or tail of a spectrum

Convolve function for collections of spectra

copy_attributes

Copy attributes

Convert transmittance into absorbance.

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

as.generic_spct

Spectral-object copy constructor

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

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

CIE xyz chromaticity coordinates 2 deg data

Convert date to time-of-day in hours

Theoretical spectrum of a clear clear material

Query if it is a waveband

Trigonometric Functions

Query if it is an spectrum is tagged

calc_source_output

Light-source spectral output

Clean a spectrum

absorptance_spct

Calculate absorptance from spectral absorptance.

date argument check and conversion

Get the "Rfr.type" attribute

Peaks or local maxima

Find peaks in a spectrum

Divide two spectra, even if the wavelengths values differ

Trim (or expand) head and/or tail

f_dispatcher_spct

Math function dispatcher for spectra

Get the "bswf.used" attribute

Get peaks and valleys in a spectrum

Rescale a spectrum using a summary function

getWhatMeasured

Get the "what.measured" attribute

fscale a spectrum

fshift a spectrum

normalized_diff_ind

Calculate a normalized index.

Integrate spectral data.

Energy-based photo-response

is.generic_spct

Query class of spectrum objects

Convert absorbance into transmittance

Multi-spct transform methods

Calculate deuterim lamp output spectrum from fitted constants

is_photon_based

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

is.generic_mspct

Query class of spectrum objects

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

l_insert_hinges

Insert wavelength values into spectral data.

Theoretical spectrum of an opaque material

black_body.spct

Theoretical black body

Wavelength maximum

Calculate response from spectral response

photons_energy_ratio

Photon:energy ratio

Average spectral data.

calc_multipliers

Spectral weights

Row-bind spectra

Query which is the class of an spectrum

filter_cps.mspct

Counts per second from a measurement of a plastic film

Spectral response of a back-thinned CCD image sensor.

Collection-of-spectra constructor

Set the "Rfr.type" attribute

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

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

Energy:energy ratio

as.generic_mspct

Collection-of-spectra copy-constructor

Wavelength range

Print a spectral object

Get the "instr.desc" attribute

Photon irradiance

getWhenMeasured

Get the "when.measured" attribute

setInstrSettings

Set the "instr.settings" attribute

Defunct functions and methods

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

Set the "scaled" attribute

Solar spectral irradiance (simulated)

mod-.generic_spct

Arithmetic Operators

Names of multi-spectra classes

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

div-.generic_spct

Arithmetic Operators

Set the "instr.desc" attribute

setWhatMeasured

Set the "what.measured" attribute

Incandescent "FEL" lamp emission spectrum

Get the "spct.version" attribute

Remove "generic_mspct" and derived class attributes.

Set the "multiple.wl" attribute

merge.generic_spct

Merge two generic_spct objects

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

Valleys or local minima

Create tagged spectrum from wavebands

Is an R object "effective"

D65.illuminant.spct

CIE D65 illuminant data

split_photon_irradiance

Photon irradiance for split spectrum regions

slash-.generic_spct

Arithmetic Operators

List-of-wavebands constructor

function to be numerically minimized

Convert spectral photon irradiance into spectral energy irradiance

summary_spct_classes

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

clear_photobio.cache

clear the spectral weights cache

Normalization of an R object

photobiology-package

'Photobiological' Calculations

v_insert_hinges

Insert wavelength values into spectral data.

w_length_range2rgb

Wavelength range to rgb color conversion

convertTimeUnit

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

c.generic_mspct

Combine collections of spectra

getInstrSettings

Get the "instr.settings" attribute

photon_irradiance

Photon irradiance

photodiode.spct

Spectral response of a GaAsP photodiode

Shift the scale of a spectrum using a summary function

Get the "Tfr.type" attribute

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

Convert photon-based quantities into energy-based quantities

Set the "bswf.used" attribute

Get the "scaled" attribute

Photon:photon ratio

Remove "generic_spct" and derived class attributes.

shared_member_class

Classes common to all collection members.

Normalize spectral data

Query whether a generic spectrum has been scaled

Sanity check of wavelengths (internal function).

Photon:energy ratio

Arithmetic Operators

getWhereMeasured

Get the "where.measured" attribute

Daily solar spectral irradiance (simulated)

Linear energy CIE 2008 luminous efficiency function 2 deg data

Convert energy-based quantities into photon-based quantities.

transmittance_spct

Calculate transmittance from spectral transmittance.

Set the "Tfr.type" attribute

Spectral-object constructor

Photon-based photo-response

Daily solar spectral irradiance (simulated)

Get the "multiple.wl" attribute

Transmittance spectrum of clear polyester film

Multiply two spectra, even if the wavelengths values differ

minus-.generic_spct

Arithmetic Operators

Query whether a generic spectrum has been normalized.

clear_body.spct

Theoretical clear body

Trim (or expand) head and/or tail

Gives irradiance from spectral irradiance.

Color of an object

checkSpctVersion

Check that the "spct.version" attribute is set

Length of object in wavelength units

Add two spectra

Map spectra to new wavelength values.

Smooth a spectrum

split_irradiance

Energy or photon irradiance for split spectrum regions

Summary of a spectral object

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

Query if an object has old class names

Upgrade one spectral object

twilight argument check and conversion

Wavelength to rgb color conversion

is.summary_generic_spct

Query class of spectrum summary objects

Find labels from "waveband" object

Waveband constructor method

time argument check and conversion

Wavelength minimum

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

white_body.spct

Theoretical white body

Spectrum to rgb color conversion

Photon or energy ratio

setWhenMeasured

Set the "when.measured" attribute

Set the "normalized" attribute

Create tagged spectrum from wavebands

Create spectrum from wavebands

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

dim.generic_mspct

Dimensions of an Object

e2quantum_multipliers

Calculate energy to quantum multipliers

getMspctVersion

Get the "mspct.version" attribute

insert_spct_hinges

Insert new wavelength values into a spectrum

normalize_range_arg

Normalize a range argument into a true numeric range

Integrated response

setWhereMeasured

Set the "where.measured" attribute

Subtract two spectra

times-.generic_spct

Arithmetic Operators

absorbance_spct

Calculate absorbance from spectral absorbance.

A.illuminant.spct

CIE A illuminant data

Convert spectral energy irradiance into spectral photon irradiance

Sanity check of a spectrum.

Linear energy CIE 2008 luminous efficiency function 10 deg data

ciexyzCMF2.spct

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

Energy:energy ratio

Energy:photon ratio

Extract or replace members of a collection of spectra

Get the "normalized" attribute

Insert wavelength values into spectral data.

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

Central wavelength value

print.summary_generic_spct

Print spectral summary

Convert an R object into a spectrum object.

Rounding of Numbers

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

split_energy_irradiance

Energy irradiance for split spectrum regions

Trim (or expand) head and/or tail

upgrade_spectra

Upgrade one or more spectral objects