Learn R Programming

⚠️There's a newer version (0.14.0) of this package.Take me there.

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. Functions for calculation of the position of the sun, times of sunrise and sunset, day length and night length are also provided.

The package supports storage and manipulation of data for radiation quantities and for optical properties of objects.

This package is the core of a suite of R packages for photobiological calculations described at the r4photobiology web site.

Copy Link

Version

Install

install.packages('photobiology')

Monthly Downloads

1,133

Version

0.9.19

License

GPL (>= 2)

Homepage

http://www.r4photobiology.info/

Maintainer

Pedro Aphalo

Last Published

March 5th, 2018

Functions in photobiology (0.9.19)

D65.illuminant.spct

CIE D65 illuminant data

FEL.BN.9101.165

Data for typical calibration lamps

Ler_leaf_trns_i.spct

Green Arabidopsis leaf spectral transmittance.

Data for typical calibration lamps

Data for typical calibration lamps

Convert transmittance into absorbance.

Convert transmittance into absorptance.

Miscellaneous Mathematical Functions

absorptance_spct

Calculate absorptance from spectral absorptance.

Guess whether insertion of hinges is needed or not

Average spectral data.

Incandescent "FEL" lamp emission spectrum

Convert spectral energy irradiance into spectral photon irradiance

Sanity check a spectrum

Convert transmittance type.

Sanity check of wavelengths (internal function).

clear_body.spct

Theoretical clear body

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

Green Arabidopsis leaf reflectance and transmittance.

Trigonometric Functions

Divide two spectra, even if the wavelengths values differ

clear_photobio.cache

Clear the spectral weights cache

A.illuminant.spct

CIE A illuminant data

Convert energy-based quantities into photon-based quantities.

Energy:energy ratio

Convert absorbance into transmittance

calc_source_output

Scaled and/or interpolated light-source spectral output

Energy:photon ratio

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

Convert spectral photon irradiance into spectral energy irradiance

Spectral response of a back-thinned CCD image sensor.

Convert spectral energy irradiance into spectral photon irradiance

Check validity of spectral objects

Clean a spectrum

Find peaks in a spectrum

Theoretical spectrum of a clear material

getInstrSettings

Get the "instr.settings" attribute

getMspctVersion

Get the "mspct.version" attribute

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

Get the "spct.version" attribute

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

e2quantum_multipliers

Calculate energy to quantum multipliers

Get the "Tfr.type" attribute

black_body.spct

Theoretical black body

Energy irradiance

Copy attributes from members of a generic_mspct

Integrate spectral data.

as.generic_mspct

Collection-of-spectra copy-constructor

Ler_leaf_rflt.spct

Green Arabidopsis leaf spectral reflectance.

absorbance_spct

Calculate absorbance from spectral absorbance.

Rescale a spectrum using a summary function

Gives irradiance from spectral irradiance.

ciexyzCMF10.spct

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

c.generic_mspct

Combine collections of spectra

calc_multipliers

Spectral weights

Ler_leaf_trns.spct

Green Arabidopsis leaf spectral transmittance.

fscale a spectrum

Collection-of-spectra constructor

Get the "Afr.type" attribute

ciexyzCMF2.spct

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

green_leaf.spct

Green birch leaf reflectance.

Clip head and/or tail of a spectrum

Linear energy CIE 2008 luminous efficiency function 10 deg data

Color of an object

is.summary_generic_spct

Query class of spectrum summary objects

Linear energy CIE 2008 luminous efficiency function 2 deg data

Times for sun positions

Query if it is an spectrum is tagged

as.generic_spct

Spectral-object copy constructor

convertTimeUnit

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

Convolve function for collections of spectra

copy_attributes

Copy attributes from one R object to another

Return the First and Last Part of an Object

Join all spectra in a collection

Normalize spectral data

Conversion from counts per second to physical quantities

Convert a solar_time object into solar_date object

interpolate_spct

Map a spectrum to new wavelength values.

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

normalize_range_arg

Normalize a range argument into a true numeric range

Extract or replace parts of a spectrum

checkMspctVersion

Check that the "mspct.version" attribute is set

Arithmetic Operators

checkSpctVersion

Check that the "spct.version" attribute is set

Is an R object "effective"

Query whether a generic spectrum has been normalized.

CIE xyz chromaticity coordinates 2 deg data

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

photobiology-package

photobiology: Photobiological Calculations

Query which is the class of an spectrum

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

Find labels from "waveband" object

Photon:energy ratio

Extract or replace members of a collection of spectra

Defunct functions and methods

dim.generic_mspct

Dimensions of an Object

Set the "multiple.wl" attribute

format.solar_time

Encode in a Common Format

Logarithms and Exponentials

formatted_range

Compute range and format it

Get the "bswf.used" attribute

Get the "instr.desc" attribute

energy_as_default

Set spectral-data options

photodiode.spct

Spectral response of a GaAsP photodiode

Multi-spct transform methods

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

div-.generic_spct

Arithmetic Operators

Shift the scale of a spectrum using a summary function

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

Energy:energy ratio

Names of multi-spectra classes

fshift a spectrum

Energy-based photo-response

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

Trim (or expand) head and/or tail of a spectrum

f_dispatcher_spct

Math function dispatcher for spectra

getWhatMeasured

Get the "what.measured" attribute

Transmittance spectrum of clear polyester film

filter_cps.mspct

Counts per second from a measurement of a plastic film

setWhatMeasured

Set the "what.measured" attribute

white_led.raw_spct

White led bulb spectrum

white_led.cps_spct

White led bulb spectrum

Photon or energy irradiance from spectral energy or photon irradiance.

Get the "Rfr.type" attribute

Get the "multiple.wl" attribute

Wavelength range

Get the "scaled" attribute

Get the "normalized" attribute

getWhenMeasured

Get the "when.measured" attribute

Set the "scaled" attribute

is.generic_mspct

Query class of spectrum objects

Get the metadata attributes

Peaks or local maxima

Convert an R object into a spectrum object.

Set the "instr.desc" attribute

getWhereMeasured

Get the "where.measured" attribute

Get peaks and valleys in a spectrum

Map spectra to new wavelength values.

Insert wavelength values into spectral data.

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

insert_spct_hinges

Insert new wavelength values into a spectrum

isValidInstrSettings

Check the "instr.settings" attribute

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

Query if it is a waveband

isValidInstrDesc

Check the "instr.desc" attribute

Convert photon-based quantities into energy-based quantities

is.generic_spct

Query class of spectrum objects

Wavelength minimum

Query if an object has old class names

Wavelength maximum

Multiply two spectra, even if the wavelengths values differ

Integrated response

merge2object_spct

Merge into object_spct

na.omit.source_spct

Handle Missing Values in Objects

RGB color values

normalized_diff_ind

Calculate a normalized index.

trimInstrSettings

Trim the "instr.settings" attribute

is_photon_based

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

split_energy_irradiance

Energy irradiance for split spectrum regions

minus-.generic_spct

Arithmetic Operators

List-of-wavebands constructor

Query whether a generic spectrum has been scaled

Normalization of an R object

Solar astronomy using Meeus' algorithm

setInstrSettings

Set the "instr.settings" attribute

mod-.generic_spct

Arithmetic Operators

Summary of a spectral object

Print a "waveband" object

Theoretical spectrum of an opaque material

Add two spectra

Set the "bswf.used" attribute

l_insert_hinges

Insert wavelength values into spectral data.

Rounding of Numbers

Photon irradiance

print.summary_generic_spct

Print spectral summary

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

Central wavelength value

Daily solar spectral irradiance (simulated)

photons_energy_ratio

Photon:energy ratio

Calculate response from spectral response

Photon-based photo-response

plus-.generic_spct

Arithmetic Operators

split_irradiance

Energy or photon irradiance for split spectrum regions

reflectance_spct

Calculate reflectance from spectral reflectance

photon_irradiance

Photon irradiance

Set the "Tfr.type" attribute

setWhenMeasured

Set the "when.measured" attribute

Print a spectral object

setWhereMeasured

Set the "where.measured" attribute

Set the "Afr.type" attribute

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

Trim (or expand) head and/or tail

Valleys or local minima

Length of object in wavelength units

w_length_range2rgb

Wavelength range to rgb color conversion

Photon:photon ratio

Spectral-object constructor

transmittance_spct

Calculate transmittance from spectral transmittance.

Local solar time

v_insert_hinges

Insert wavelength values into spectral data.

print.solar_time

Print solar time and solar date objects

summary_spct_classes

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

Daily solar spectral irradiance (simulated)

upgrade_spectra

Upgrade one or more spectral objects

Set the "Rfr.type" attribute

Trim the "instr.desc" attribute

Time difference between two time zones

Photo:photon ratio

Waveband constructor method

Spectral irradiance to rgb color conversion

Use photobiology options

split_photon_irradiance

Photon irradiance for split spectrum regions

Set the "normalized" attribute

Solar spectral irradiance (simulated)

Create tagged spectrum from wavebands

Wavelength to rgb color conversion

verbose_as_default

Set error reporting options

Solar spectral irradiance (simulated)

twilight argument check and conversion

Photon or energy ratio

Remove "generic_spct" and derived class attributes.

Upgrade one spectral object

Create spectrum from wavebands

Create tagged spectrum from wavebands

shared_member_class

Classes common to all collection members.

Row-bind spectra

Remove "generic_mspct" and derived class attributes.

Smooth a spectrum

slash-.generic_spct

Arithmetic Operators

Trim (or expand) head and/or tail

Trim head and/or tail of a spectrum

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

Subtract two spectra

times-.generic_spct

Arithmetic Operators

wb_trim_as_default

Set computation options

white_body.spct

Theoretical white body

yellow_gel.spct

Transmittance spectrum of yellow theatrical gel.

white_led.source_spct

White led bulb spectrum

Calculate deuterium lamp output spectrum from fitted constants

Data for typical calibration lamps