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photobiology

Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Functions (303)

A.illuminant.spct

CIE A illuminant data

A2T

Convert absorbance into transmittance

Convert transmittance into absorptance.

Data for typical calibration lamps

Data for typical calibration lamps

Data for typical calibration lamps

D2_spectrum

Calculate deuterium lamp output spectrum from fitted constants

D65.illuminant.spct

CIE D65 illuminant data

Evapotranspiration

FEL.BN.9101.165

Data for typical calibration lamps

FEL_spectrum

Incandescent "FEL" lamp emission spectrum

Ler_leaf.spct

Green Arabidopsis leaf reflectance and transmittance.

Ler_leaf_rflt.spct

Green Arabidopsis leaf spectral reflectance.

Ler_leaf_trns.spct

Green Arabidopsis leaf spectral transmittance.

Ler_leaf_trns_i.spct

Green Arabidopsis leaf spectral transmittance.

Miscellaneous Mathematical Functions

Reflectance at a planar boundary

T2A

Convert transmittance into absorbance.

Convert transmittance into absorptance.

Trig

Trigonometric Functions

Absorbance

absorbance_spct

Calculate absorbance from spectral absorbance.

absorptance

Absorptance

absorptance_spct

Calculate absorptance from spectral absorptance.

adaptive_smoothing

Custom smoothing

add_attr2tb

Copy attributes from members of a generic_mspct

Convert filter quantities.

as.calibration_mspct

Coerce to a collection-of-spectra

as.calibration_spct

Coerce to a spectrum

as.chroma_mspct

Coerce to a collection-of-spectra

as.chroma_spct

Coerce to a spectrum

as.cps_mspct

Coerce to a collection-of-spectra

as.cps_spct

Coerce to a spectrum

as.filter_mspct

Coerce to a collection-of-spectra

as.filter_spct

Coerce to a spectrum

as.generic_mspct

Coerce to a collection-of-spectra

as.generic_spct

Coerce to a spectrum

as.matrix-mspct

Coerce a collection of spectra into a matrix

as.object_mspct

Coerce to a collection-of-spectra

as.object_spct

Coerce to a spectrum

as.raw_mspct

Coerce to a collection-of-spectra

as.raw_spct

Coerce to a spectrum

as.reflector_mspct

Coerce to a collection-of-spectra

as.reflector_spct

Coerce to a spectrum

as.response_mspct

Coerce to a collection-of-spectra

as.response_spct

Coerce to a spectrum

as.solar_date

Convert a solar_time object into solar_date object

as.source_mspct

Coerce to a collection-of-spectra

as.source_spct

Coerce to a spectrum

Convert spectral photon irradiance into spectral energy irradiance

Convert spectral energy irradiance into spectral photon irradiance

as_quantum_mol

Convert spectral energy irradiance into spectral photon irradiance

Convert datetime to time-of-day

auto_hinges

Guess whether insertion of hinges is needed or not

average_spct

Average spectral data.

beesxyzCMF.spct

Honeybee xyz chromaticity colour matching function data

black_body.spct

Theoretical black body

Combine collections of spectra

calc_multipliers

Spectral weights

calc_source_output

Scaled and/or interpolated light-source spectral output

Spectral response of a back-thinned CCD image sensor.

checkMspctVersion

Check that the "mspct.version" attribute is set

checkSpctVersion

Check that the "spct.version" attribute is set

checkTimeUnit

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

Check validity of spectral objects

check_spectrum

Sanity check a spectrum

check_w.length

Sanity check of wavelengths (internal function).

ciev10.spct

Linear energy CIE 2008 luminous efficiency function 10 deg data

Linear energy CIE 2008 luminous efficiency function 2 deg data

ciexyzCC10.spct

CIE xyz chromaticity coordinates (CC) 10 deg data

ciexyzCC2.spct

CIE xyz chromaticity coordinates 2 deg data

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

Query which is the class of a spectrum

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

Clean a spectrum

Theoretical spectrum of a clear material

clear_body.spct

Theoretical clear body

clear_photobio.cache

Clear the spectral weights cache

Clip head and/or tail of a spectrum

collect2mspct

Form a new collection

Color of an object

compare_spct

Coarse-grained comparison of two spectra

cone_fundamentals10.spct

Ten-degree cone fundaamentals

convertTfrType

Convert the "Tfr.type" attribute

convertThickness

Convert the "thickness" attribute of an existing filter_spct object.

convertTimeUnit

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

convolve_each

Convolve function for collections of spectra

copy_attributes

Copy attributes

Conversion from counts per second to physical quantities

Times for sun positions

Defunct functions and methods

Remove spikes from spectrum

diffraction_single_slit

Diffraction

dim.generic_mspct

Dimensions of an Object

div-.generic_spct

Arithmetic Operators

div_spectra

Divide two spectra, even if the wavelengths values differ

drop_user_cols

Drop user columns

e2q

Convert energy-based quantities into photon-based quantities.

e2qmol_multipliers

Calculate energy to quantum (mol) multipliers

e2quantum_multipliers

Calculate energy to quantum multipliers

Energy fluence

Energy irradiance

Energy:energy ratio

Energy-based photo-response

enable_check_spct

Enable or disable checks

energy_as_default

Set spectral-data options

energy_irradiance

Calculate (energy) irradiance from spectral irradiance

energy_ratio

Energy:energy ratio

Energy:photon ratio

Expanse

Extract or replace parts of a spectrum

extract_mspct

Extract or replace members of a collection of spectra

f_dispatcher_spct

Math function dispatcher for spectra

filter_cps.mspct

Counts per second from a measurement of a plastic film

findMultipleWl

Find repeated w.length values

Find peaks in a spectrum

find_spikes

Find spikes

Find wavelength values in a spectrum

Refine position and value of extremes by fitting

Fluence

format.solar_time

Encode in a Common Format

format.tod_time

Encode in a Common Format

formatted_range

Compute range and format it

Rescale a spectrum using a summary function

fscale_spct

fscale a spectrum

Shift the scale of a spectrum using a summary function

fshift_spct

fshift a spectrum

generic_mspct

Collection-of-spectra constructor

getBSWFUsed

Get the "bswf.used" attribute

getFilterProperties

Get the "filter.properties" attribute

getHowMeasured

Get the "how.measured" attribute

getIdFactor

Get the "idfactor" attribute

getInstrDesc

Get the "instr.desc" attribute

getInstrSettings

Get the "instr.settings" attribute

getMspctVersion

Get the "mspct.version" attribute

getMultipleWl

Get the "multiple.wl" attribute

getNormalized

Get the "normalized" attribute

getResponseType

Get the "response.type" attribute

Get the "Rfr.type" attribute

Get the "scaled" attribute

getSpctVersion

Get the "spct.version" attribute

Get the "Tfr.type" attribute

getTimeUnit

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

getWhatMeasured

Get the "what.measured" attribute

getWhenMeasured

Get the "when.measured" attribute

getWhereMeasured

Get the "where.measured" attribute

get_attributes

Get the metadata attributes

Get peaks and valleys in a spectrum

green_leaf.spct

Green birch leaf reflectance.

Return the First and Last Part of an Object

insert_hinges

Insert wavelength values into spectral data.

insert_spct_hinges

Insert new wavelength values into a spectrum

integrate_spct

Integrate spectral data.

integrate_xy

Gives irradiance from spectral irradiance.

interpolate_spct

Map a spectrum to new wavelength values.

interpolate_spectrum

Calculate spectral values at a different set of wavelengths

interpolate_wl

Map spectra to new wavelength values.

Irradiance

irrad_extraterrestrial

Extraterrestrial irradiance

Photon or energy irradiance from spectral energy or photon irradiance.

is.generic_mspct

Query class of spectrum objects

is.generic_spct

Query class of spectrum objects

is.old_spct

Query if an object has old class names

is.solar_time

Query class

is.summary_generic_spct

Query class of spectrum summary objects

is.waveband

Query if it is a waveband

isValidInstrDesc

Check the "instr.desc" attribute

isValidInstrSettings

Check the "instr.settings" attribute

is_absorbance_based

Query if a spectrum contains absorbance or transmittance data

is_effective

Is an R object "effective"

is_normalized

Query whether a generic spectrum has been normalized.

is_photon_based

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

Query whether a generic spectrum has been scaled

Query if a spectrum is tagged

Join all spectra in a collection

Solar astronomy using Meeus' algorithm

l_insert_hinges

Insert wavelength values into spectral data.

Find labels from "waveband" object

log

Logarithms and Exponentials

max

Wavelength maximum

merge2object_spct

Merge into object_spct

merge_attributes

Merge and copy attributes

Midpoint

min

Wavelength minimum

minus-.generic_spct

Arithmetic Operators

mod-.generic_spct

Arithmetic Operators

Multi-spct transform methods

mspct_classes

Names of multi-spectra classes

Handle Missing Values in Objects

net_irradiance

Net radiation flux

normalization

Normalization of an R object

Normalize spectral data

normalize_range_arg

Normalize a range argument into a true numeric range

normalized_diff_ind

Calculate a normalized index.

opaque.spct

Theoretical spectrum of an opaque material

oper_spectra

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

Peaks or local maxima

photobiology-package

photobiology: Photobiological Calculations

photodiode.spct

Spectral response of a GaAsP photodiode

photon_irradiance

Photon irradiance

photon_ratio

Photo:photon ratio

photons_energy_ratio

Photon:energy ratio

plus-.generic_spct

Arithmetic Operators

polyester.spct

Transmittance spectrum of clear polyester film

pow-.generic_spct

Arithmetic Operators

Print a spectral object

print.solar_time

Print solar time and solar date objects

print.summary_generic_spct

Print spectral summary

print.tod_time

Print time-of-day objects

print.waveband

Print a "waveband" object

prod_spectra

Multiply two spectra, even if the wavelengths values differ

q2e

Convert photon-based quantities into energy-based quantities

Photon fluence

Photon irradiance

Photon:photon ratio

Photon-based photo-response

Photon:energy ratio

Packages in R for Photobiology suite

Wavelength range

Row-bind spectra

reflectance

Reflectance

reflectance_spct

Calculate reflectance from spectral reflectance

relative_AM

Relative Air Mass (AM)

replace_bad_pixs

Replace bad pixels in a spectrum

Calculate response from spectral response

Integrated response

RGB color values

rmDerivedMspct

Remove "generic_mspct" and derived class attributes.

rmDerivedSpct

Remove "generic_spct" and derived class attributes.

Rounding of Numbers

rowwise functions for collections of spectra

s_e_irrad2rgb

Spectral irradiance to rgb color conversion

Mean from collection of spectra

Mean and standard error from collection of spectra

Median of a collection of spectra

Product from collection of spectra

Range of a collection of spectra

s_sd

Standard Deviation of a collection of spectra

s_se

Standard Error of a collection of spectra

Sum from collection of spectra

Variance of a collection of spectra

Standard error of the mean

select_spct_attributes

Merge user supplied attribute names with default ones

setBSWFUsed

Set the "bswf.used" attribute

setFilterProperties

Set the "filter.properties" attribute

setGenericSpct

Convert an R object into a spectrum object.

setHowMeasured

Set the "how.measured" attribute

setIdFactor

Set the "idfactor" attribute

setInstrDesc

Set the "instr.desc" attribute

setInstrSettings

Set the "instr.settings" attribute

setMultipleWl

Set the "multiple.wl" attribute

setNormalized

Set the "normalized" and "normalization" attributes

setResponseType

Set the "response.type" attribute

Set the "Rfr.type" attribute

Set the "scaled" attribute

Set the "Tfr.type" attribute

setTimeUnit

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

setWhatMeasured

Set the "what.measured" attribute

setWhenMeasured

Set the "when.measured" attribute

setWhereMeasured

Set the "where.measured" attribute

shared_member_class

Classes common to all collection members.

sign

Sign

sinc

sinc

slash-.generic_spct

Arithmetic Operators

smooth_spct

Smooth a spectrum

Local solar time

source_spct

Spectral-object constructor

spct_attr2tb

Copy attributes into a tibble

spct_classes

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

spct_metadata

Access metadata

Spikes

split2mspct

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

split_bands

List-of-wavebands constructor

split_energy_irradiance

Energy irradiance for split spectrum regions

split_irradiance

Energy or photon irradiance for split spectrum regions

split_photon_irradiance

Photon irradiance for split spectrum regions

Stepsize

Subsetting spectra

subset2mspct

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

subt_spectra

Subtract two spectra

sum_spectra

Add two spectra

Summary of a spectral object

summary_spct_classes

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

sun.daily.data

Daily solar spectral irradiance (simulated)

sun.daily.spct

Daily solar spectral irradiance (simulated)

Solar spectral irradiance (simulated)

Solar spectral irradiance (simulated)

Solar angles

tag

Tag a spectrum

Thin the density of wavelength values

times-.generic_spct

Arithmetic Operators

transmittance

Transmittance

transmittance_spct

Calculate transmittance from spectral transmittance.

trimInstrDesc

Trim the "instr.desc" attribute

trimInstrSettings

Trim the "instr.settings" attribute

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

Trim (or expand) head and/or tail

trim_waveband

Trim (or expand) head and/or tail

Trim head and/or tail of a spectrum

twilight2angle

twilight argument check and conversion

tz_time_diff

Time difference between two time zones

uncollect2spct

Extract all members from a collection

photobiology

Photobiological Calculations

v0.10.10

GPL (>= 2)

Authors

Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb], Agnese Fazio [ctb]

Initial release

2022-03-24

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