photobiology0.14.1 package

Convert absorbance into transmittance

Calculate absorbance from spectral absorbance.

Absorbance

Calculate absorptance from spectral absorptance.

Absorptance

Custom smoothing

Copy attributes from members of a generic_mspct

Convert transmittance into absorptance.

Convert filter quantities.

Convert spectral photon irradiance into spectral energy irradiance

Convert spectral energy irradiance into spectral photon irradiance

Convert spectral energy irradiance into spectral photon irradiance

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce or convert into a filter spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce a collection of spectra into a matrix

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Coerce to a collection-of-spectra

Coerce to a solute spectrum

Coerce to a collection-of-spectra

Coerce to a spectrum

Guess whether insertion of hinges is needed or not

Average spectral data.

Honeybee xyz chromaticity colour matching function data

Combine collections of spectra

Spectral weights

Scaled and/or interpolated light-source spectral output

Spectral response of a back-thinned CCD image sensor.

check and rename variables

Check validity of spectral objects

Sanity check a spectrum

Sanity check of wavelengths (internal function).

Check consistency of wavelength step size

Check that the "mspct.version" attribute is set

Check that the "spct.version" attribute is set

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

Query which is the class of a spectrum

Clean a spectrum

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

Clear the spectral weights cache

Theoretical spectrum of clear and apaque materials

Clip head and/or tail of a spectrum

Form a new collection

Color of an object

Coarse-grained comparison of two spectra

Convert the "Tfr.type" attribute

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

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

Convolve function for collections of spectra

Copy attributes

Conversion from counts per second to physical quantities

Calculate deuterium lamp output spectrum from fitted constants

Data for typical calibration lamps

Defunct functions and methods

Remove a previously applied normalization

Remove spikes from spectrum

Diffraction

Dimensions of an Object

Divide two spectra, even if the wavelengths values differ

Arithmetic Operators

Drop user columns

Energy fluence

Energy:energy fraction

Energy irradiance

Energy:energy ratio

Energy-based photo-response

Convert energy-based quantities into photon-based quantities.

Calculate energy to quantum (mol) multipliers

Calculate energy to quantum multipliers

Enable or disable checks

Set spectral-data options

Calculate (energy) irradiance from spectral irradiance

Energy:energy ratio

Energy:photon ratio

Expanse

Extract or replace members of a collection of spectra

Extract or replace parts of a spectrum

Math function dispatcher for spectra

Incandescent "FEL" lamp emission spectrum

Counts per second from a measurement of a plastic film

Find local maxima or global maximum (peaks)

Find spikes

Find wavelength values in a spectrum

Find repeated w.length values

Refine position and value of extremes by fitting

Fluence

Compute range and format it

fscale a spectrum

Rescale a spectrum using a summary function

fshift a spectrum

Shift the scale of a spectrum using a summary function

Collection-of-spectra constructor

Get the metadata attributes

Get peaks and valleys from a spectrum

Get the "filter.properties" attribute

Get the "how.measured" attribute

Get the "idfactor" attribute

Get the "instr.desc" attribute

Get the "instr.settings" attribute

Get the "K.type" attribute

Get the "mspct.version" attribute

Get the "multiple.wl" attribute

Query the "normalized" and "normalization" attributes

Get the "scaled" attribute

Get the "solute.properties" attribute

Get the "spct.version" attribute

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

Get the "what.measured" attribute

Get the "when.measured" attribute

Get the "where.measured" attribute

Return the First and Last Parts of an Object

Irradiance

Insert wavelength values into spectral data.

Insert new wavelength values into a spectrum

Integrate spectral data.

Gives irradiance from spectral irradiance.

Map a spectrum to new wavelength values.

Calculate spectral values at a different set of wavelengths

Map spectra to new wavelength values.

Irradiance

Photon or energy irradiance from spectral energy or photon irradiance.

Query if a spectrum contains absorbance or transmittance data

Is an R object "effective"

Query if a spectrum contains mole or mass based data

Query whether a generic spectrum has been normalized.

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

Query whether a generic spectrum has been scaled

Query if a spectrum is tagged

Query class of spectrum objects

Query class of spectrum objects

Query if an object has old class names

Query class of spectrum summary objects

Query if it is a waveband

Check the "instr.desc" attribute

Check the "instr.settings" attribute

Join all spectra in a collection

Solar astronomy using Meeus' algorithm

Insert wavelength values into spectral data.

Find labels from "waveband" object

Green Arabidopsis leaf reflectance and transmittance.

Logarithms and Exponentials

Column or variable labels

Make wavelengths consistent

Miscellaneous Mathematical Functions

Wavelength maximum

Merge and copy attributes

Merge into object_spct

Midpoint

Wavelength minimum

Arithmetic Operators

Arithmetic Operators

Multi-spct transform methods

Names of multi-spectra classes

Handle Missing Values in Objects

Normalization of an R object

Normalize a range argument into a true numeric range

Normalize spectral data

Calculate a normalized difference.

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

Peaks or local maxima

Molar spectral attenuation coefficient of phenylalanine

photobiology: Photobiological Calculations

Spectral response of a GaAsP photodiode

Photon irradiance

Photo:photon ratio

Photon:energy ratio

Arithmetic Operators

Arithmetic Operators

Print spectral objects

Print methods for metadata records

Print spectral summary

Print a "waveband" object

Multiply two spectra, even if the wavelengths values differ

Random sample of spectra

Photon fluence

Photon:photon fraction

Photon irradiance

Photon:photon ratio

Photon-based photo-response

Convert photon-based quantities into energy-based quantities

Photon:energy ratio

Packages in R for Photobiology suite

Internal utility range-check functions

Wavelength range

Row-bind spectra

Calculate reflectance from spectral reflectance

Reflectance

Replace bad pixels in a spectrum

Calculate response from spectral response

Integrated response

reflectance:reflectance fraction

Reflectance at a planar boundary

reflectance:reflectance normalised difference

reflectance:reflectance ratio

RGB color values

Remove "generic_mspct" and derived class attributes.

Remove "generic_spct" and derived class attributes.

Rounding of Numbers

rowwise functions for collections of spectra

Spectral irradiance to rgb color conversion

Mean plus and minus standard error from collection of spectra

Mean and standard error from collection of spectra

Mean from collection of spectra

Median of a collection of spectra

Product from collection of spectra

Quantiles of a collection of spectra

Range of a collection of spectra

Standard Deviation of a collection of spectra

Standard Error of a collection of spectra

Sum from collection of spectra

Variance of a collection of spectra

Standard error of the mean

Standard error of the mean

Standard error of the mean

Merge user supplied attribute names with default ones

The "bswf.used" attribute

Set the "filter.properties" attribute

Convert an R object into a spectrum object.

Set the "how.measured" attribute

Set the "idfactor" attribute

Set the "instr.desc" attribute

Set the "instr.settings" attribute

Set the "K.type" attribute

Set the "multiple.wl" attribute

Set the "normalized" and "normalization" attributes

Set the "response.type" attribute

The "Rfr.type" attribute

Set the "scaled" attribute

Set the "solute.properties" attribute

The "Tfr.type" attribute

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

Set the "what.measured" attribute

Set the "when.measured" attribute

Set the "where.measured" attribute

Classes common to all collection members.

Sign

sinc

Arithmetic Operators

Smooth a spectrum

Spectral-object constructors

Copy attributes into a tibble

Function returning a vector containing the names of spectra classes.

Access metadata

Convert spectrum from wide to long form

Spikes

List-of-wavebands constructor

Energy irradiance for split spectrum regions

Energy or photon irradiance for split spectrum regions

Photon irradiance for split spectrum regions

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

Stepsize

Subset the metadata attributes

Subsetting spectra

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

Subtract two spectra

Add two spectra

Function that returns a vector containing the names of spectral summar...

Summary of one or more spectra

Daily solar spectral irradiance (simulated)

Time series of solar spectral irradiance (measured)

Solar spectral irradiance (simulated)

Convert transmittance into absorbance.

Convert transmittance into absorptance.

Tag a spectrum

transmittance:transmittance fraction

transmittance:transmittance normalised difference

transmittance:transmittance ratio

Thin the density of wavelength values

Arithmetic Operators

Calculate transmittance from spectral transmittance.

Transmittance

Trigonometric Functions

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

Trim (or expand) head and/or tail

Trim (or expand) head and/or tail

Trim head and/or tail of a spectrum

Trim the "instr.desc" attribute

Trim the "instr.settings" attribute

Transmittance spectrum of plastic films

Compute two irrads for ratio, fraction or normalised difference

Compute two reflectances for ratio, fraction or normalised difference

Spectral response of two light sensors.

Compute two transmittances for ratio, fraction or normalised differenc...

Extract all members from a collection

Remove tags

Upgrade one spectral object

Upgrade one or more spectral objects

Use photobiology options

Insert spectral data values at new wavelength values.

Overwrite spectral data values at existing wavelength values.

Valleys or local minima

Set error reporting options

Wavelength range to rgb color conversion

Wavelength to rgb color conversion

Molar spectral attenuation coefficient of water

Photon or energy ratio

Waveband constructor method

Set computation options

Create tagged spectrum from wavebands

Create spectrum from wavebands

Create tagged spectrum from wavebands

White led bulb spectrum

Wavelength conversions

Find wavelengths values corresponding to a target spectral value