Package index

Methods for the computation of non-spectral derived quantities from spectra. Each spectrum is described by one or up to a few scalar values resulting from integration or averaging of spectral values over wavelengths, or other properties.

irrad(): Irradiance

e_irrad(): Energy irradiance

q_irrad(): Photon irradiance

fluence(): Fluence

e_fluence(): Energy fluence

q_fluence(): Photon fluence

illuminance(): Irradiance

response(): Integrated response

e_response(): Energy-based photo-response

q_response(): Photon-based photo-response

absorbance(): Absorbance

absorptance(): Absorptance

transmittance(): Transmittance

reflectance(): Reflectance

average_spct(): Average spectral data.

integrate_spct(): Integrate spectral data.

color_of() colour_of() color() fast_color_of_wl() fast_color_of_wb(): Color of an object

rgb_spct(): RGB color values

e_ratio(): Energy:energy ratio

q_ratio(): Photon:photon ratio

eq_ratio(): Energy:photon ratio

qe_ratio(): Photon:energy ratio

e_fraction(): Energy:energy fraction

q_fraction(): Photon:photon fraction

Tfr_ratio(): transmittance:transmittance ratio

Tfr_fraction(): transmittance:transmittance fraction

Tfr_normdiff(): transmittance:transmittance normalised difference

Rfr_ratio(): reflectance:reflectance ratio

Rfr_fraction(): reflectance:reflectance fraction

Rfr_normdiff(): reflectance:reflectance normalised difference

Methods for querying about the wavelength values of spectra and wavebands. Each spectrum or wavebdand is described by one or two scalar values.

wl_min() min(<waveband>) min(<generic_spct>) min(<generic_mspct>): Wavelength minimum

wl_max() max(<waveband>) max(<generic_spct>) max(<generic_mspct>): Wavelength maximum

wl_range() range(<waveband>) range(<generic_spct>) range(<generic_mspct>): Wavelength range

spread() wl_expanse() expanse(): Expanse

wl_midpoint() midpoint(): Midpoint

wl_stepsize() stepsize(): Stepsize

Statistical summaries from groups of spectra

Methods that compute statistical summaries of spectral data, treating individual spectra as replicates or sampled members from a population of spectra. A summary spectrum or fewer spectra than input are returned.

compare_spct(): Coarse-grained comparison of two spectra

s_sum(): Sum from collection of spectra

s_prod(): Product from collection of spectra

s_mean(): Mean from collection of spectra

s_median(): Median of a collection of spectra

s_range(): Range of a collection of spectra

s_var(): Variance of a collection of spectra

s_sd(): Standard Deviation of a collection of spectra

s_se(): Standard Error of a collection of spectra

s_mean_se(): Mean and standard error from collection of spectra

s_mean_se_band(): Mean plus and minus standard error from collection of spectra

pull_sample(): Random sample of spectra

Metadata attributes

Methods for setting and querying metadata from spectral objects.

is_photon_based() is_energy_based(): Query if a spectrum contains photon- or energy-based data.

setBSWFUsed() getBSWFUsed(): The "bswf.used" attribute

is_effective(): Is an R object "effective"

getInstrDesc() instr_descriptor(): Get the "instr.desc" attribute

setInstrDesc() `instr_descriptor<-`(): Set the "instr.desc" attribute

trimInstrDesc(): Trim the "instr.desc" attribute

isValidInstrDesc(): Check the "instr.desc" attribute

getInstrSettings() instr_settings(): Get the "instr.settings" attribute

setInstrSettings() `instr_settings<-`(): Set the "instr.settings" attribute

trimInstrSettings(): Trim the "instr.settings" attribute

isValidInstrSettings(): Check the "instr.settings" attribute

getMultipleWl() multiple_wl(): Get the "multiple.wl" attribute

setMultipleWl() `multiple_wl<-`(): Set the "multiple.wl" attribute

getNormalized() getNormalised() getNormalization() getNormalisation(): Query the "normalized" and "normalization" attributes

setNormalized() setNormalised(): Set the "normalized" and "normalization" attributes

is_normalized() is_normalised(): Query whether a generic spectrum has been normalized.

getScaled() getScaling(): Get the "scaled" attribute

setScaled(): Set the "scaled" attribute

is_scaled(): Query whether a generic spectrum has been scaled

setRfrType() getRfrType(): The "Rfr.type" attribute

getFilterProperties() filter_properties(): Get the "filter.properties" attribute

setFilterProperties() `filter_properties<-`(): Set the "filter.properties" attribute

getSoluteProperties() solute_properties(): Get the "solute.properties" attribute

setSoluteProperties() `solute_properties<-`(): Set the "solute.properties" attribute

setTfrType() getTfrType(): The "Tfr.type" attribute

f_mspct() mutate_mspct() calc_filter_multipliers() T2T() getAfrType() setAfrType() sample_spct() sample_mspct(): Defunct functions and methods

is_absorbance_based() is_absorptance_based() is_transmittance_based(): Query if a spectrum contains absorbance or transmittance data

getKType(): Get the "K.type" attribute

setKType(): Set the "K.type" attribute

is_mole_based() is_mass_based(): Query if a spectrum contains mole or mass based data

getTimeUnit(): Get the "time.unit" attribute of an existing source_spct object

setTimeUnit(): Set the "time.unit" attribute of an existing source_spct object

setResponseType() getResponseType(): Set the "response.type" attribute

getWhatMeasured() what_measured(): Get the "what.measured" attribute

setWhatMeasured() `what_measured<-`(): Set the "what.measured" attribute

getWhenMeasured() when_measured(): Get the "when.measured" attribute

setWhenMeasured() `when_measured<-`(): Set the "when.measured" attribute

getWhereMeasured() where_measured(): Get the "where.measured" attribute

setWhereMeasured() `where_measured<-`(): Set the "where.measured" attribute

getHowMeasured() how_measured(): Get the "how.measured" attribute

setHowMeasured() `how_measured<-`(): Set the "how.measured" attribute

getIdFactor() id_factor(): Get the "idfactor" attribute

setIdFactor() `id_factor<-`(): Set the "idfactor" attribute

is_tagged(): Query if a spectrum is tagged

dim(<generic_mspct>) `dim<-`(<generic_mspct>): Dimensions of an Object

labels(<waveband>) labels(<generic_spct>): Find labels from "waveband" object

add_attr2tb() when_measured2tb() geocode2tb() lonlat2tb() lon2tb() lat2tb() address2tb() what_measured2tb() how_measured2tb() normalized2tb() scaled2tb() instr_desc2tb() instr_settings2tb() BSWF_used2tb() filter_properties2tb() solute_properties2tb() Tfr_type2tb() Rfr_type2tb() time_unit2tb() comment2tb(): Copy attributes from members of a generic_mspct

spct_attr2tb(): Copy attributes into a tibble

spct_metadata(): Access metadata

Spectral features

Methods for detection of specific features in spectra.

peaks(): Peaks or local maxima

valleys(): Valleys or local minima

wls_at_target(): Find wavelengths values corresponding to a target spectral value

spikes(): Spikes

Non-summary methods for transforming or modifying the radiation-related quantity of spectral data objects.

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

despike(): Remove spikes from spectrum

normalize() normalise(): Normalize spectral data

normalization(): Normalization of an R object

fscale(): Rescale a spectrum using a summary function

fshift(): Shift the scale of a spectrum using a summary function

convertTimeUnit(): Convert the "time.unit" attribute of an existing source_spct object

e2q(): Convert energy-based quantities into photon-based quantities.

q2e(): Convert photon-based quantities into energy-based quantities

T2A(): Convert transmittance into absorbance.

A2T(): Convert absorbance into transmittance

T2Afr(): Convert transmittance into absorptance.

Afr2T(): Convert transmittance into absorptance.

any2T() any2A() any2Afr(): Convert filter quantities.

convertTfrType(): Convert the "Tfr.type" attribute

convertThickness(): Convert the "thickness" attribute of an existing filter_spct object.

tag(): Tag a spectrum

untag(): Remove tags

cps2irrad() cps2Rfr() cps2Tfr(): Conversion from counts per second to physical quantities

smooth_spct(): Smooth a spectrum

Non-summary methods for transforming or modifying the wavelengths of spectral data objects.

insert_hinges(): Insert wavelength values into spectral data.

interpolate_wl(): Map spectra to new wavelength values.

interpolate_spct() interpolate_mspct(): Map a spectrum to new wavelength values.

clip_wl(): Clip head and/or tail of a spectrum

thin_wl(): Thin the density of wavelength values

trim_wl(): Trim head and/or tail of a spectrum

trim_spct() trim_mspct() trim2overlap() extend2extremes(): Trim (or expand) head and/or tail of a spectrum

na.omit(<generic_spct>) na.omit(<source_spct>) na.omit(<response_spct>) na.omit(<filter_spct>) na.omit(<reflector_spct>) na.omit(<object_spct>) na.omit(<solute_spct>) na.omit(<cps_spct>) na.omit(<raw_spct>) na.omit(<chroma_spct>) na.omit(<generic_mspct>) na.exclude(<generic_spct>) na.exclude(<source_spct>) na.exclude(<response_spct>) na.exclude(<filter_spct>) na.exclude(<reflector_spct>) na.exclude(<object_spct>) na.exclude(<solute_spct>) na.exclude(<cps_spct>) na.exclude(<raw_spct>) na.exclude(<chroma_spct>) na.exclude(<generic_mspct>): Handle Missing Values in Objects

wl2wavenumber() wavenumber2wl() wl2frequency() frequency2wl() wl2energy() energy2wl(): Wavelength conversions

Mathematical operators and functions for spectra

Specializations of all R’s mathematical functions and operators for spectral objects.

`+`(<generic_spct>): Arithmetic Operators

`%/%`(<generic_spct>): Arithmetic Operators

`-`(<generic_spct>): Arithmetic Operators

`%%`(<generic_spct>): Arithmetic Operators

`/`(<generic_spct>): Arithmetic Operators

`*`(<generic_spct>): Arithmetic Operators

`^`(<generic_spct>): Arithmetic Operators

cos(<generic_spct>) sin(<generic_spct>) tan(<generic_spct>) acos(<generic_spct>) asin(<generic_spct>) atan(<generic_spct>): Trigonometric Functions

log(<generic_spct>) log2(<generic_spct>) log10(<generic_spct>) exp(<generic_spct>): Logarithms and Exponentials

sqrt(<generic_spct>) abs(<generic_spct>): Miscellaneous Mathematical Functions

sign(<generic_spct>): Sign

round(<generic_spct>) signif(<generic_spct>) ceiling(<generic_spct>) floor(<generic_spct>) trunc(<generic_spct>): Rounding of Numbers

Extract, replace and combine

Functions and operators, both specializations of R’s ones and new ones specific to spectra and collections of spectra.

`[`(<generic_spct>) `[`(<raw_spct>) `[`(<cps_spct>) `[`(<source_spct>) `[`(<response_spct>) `[`(<filter_spct>) `[`(<reflector_spct>) `[`(<solute_spct>) `[`(<object_spct>) `[`(<chroma_spct>) `[<-`(<generic_spct>) `$<-`(<generic_spct>): Extract or replace parts of a spectrum

`[`(<generic_mspct>) `[<-`(<generic_mspct>) `$<-`(<generic_mspct>) `[[<-`(<generic_mspct>): Extract or replace members of a collection of spectra

subset(<generic_spct>): Subsetting spectra

c(<generic_mspct>): Combine collections of spectra

rbindspct(): Row-bind spectra

merge2object_spct(): Merge into object_spct

split2mspct() split2source_mspct() split2response_mspct() split2filter_mspct() split2reflector_mspct() split2solute_mspct() split2cps_mspct() split2raw_mspct() split2calibration_mspct(): Convert a 'wide' or untidy data frame into a collection of spectra

subset2mspct(): Convert 'long' or tidy spectral data into a collection of spectra

join_mspct(): Join all spectra in a collection

Apply

Apply functions for collections of spectra.

msmsply() msdply() mslply() msaply(): Multi-spct transform methods

convolve_each(): Convolve function for collections of spectra

Options

Convenience functions for setting R options recognized by functions in the ‘r4photobiology’ suite of R packages.

using_Tfr() using_Afr() using_A() using_energy() using_photon() using_quantum(): Use photobiology options

energy_as_default() photon_as_default() quantum_as_default() Tfr_as_default() Afr_as_default() A_as_default() unset_radiation_unit_default() unset_filter_qty_default() unset_user_defaults(): Set spectral-data options

wb_trim_as_default() use_cached_mult_as_default(): Set computation options

verbose_as_default() strict_range_as_default(): Set error reporting options

Astronomy

Astronomical computations of interest in photobiology and meteorology.

solar_time(): Local solar time

as.solar_date(): Convert a solar_time object into solar_date object

is.solar_time() is.solar_date(): Query class

as_tod(): Convert datetime to time-of-day

format(<tod_time>): Encode in a Common Format

print(<tod_time>): Print time-of-day objects

tz_time_diff(): Time difference between two time zones

day_night() day_night_fast() is_daytime() noon_time() sunrise_time() sunset_time() day_length() night_length(): Times for sun positions

sun_angles() sun_angles_fast() sun_elevation() sun_zenith_angle() sun_azimuth() distance_to_sun(): Solar angles

format(<solar_time>): Encode in a Common Format

print(<solar_time>) print(<solar_date>): Print solar time and solar date objects

validate_geocode() is_valid_geocode() length_geocode() na_geocode(): Validate a geocode

irrad_extraterrestrial(): Extraterrestrial irradiance

Atmosphere

Computations related to water vapour in air, and on equivalent air mass at different solar elevations.

water_vp_sat() water_dp() water_fp() water_vp2mvc() water_mvc2vp() water_vp2RH() water_RH2vp() water_vp_sat_slope() psychrometric_constant(): Water vapour pressure

relative_AM(): Relative Air Mass (AM)

ET_ref() ET_ref_day(): Evapotranspiration

net_irradiance(): Net radiation flux

Optics

Computations related to radiation physics.

diffraction_single_slit() diffraction_double_slit(): Diffraction

Rfr_from_n() Rfr_p_from_n() Rfr_s_from_n(): Reflectance at a planar boundary

Datasets

Spectral data used in documentation examples and unit tests

Data for light sources

Spectral irradiance data for daylight and artificial light

sun.spct sun.data: Solar spectral irradiance (simulated)

sun_daily.spct sun_daily.data sun.daily.spct sun.daily.data: Daily solar spectral irradiance (simulated)

sun_evening.spct sun_evening.mspct: Time series of solar spectral irradiance (measured)

white_led.source_spct white_led.cps_spct white_led.raw_spct: White led bulb spectrum

phenylalanine.spct: Molar spectral attenuation coefficient of phenylalanine

water.spct: Molar spectral attenuation coefficient of water

A.illuminant.spct: CIE A illuminant data

D50.illuminant.spct: CIE D50 illuminant data

D65.illuminant.spct: CIE D65 illuminant data

FEL_spectrum(): Incandescent "FEL" lamp emission spectrum

D2_spectrum(): Calculate deuterium lamp output spectrum from fitted constants

D2.UV653 D2.UV586 D2.UV654 FEL.BN.9101.165: Data for typical calibration lamps

Data for real and theoretical objects

Spectral transmittance, spectral reflectance and spectral absorptance data for real and theoretical objects

two_filters.spct two_filters.mspct polyester.spct yellow_gel.spct: Transmittance spectrum of plastic films

clear.spct opaque.spct: Theoretical spectrum of clear and apaque materials

green_leaf.spct: Green birch leaf reflectance.

Ler_leaf.spct Ler_leaf_rflt.spct Ler_leaf_trns.spct Ler_leaf_trns_i.spct: Green Arabidopsis leaf reflectance and transmittance.

black_body.spct white_body.spct clear_body.spct: Theoretical optical bodies

Data for light sensors

ccd.spct: Spectral response of a back-thinned CCD image sensor.

photodiode.spct: Spectral response of a GaAsP photodiode

Data for human vision

Data for the spectral response of the human eye as used in different computaions related to illumination and vision

ciev10.spct: Linear energy CIE 2008 luminous efficiency function 10 deg data

ciev2.spct: 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

cone_fundamentals10.spct cone_fundamentals10.mspct: Ten-degree cone fundamentals

Data for animal vision

Data for the spectral response of bee vision

beesxyzCMF.spct: Honeybee xyz chromaticity colour matching function data

Utility data

List of packages in the R for Photobiology suite

r4p_pkgs: Packages in R for Photobiology suite

Housekeeping and helper functions

Utilities mainly used internally in the ‘r4photobiology’ suite of R packages, but safe to use in user code.

check_spct(): Check validity of spectral objects

enable_check_spct() disable_check_spct() set_check_spct(): Enable or disable checks

check_w.length(): Sanity check of wavelengths (internal function).

checkTimeUnit(): Check the "time.unit" attribute of an existing source_spct object

copy_attributes(): Copy attributes

merge_attributes(): Merge and copy attributes

formatted_range(): Compute range and format it

normalize_range_arg(): Normalize a range argument into a true numeric range

collect2mspct(): Form a new collection

spct_wide2long(): Convert spectrum from wide to long form

uncollect2spct(): Extract all members from a collection

drop_user_cols(): Drop user columns

getSpctVersion(): Get the "spct.version" attribute

getMspctVersion(): Get the "mspct.version" attribute

is.old_spct(): Query if an object has old class names

upgrade_spct(): Upgrade one spectral object

upgrade_spectra(): Upgrade one or more spectral objects

f_mspct() mutate_mspct() calc_filter_multipliers() T2T() getAfrType() setAfrType() sample_spct() sample_mspct(): Defunct functions and methods

Low-level functions

Internal functions available for use by developers when maximum flexibility is needed. They are not meant for everyday use as they lack error handling and data validation features.

as_energy(): Convert spectral photon irradiance into spectral energy irradiance

as_quantum(): Convert spectral energy irradiance into spectral photon irradiance

as_quantum_mol(): Convert spectral energy irradiance into spectral photon irradiance

calc_multipliers(): Spectral weights

calc_source_output(): Scaled and/or interpolated light-source spectral output

check_spectrum(): Sanity check a spectrum

copy_attributes(): Copy attributes

div_spectra(): Divide two spectra, even if the wavelengths values differ

e2qmol_multipliers(): Calculate energy to quantum (mol) multipliers

e2quantum_multipliers(): Calculate energy to quantum multipliers

energy_irradiance(): Calculate (energy) irradiance from spectral irradiance

energy_ratio(): Energy:energy ratio

findMultipleWl(): Find repeated w.length values

find_peaks(): Find peaks in a spectrum

find_spikes(): Find spikes

find_wls(): Find wavelength values in a spectrum

fit_peaks() fit_valleys(): Refine position and value of extremes by fitting

get_attributes(): Get the metadata attributes

get_peaks() get_valleys(): Get peaks and valleys in a spectrum

insert_spct_hinges(): Insert new wavelength values into a spectrum

integrate_xy(): Gives irradiance from spectral irradiance.

interpolate_spectrum(): Calculate spectral values at a different set of wavelengths

irradiance(): Photon or energy irradiance from spectral energy or photon irradiance.

merge_attributes(): Merge and copy attributes

normalized_diff_ind() normalised_diff_ind() NDxI(): Calculate a normalized difference.

oper_spectra(): Binary operation on two spectra, even if the wavelengths values differ

photon_irradiance(): Photon irradiance

photon_ratio(): Photo:photon ratio

photons_energy_ratio(): Photon:energy ratio

prod_spectra(): Multiply two spectra, even if the wavelengths values differ

replace_bad_pixs(): Replace bad pixels in a spectrum

s_e_irrad2rgb(): Spectral irradiance to rgb color conversion

select_spct_attributes() spct_attributes(): Merge user supplied attribute names with default ones

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

subt_spectra(): Subtract two spectra

sum_spectra(): Add two spectra

trim_tails(): Trim (or expand) head and/or tail

trim_waveband(): Trim (or expand) head and/or tail

v_insert_hinges(): Insert spectral data values at new wavelength values.

v_replace_hinges(): Overwrite spectral data values at existing wavelength values.

w_length_range2rgb(): Wavelength range to rgb color conversion

w_length2rgb(): Wavelength to rgb color conversion

waveband_ratio(): Photon or energy ratio

Package overview

Radiation

Waveband and spectral weighting functions

Individual spectra

Collections of spectra

summary() and print() methods for spectra

Summary quantities from individual spectra, related to spectral values

Summary quantities from individual spectra and wavebands, related to wavelength