Package 'photobiology'

Description

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. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) doi:10.19232/uv4pb.2015.1.14.

Details

Package ‘photobiology’ is at the core of a suite of R packages supporting computations and plotting relevant to photobiology (described at https://www.r4photobiology.info/). Package 'photobiology' has its main focus in the characterization of the light environment, the description of optical properties of objects and substances and description of light responses of organisms and devices used to measure light. The facilities for spectral data storage and manipulations are widely useful in photobiology, chemistry, geophysics, radiation climatology and remote sensing. Astronomical computations for the sun are also implemented. The design of object classes for spectral data supports reproducibility by facilitating the consistent use of units and physical quantities and consistent embedding of metadata. Data are expressed throughout using SI base units, except for wavelengths which are consistently expressed in nanometres [$nm$]. Please see the vignette 0: The R for photobiology Suite for a description of the suite.

Acknowledgements

This work was funded by the Academy of Finland (decision 252548). COST Action FA9604 ‘UV4Growth’ facilitated discussions and exchanges of ideas that lead to the development of this package. The contributions of Andy McLeod, Lars Olof Björn, Nigel Paul, Lasse Ylianttila, T. Matthew Robson and Titta Kotilainen were specially significant. Tutorials by Hadley Wickham and comments on my presentation at UseR!2015 allowed me to significantly improve the coding and functionality.

Author(s)

Maintainer: Pedro J. Aphalo [email protected] (ORCID)

Other contributors:

• Titta K. Kotilainen (ORCID) [contributor]

• Glenn Davis [email protected] [contributor]

• Agnese Fazio [email protected] [contributor]

References

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. xx + 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). Open access PDF download available at doi:10.31885/9789521083631.

Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. doi:10.19232/uv4pb.2015.1.14.

Maia, R., Eliason, C. M., Bitton, P. P., Doucet, S. M., Shawkey, M. D. (2013) pavo: an R package for the analysis, visualization and organization of spectral data. Methods in Ecology and Evolution, 4(10):906-913. doi:10.1111/2041-210X.12069.

See Also

Useful links:

• https://docs.r4photobiology.info/photobiology/

• https://github.com/aphalo/photobiology

• Report bugs at https://github.com/aphalo/photobiology/issues

Examples

# irradiance of the whole spectrum
irrad(sun.spct)
# photon irradiance 400 nm to 700 nm
q_irrad(sun.spct, waveband(c(400,700)))
# energy irradiance 400 nm to 700 nm
e_irrad(sun.spct, waveband(c(400,700)))
# simulating the effect of a filter on solar irradiance
e_irrad(sun.spct * yellow_gel.spct, waveband(c(400,500)))
e_irrad(sun.spct * yellow_gel.spct, waveband(c(500,700)))
# daylength
sunrise_time(lubridate::today(tzone = "Europe/Helsinki"),
             tz = "Europe/Helsinki",
             geocode = data.frame(lat = 60, lon = 25),
             unit.out = "hour")
day_length(lubridate::today(tzone = "Europe/Helsinki"),
           tz = "Europe/Helsinki",
           geocode = data.frame(lat = 60, lon = 25),
           unit.out = "hour")
# colour as seen by humans
color_of(sun.spct)
color_of(sun.spct * yellow_gel.spct)
# filter transmittance
transmittance(yellow_gel.spct)
transmittance(yellow_gel.spct, waveband(c(400,500)))
transmittance(yellow_gel.spct, waveband(c(500,700)))

Description

Power operator for spectra.

Usage

## S3 method for class 'generic_spct'
e1 ^ e2

Arguments

See Also

Other math operators and functions: MathFun, convolve_each(), div-.generic_spct, log(), minus-.generic_spct, mod-.generic_spct, plus-.generic_spct, round(), sign(), slash-.generic_spct, times-.generic_spct

Description

A dataset containing wavelengths at a 5 nm interval (300 nm to 830 nm) and the corresponding spectral energy irradiance normalized to 1 at 560 nm. Spectrum approximates typical, domestic, tungsten-filament lighting and 'corresponds' to a black body a 2856 K. CIE standard illuminant A is intended to represent typical, domestic, tungsten-filament lighting. Original data from CIE downloaded on 2024-11-30.

Usage

A.illuminant.spct

Format

A source spectrum with 531 rows and 2 variables.

• w.length (nm)

• s.e.irrad (rel. units)

Note

This and other CIE illuminant spectra can be downloaded from https://cie.co.at/data-tables as .CSV files.

Author(s)

CIE

References

CIE 2018, CIE standard illuminant A - 1 nm, International Commission on Illumination (CIE), Vienna, Austria, doi:10.25039/CIE.DS.8jsxjrsn.

See Also

Other Spectral data examples: D50.illuminant.spct, D65.illuminant.spct, Ler_leaf.spct, black_body.spct, ccd.spct, clear.spct, filter_cps.mspct, green_leaf.spct, phenylalanine.spct, photodiode.spct, sun.spct, sun_daily.spct, sun_evening.spct, two_filters.spct, two_sensors.mspct, water.spct, white_led.source_spct

Examples

A.illuminant.spct

Description

Function that converts absorbance (a.u.) into transmittance (fraction).

Usage

A2T(x, action, byref, ...)

## Default S3 method:
A2T(x, action = NULL, byref = FALSE, ...)

## S3 method for class 'numeric'
A2T(x, action = NULL, byref = FALSE, ...)

## S3 method for class 'filter_spct'
A2T(x, action = "add", byref = FALSE, ...)

## S3 method for class 'filter_mspct'
A2T(x, action = "add", byref = FALSE, ..., .parallel = FALSE, .paropts = NULL)

Arguments

Value

A copy of x with a column Tfr added and A and Afr possibly deleted except for w.length. If action = "replace", in all cases, the additional columns are removed, even if no column needs to be added.

Methods (by class)

• A2T(default): Default method for generic function

• A2T(numeric): method for numeric vectors

• A2T(filter_spct): Method for filter spectra

• A2T(filter_mspct): Method for collections of filter spectra

See Also

Other quantity conversion functions: Afr2T(), T2A(), T2Afr(), any2T(), as_quantum(), e2q(), e2qmol_multipliers(), e2quantum_multipliers(), q2e()

Description

Function to calculate the mean, total, or other summary of absorbance for spectral data stored in a filter_spct or in an object_spct.

Usage

absorbance(spct, w.band, quantity, wb.trim, use.hinges, ...)

## Default S3 method:
absorbance(spct, w.band, quantity, wb.trim, use.hinges, ...)

## S3 method for class 'filter_spct'
absorbance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...
)

## S3 method for class 'object_spct'
absorbance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...
)

## S3 method for class 'filter_mspct'
absorbance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'object_mspct'
absorbance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

Value

A named numeric vector in the case of methods for individual spectra, with one value for each waveband passed to parameter w.band. A data.frame in the case of collections of spectra, containing one column for each waveband object, an index column with the names of the spectra, and optionally additional columns with metadata values retrieved from the attributes of the member spectra.

By default values are only integrated, but depending on the argument passed to parameter quantity they can be re-expressed as relative fractions or percentages. In the case of vector output, names attribute is set to the name of the corresponding waveband unless a named list is supplied in which case the names of the list members are used.

Methods (by class)

• absorbance(default): Default for generic function

• absorbance(filter_spct): Specialization for filter spectra

• absorbance(object_spct): Specialization for object spectra

• absorbance(filter_mspct): Calculates absorbance from a filter_mspct

• absorbance(object_mspct): Calculates absorbance from a object_mspct

Note

The use.hinges parameter controls speed optimization. The defaults should be suitable in most cases. Only the range of wavelengths in the wavebands is used and all BSWFs are ignored.

Examples

absorbance(polyester.spct, new_waveband(400,700))
absorbance(yellow_gel.spct, new_waveband(400,700))
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3))
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "average")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "total")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative.pc")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution.pc")

Description

Function to calculate the mean, total, or other summary of absorptance for spectral data stored in a filter_spct or in an object_spct. Absorptance is a different quantity than absorbance.

Usage

absorptance(spct, w.band, quantity, wb.trim, use.hinges, ...)

## Default S3 method:
absorptance(spct, w.band, quantity, wb.trim, use.hinges, ...)

## S3 method for class 'filter_spct'
absorptance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...
)

## S3 method for class 'object_spct'
absorptance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...
)

## S3 method for class 'filter_mspct'
absorptance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx"
)

## S3 method for class 'object_mspct'
absorptance(
  spct,
  w.band = NULL,
  quantity = "average",
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = NULL,
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

Value

A named numeric vector in the case of methods for individual spectra, with one value for each waveband passed to parameter w.band. A data.frame in the case of collections of spectra, containing one column for each waveband object, an index column with the names of the spectra, and optionally additional columns with metadata values retrieved from the attributes of the member spectra.

By default values are only integrated, but depending on the argument passed to parameter quantity they can be re-expressed as relative fractions or percentages. In the case of vector output, names attribute is set to the name of the corresponding waveband unless a named list is supplied in which case the names of the list members are used.

Methods (by class)

• absorptance(default): Default for generic function

• absorptance(filter_spct): Specialization for filter spectra

• absorptance(object_spct): Specialization for object spectra

• absorptance(filter_mspct): Calculates absorptance from a filter_mspct

• absorptance(object_mspct): Calculates absorptance from a object_mspct

Note

The use.hinges parameter controls speed optimization. The defaults should be suitable in most cases. Only the range of wavelengths in the wavebands is used and all BSWFs are ignored.

Examples

absorptance(black_body.spct, new_waveband(400,500))
absorptance(white_body.spct, new_waveband(300,400))
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3))
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "average")
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "total")
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative")
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative.pc")
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution")
absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution.pc")

Description

Copy metadata attributes from members of a generic_mspct object into a data.frame or a tibble.

Usage

add_attr2tb(
  tb = NULL,
  mspct,
  col.names = NULL,
  idx = "spct.idx",
  unnest = FALSE
)

when_measured2tb(mspct, tb = NULL, col.names = "when.measured", idx = NULL)

geocode2tb(mspct, tb = NULL, col.names = "geocode", idx = "spct.idx")

lonlat2tb(mspct, tb = NULL, col.names = c("lon", "lat"), idx = "spct.idx")

lon2tb(mspct, tb = NULL, col.names = "lon", idx = "spct.idx")

lat2tb(mspct, tb = NULL, col.names = "lat", idx = "spct.idx")

address2tb(mspct, tb = NULL, col.names = "address", idx = "spct.idx")

what_measured2tb(
  mspct,
  tb = NULL,
  col.names = "what.measured",
  idx = "spct.idx"
)

how_measured2tb(mspct, tb = NULL, col.names = "how.measured", idx = "spct.idx")

normalized2tb(mspct, tb = NULL, col.names = "normalized", idx = "spct.idx")

scaled2tb(mspct, tb = NULL, col.names = "scaled", idx = "spct.idx")

instr_desc2tb(
  mspct,
  tb = NULL,
  col.names = "instr.desc",
  fields = TRUE,
  idx = "spct.idx"
)

instr_settings2tb(
  mspct,
  tb = NULL,
  col.names = "instr.settings",
  fields = TRUE,
  idx = "spct.idx"
)

BSWF_used2tb(mspct, tb = NULL, col.names = "bswf.used", idx = "spct.idx")

filter_properties2tb(
  mspct,
  tb = NULL,
  col.names = "filter.properties",
  idx = "spct.idx"
)

solute_properties2tb(
  mspct,
  tb = NULL,
  col.names = "solute.properties",
  idx = "spct.idx"
)

Tfr_type2tb(mspct, tb = NULL, col.names = "Tfr.type", idx = "spct.idx")

Rfr_type2tb(mspct, tb = NULL, col.names = "Rfr.type", idx = "spct.idx")

time_unit2tb(mspct, tb = NULL, col.names = "time.unit", idx = "spct.idx")

comment2tb(mspct, tb = NULL, col.names = "comment", idx = "spct.idx")

multiple_wl2tb(mspct, tb = NULL, col.names = "multiple.wl", idx = "spct.idx")

Arguments

Details

Each attribute is by default copied to a column in a tibble or a data.frame. If the argument for tb is NULL, as by default, a new tibble will be created. If an existing data.frame or tibble is passed as argument, new columns are added to it. However, the number of rows in the argument passed to tb must match the number of spectra in the argument passed to mspct. Only in the case of methods add_attr2tb() and spct_metadata() if the argument to col.names is a named vector, the names of members are used as names for the columns created. This permits setting any valid name for the new columns. If the members of the vector passed to col.names have no names, then the value is interpreted as the name of the attributes to add, and also used as name for the new column.

Valid values accepted as argument to col.names are NULL, or a vector containing one or more of the following character strings: "lon", "lat", "address", "geocode", "where.measured", "when.measured", "what.measured", "how.measured", "comment", "normalised", "normalized", "scaled", "bswf.used", "instr.desc", "instr.sn", solute.properties, "filter.properties", "Tfr.type", "Rfr.type", "time.unit", bswf.used, multiple.wl. Invalid character values are ignored with a warning.

Value

A data.frame or a tibble With the metadata attributes in separate new variables.

Note

The order of the first two arguments is reversed in add_attr2tb(), when_measured2tb(), what_measured2tb(), etc., compared to attribute query functions, such as spct_metadata, when_measured(), what_measured(), how_measured(), etc. This is to allow the use of add_attr2tb() and related functions in 'pipes' to add metadata to summaries computed at earlier steps in the pipe.

See Also

Other measurement metadata functions: getFilterProperties(), getHowMeasured(), getInstrDesc(), getInstrSettings(), getSensorProperties(), getSoluteProperties(), getWhatMeasured(), getWhenMeasured(), getWhereMeasured(), get_attributes(), isValidInstrDesc(), isValidInstrSettings(), select_spct_attributes(), setFilterProperties(), setHowMeasured(), setInstrDesc(), setInstrSettings(), setSensorProperties(), setSoluteProperties(), setWhatMeasured(), setWhenMeasured(), setWhereMeasured(), spct_attr2tb(), spct_metadata(), subset_attributes(), trimInstrDesc(), trimInstrSettings()

Examples

# Add attributes to irradiance
## from collection of spectra
e_irrad(sun_evening.mspct) |>
  add_attr2tb(sun_evening.mspct,
              c(when.measured = "time"))

## from spectra in long form
e_irrad(sun_evening.spct) |>
  add_attr2tb(sun_evening.spct,
              c(when.measured = "time"))

# Add attributes to transmittance
## from collection of spectra
transmittance(two_filters.mspct) |>
  add_attr2tb(two_filters.mspct, col.names = "what.measured")

transmittance(two_filters.mspct) |>
  add_attr2tb(two_filters.mspct,
              col.names = c("filter.properties", "what.measured"),
              unnest = TRUE)

# Create a new data frame
add_attr2tb(mspct = two_filters.mspct,
            idx = "filter",
            col.names = c("filter.properties", "what.measured"),
            unnest = TRUE)

Description

Function that converts transmittance (fraction) into absorptance (fraction). If reflectance (fraction) is available, it allows conversions between internal and total absorptance.

Usage

Afr2T(x, action, byref, clean, ...)

## Default S3 method:
Afr2T(x, action = NULL, byref = FALSE, clean = FALSE, ...)

## S3 method for class 'numeric'
Afr2T(x, action = NULL, byref = FALSE, clean = FALSE, Rfr = NA_real_, ...)

## S3 method for class 'filter_spct'
Afr2T(x, action = "add", byref = FALSE, clean = FALSE, ...)

## S3 method for class 'object_spct'
Afr2T(x, action = "add", byref = FALSE, clean = FALSE, ...)

## S3 method for class 'filter_mspct'
Afr2T(
  x,
  action = "add",
  byref = FALSE,
  clean = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'object_mspct'
Afr2T(
  x,
  action = "add",
  byref = FALSE,
  clean = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

Value

A copy of x with a column Tfr added and other columns possibly deleted except for w.length. If action = "replace", in all cases, the additional columns are removed, even if no column needs to be added.

Methods (by class)

• Afr2T(default): Default method for generic function

• Afr2T(numeric): Default method for generic function

• Afr2T(filter_spct): Method for filter spectra

• Afr2T(object_spct): Method for object spectra

• Afr2T(filter_mspct): Method for collections of filter spectra

• Afr2T(object_mspct): Method for collections of object spectra

See Also

Other quantity conversion functions: A2T(), T2A(), T2Afr(), any2T(), as_quantum(), e2q(), e2qmol_multipliers(), e2quantum_multipliers(), q2e()

Examples

T2Afr(Ler_leaf.spct)

Description

Functions that convert or add related physical quantities to filter_spct or object_spct objects. transmittance (fraction) into absorptance (fraction).

Usage

any2T(x, action = "add", clean = FALSE)

any2A(x, action = "add", clean = FALSE)

any2Afr(x, action = "add", clean = FALSE)

Arguments

Details

These functions are dispatchers for A2T, Afr2T, T2A, and T2Afr. The dispatch is based on the names of the variables stored in x. They do not support in-place modification of x.

Value

A copy of x with the columns for the different quantities added or replaced. If action = "replace", in all cases, the additional columns are removed, even if no column needs to be added.

See Also

Other quantity conversion functions: A2T(), Afr2T(), T2A(), T2Afr(), as_quantum(), e2q(), e2qmol_multipliers(), e2quantum_multipliers(), q2e()

Examples

any2Afr(Ler_leaf.spct)
any2T(Ler_leaf.spct)
any2T(polyester.spct)

Description

Convert a spectral photon irradiance [$mol\,s^{-1}\,m^{-2}\,nm^{-1}$] into a spectral energy irradiance [$W\,m^{-2}\,nm^{-1}$].

Usage

as_energy(w.length, s.qmol.irrad)

Arguments

Value

A numeric vector of spectral (energy) irradiances.

See Also

Other low-level functions operating on numeric vectors.: as_quantum_mol(), calc_multipliers(), div_spectra(), energy_irradiance(), energy_ratio(), insert_hinges(), integrate_xy(), interpolate_spectrum(), irradiance(), l_insert_hinges(), oper_spectra(), photon_irradiance(), photon_ratio(), photons_energy_ratio(), prod_spectra(), s_e_irrad2rgb(), split_energy_irradiance(), split_photon_irradiance(), subt_spectra(), sum_spectra(), trim_tails(), v_insert_hinges(), v_replace_hinges()

Examples

with(sun.spct, as_energy(w.length, s.q.irrad))

Description

Convert spectral energy irradiance [W m-2 nm-1] into spectral photon irradiance expressed as number of photons [s-1 m-2 nm-1]

Usage

as_quantum(w.length, s.e.irrad)

Arguments

Value

A numeric vector of spectral photon irradiances.

See Also

Other quantity conversion functions: A2T(), Afr2T(), T2A(), T2Afr(), any2T(), e2q(), e2qmol_multipliers(), e2quantum_multipliers(), q2e()

Examples

with(sun.data, as_quantum(w.length, s.e.irrad))

Description

Convert spectral energy irradiance [$W\,m^{-2}\,nm^{-1}$] into a spectral photon irradiance expressed in number of molds of photons [$mol\,s^{-1}\,m^{-2}\,nm^{-1}$].

Usage

as_quantum_mol(w.length, s.e.irrad)

Arguments

Value

a numeric vector of spectral photon irradiances.

See Also

Other low-level functions operating on numeric vectors.: as_energy(), calc_multipliers(), div_spectra(), energy_irradiance(), energy_ratio(), insert_hinges(), integrate_xy(), interpolate_spectrum(), irradiance(), l_insert_hinges(), oper_spectra(), photon_irradiance(), photon_ratio(), photons_energy_ratio(), prod_spectra(), s_e_irrad2rgb(), split_energy_irradiance(), split_photon_irradiance(), subt_spectra(), sum_spectra(), trim_tails(), v_insert_hinges(), v_replace_hinges()

Examples

with(sun.data, as_quantum_mol(w.length, s.e.irrad))

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.calibration_mspct(x, ...)

## Default S3 method:
as.calibration_mspct(x, ...)

## S3 method for class 'data.frame'
as.calibration_mspct(x, ...)

## S3 method for class 'calibration_spct'
as.calibration_mspct(x, ...)

## S3 method for class 'list'
as.calibration_mspct(x, ..., ncol = 1, byrow = FALSE)

## S3 method for class 'matrix'
as.calibration_mspct(
  x,
  w.length,
  spct.data.var = "irrad.mult",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a calibration_mspctt object.

Methods (by class)

• as.calibration_mspct(default):

• as.calibration_mspct(data.frame):

• as.calibration_mspct(calibration_spct):

• as.calibration_mspct(list):

• as.calibration_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.calibration_spct(x, ...)

## Default S3 method:
as.calibration_spct(x, ...)

Arguments

Value

A copy of x converted into a calibration_spct object.

Methods (by class)

• as.calibration_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.chroma_mspct(x, ...)

## Default S3 method:
as.chroma_mspct(x, ...)

## S3 method for class 'data.frame'
as.chroma_mspct(x, ...)

## S3 method for class 'chroma_spct'
as.chroma_mspct(x, ...)

## S3 method for class 'list'
as.chroma_mspct(x, ..., ncol = 1, byrow = FALSE)

Arguments

Value

A copy of x converted into a chroma_mspct object.

Methods (by class)

• as.chroma_mspct(default):

• as.chroma_mspct(data.frame):

• as.chroma_mspct(chroma_spct):

• as.chroma_mspct(list):

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.chroma_spct(x, ...)

## Default S3 method:
as.chroma_spct(x, ...)

Arguments

Value

A copy of x converted into a chroma_spct object.

Methods (by class)

• as.chroma_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.cps_mspct(x, ...)

## Default S3 method:
as.cps_mspct(x, ...)

## S3 method for class 'data.frame'
as.cps_mspct(x, ...)

## S3 method for class 'cps_spct'
as.cps_mspct(x, ...)

## S3 method for class 'list'
as.cps_mspct(x, ..., ncol = 1, byrow = FALSE)

## S3 method for class 'matrix'
as.cps_mspct(
  x,
  w.length,
  spct.data.var = "cps",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a cps_mspct object.

Methods (by class)

• as.cps_mspct(default):

• as.cps_mspct(data.frame):

• as.cps_mspct(cps_spct):

• as.cps_mspct(list):

• as.cps_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.cps_spct(x, ...)

## Default S3 method:
as.cps_spct(x, ...)

Arguments

Value

A copy of x converted into a cps_spct object.

Methods (by class)

• as.cps_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.filter_mspct(x, ...)

## Default S3 method:
as.filter_mspct(x, ...)

## S3 method for class 'data.frame'
as.filter_mspct(x, Tfr.type = c("total", "internal"), strict.range = TRUE, ...)

## S3 method for class 'filter_spct'
as.filter_mspct(x, ...)

## S3 method for class 'list'
as.filter_mspct(
  x,
  Tfr.type = c("total", "internal"),
  strict.range = TRUE,
  ...,
  ncol = 1,
  byrow = FALSE
)

## S3 method for class 'matrix'
as.filter_mspct(
  x,
  w.length,
  spct.data.var = "Tfr",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a filter_mspct object.

Methods (by class)

• as.filter_mspct(default):

• as.filter_mspct(data.frame):

• as.filter_mspct(filter_spct):

• as.filter_mspct(list):

• as.filter_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a possibly modified copy of an R object with its class set to a filter spectrum. In the case of conversion from a solute_spct object, compute the spectral quantity based on additional input from user.

Usage

as.filter_spct(x, ...)

## Default S3 method:
as.filter_spct(
  x,
  Tfr.type = c("total", "internal"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

## S3 method for class 'solute_spct'
as.filter_spct(
  x,
  Tfr.type = "internal",
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  Rfr.constant = NA_real_,
  comment = NULL,
  molar.concentration = NULL,
  mass.concentration = NULL,
  path.length = 1,
  ...
)

Arguments

Value

A copy of x converted into a filter_spct. object.

Methods (by class)

• as.filter_spct(default):

• as.filter_spct(solute_spct):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.generic_mspct(x, ...)

## Default S3 method:
as.generic_mspct(x, ...)

## S3 method for class 'data.frame'
as.generic_mspct(x, force.spct.class = FALSE, ...)

## S3 method for class 'generic_spct'
as.generic_mspct(x, force.spct.class = FALSE, ...)

## S3 method for class 'list'
as.generic_mspct(x, force.spct.class = FALSE, ..., ncol = 1, byrow = FALSE)

## S3 method for class 'matrix'
as.generic_mspct(
  x,
  w.length,
  member.class,
  spct.data.var,
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

mat2mspct(
  x,
  w.length,
  member.class,
  spct.data.var,
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a generic_mspct object.

Methods (by class)

• as.generic_mspct(default):

• as.generic_mspct(data.frame):

• as.generic_mspct(generic_spct):

• as.generic_mspct(list):

• as.generic_mspct(matrix):

Note

Members of generic_mspct objects can be heterogeneous: they can belong to any class derived from generic_spct and class is not enforced. When x is a list of data frames force.spct.class = TRUE needs to be supplied. When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum, or convert an R object of a different class into one of the spectral classes.

Usage

as.generic_spct(x, ...)

## Default S3 method:
as.generic_spct(x, ...)

Arguments

Details

Data frames, tibbles and similar objects are accepted as input if the column names are those expected by the matching class setting functions. An exception, is that an additional method specialization for conversion of waveband objects into response_spct objects is also defined.

Value

A copy of x converted into a generic_spct object.

Methods (by class)

• as.generic_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Convert an object of class generic_mspct or a derived class into an R matrix with wavelengths saved as an attribute and spectral data in rows or columns.

Usage

## S3 method for class 'generic_mspct'
as.matrix(x, spct.data.var, byrow = attr(x, "mspct.byrow"), ...)

mspct2mat(x, spct.data.var, byrow = attr(x, "mspct.byrow"), ...)

Arguments

Warning!

This conversion preserves the spectral data but discards almost all the metadata contained in the spectral objects. In other words a matrix created with this function cannot be used to recreate the original object unless the same metadata is explicitly supplied when converting the matrix into new collection of spectra.

Note

Only collections of spectra containing spectra with exactly the same w.length values can by converted. If needed, the spectra can be re-expressed before attempting the conversion to a matrix.

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.object_mspct(x, ...)

## Default S3 method:
as.object_mspct(x, ...)

## S3 method for class 'data.frame'
as.object_mspct(
  x,
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  strict.range = TRUE,
  ...
)

## S3 method for class 'object_spct'
as.object_mspct(x, ...)

## S3 method for class 'list'
as.object_mspct(
  x,
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  strict.range = TRUE,
  ...,
  ncol = 1,
  byrow = FALSE
)

Arguments

Value

A copy of x converted into a object_mspct object.

Methods (by class)

• as.object_mspct(default):

• as.object_mspct(data.frame):

• as.object_mspct(object_spct):

• as.object_mspct(list):

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.object_spct(x, ...)

## Default S3 method:
as.object_spct(
  x,
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

Arguments

Value

A copy of x converted into a object_spct object.

Methods (by class)

• as.object_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.raw_mspct(x, ...)

## Default S3 method:
as.raw_mspct(x, ...)

## S3 method for class 'data.frame'
as.raw_mspct(x, ...)

## S3 method for class 'raw_spct'
as.raw_mspct(x, ...)

## S3 method for class 'list'
as.raw_mspct(x, ..., ncol = 1, byrow = FALSE)

## S3 method for class 'matrix'
as.raw_mspct(
  x,
  w.length,
  spct.data.var = "counts",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a raw_mspct object.

Methods (by class)

• as.raw_mspct(default):

• as.raw_mspct(data.frame):

• as.raw_mspct(raw_spct):

• as.raw_mspct(list):

• as.raw_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.raw_spct(x, ...)

## Default S3 method:
as.raw_spct(x, ...)

Arguments

Value

A copy of x converted into a raw_spct object.

Methods (by class)

• as.raw_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.reflector_mspct(x, ...)

## Default S3 method:
as.reflector_mspct(x, ...)

## S3 method for class 'data.frame'
as.reflector_mspct(
  x,
  Rfr.type = c("total", "specular"),
  strict.range = TRUE,
  ...
)

## S3 method for class 'reflector_spct'
as.reflector_mspct(x, ...)

## S3 method for class 'list'
as.reflector_mspct(
  x,
  Rfr.type = c("total", "specular"),
  strict.range = TRUE,
  ...,
  ncol = 1,
  byrow = FALSE
)

## S3 method for class 'matrix'
as.reflector_mspct(
  x,
  w.length,
  spct.data.var = "Rfr",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a reflector_mspct object.

Methods (by class)

• as.reflector_mspct(default):

• as.reflector_mspct(data.frame):

• as.reflector_mspct(reflector_spct):

• as.reflector_mspct(list):

• as.reflector_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.response_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.reflector_spct(x, ...)

## Default S3 method:
as.reflector_spct(
  x,
  Rfr.type = c("total", "specular"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

Arguments

Value

A copy of x converted into a reflector_spct object.

Methods (by class)

• as.reflector_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.response_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.response_mspct(x, ...)

## Default S3 method:
as.response_mspct(x, ...)

## S3 method for class 'data.frame'
as.response_mspct(x, time.unit = "second", ...)

## S3 method for class 'response_spct'
as.response_mspct(x, ...)

## S3 method for class 'list'
as.response_mspct(x, time.unit = "second", ..., ncol = 1, byrow = FALSE)

## S3 method for class 'matrix'
as.response_mspct(
  x,
  w.length,
  spct.data.var = "s.e.response",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a response_mspct object.

Methods (by class)

• as.response_mspct(default):

• as.response_mspct(data.frame):

• as.response_mspct(response_spct):

• as.response_mspct(list):

• as.response_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.solute_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.response_spct(x, ...)

## Default S3 method:
as.response_spct(x, time.unit = "second", ...)

## S3 method for class 'waveband'
as.response_spct(
  x,
  time.unit = "second",
  w.length = NULL,
  fill = 0,
  unit.in = getOption("photobiology.radiation.unit", default = "energy"),
  unit.out = unit.in,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  na.rm = FALSE,
  ...
)

Arguments

Value

A copy of x converted into a response_spct object.

Methods (by class)

• as.response_spct(default):

• as.response_spct(waveband):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.solute_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.solute_mspct(x, ...)

## Default S3 method:
as.solute_mspct(x, ...)

## S3 method for class 'data.frame'
as.solute_mspct(
  x,
  K.type = c("attenuation", "absorption", "scattering"),
  strict.range = TRUE,
  ...
)

## S3 method for class 'solute_spct'
as.solute_mspct(x, ...)

## S3 method for class 'list'
as.solute_mspct(
  x,
  K.type = c("attenuation", "absorption", "scattering"),
  strict.range = TRUE,
  ...,
  ncol = 1,
  byrow = FALSE
)

## S3 method for class 'matrix'
as.solute_mspct(
  x,
  w.length,
  spct.data.var = "K.mole",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a filter_mspct object.

Methods (by class)

• as.solute_mspct(default):

• as.solute_mspct(data.frame):

• as.solute_mspct(solute_spct):

• as.solute_mspct(list):

• as.solute_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.source_mspct(), split2mspct(), subset2mspct()

Description

Return a possibly modified copy of an R object with its class set to solute_spct (a solute spectrum). In the case of conversion from a filter_spct object, compute spectral molar attenuation based on additional input from user.

Usage

as.solute_spct(x, ...)

## Default S3 method:
as.solute_spct(
  x,
  K.type = c("attenuation", "absorption", "scattering"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

## S3 method for class 'filter_spct'
as.solute_spct(
  x,
  K.type = c("attenuation", "absorption", "scattering"),
  name = NA_character_,
  mass = NA_character_,
  formula = NULL,
  structure = grDevices::as.raster(matrix()),
  ID = NA_character_,
  solvent.name = NA_character_,
  solvent.ID = NA_character_,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  comment = NULL,
  molar.concentration = NULL,
  mass.concentration = NULL,
  path.length = 1,
  ...
)

Arguments

Value

A copy of x converted into a solute_spct object.

Methods (by class)

• as.solute_spct(default):

• as.solute_spct(filter_spct):

See Also

setSoluteSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.source_spct(), source_spct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.source_mspct(x, ...)

## Default S3 method:
as.source_mspct(x, ...)

## S3 method for class 'data.frame'
as.source_mspct(
  x,
  time.unit = c("second", "day", "exposure"),
  bswf.used = c("none", "unknown"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

## S3 method for class 'source_spct'
as.source_mspct(x, ...)

## S3 method for class 'list'
as.source_mspct(
  x,
  time.unit = c("second", "day", "exposure"),
  bswf.used = c("none", "unknown"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...,
  ncol = 1,
  byrow = FALSE
)

## S3 method for class 'matrix'
as.source_mspct(
  x,
  w.length,
  spct.data.var = "s.e.irrad",
  multiplier = 1,
  byrow = NULL,
  spct.names = "spct_",
  ...
)

Arguments

Value

A copy of x converted into a source_mspct object.

Methods (by class)

• as.source_mspct(default):

• as.source_mspct(data.frame):

• as.source_mspct(source_spct):

• as.source_mspct(list):

• as.source_mspct(matrix):

Note

When x is a square matrix an explicit argument is needed for byrow to indicate how data in x should be read. In every case the length of the w.length vector must match one of the dimensions of x.

See Also

Other Coercion methods for collections of spectra: as.calibration_mspct(), as.chroma_mspct(), as.cps_mspct(), as.filter_mspct(), as.generic_mspct(), as.object_mspct(), as.raw_mspct(), as.reflector_mspct(), as.response_mspct(), as.solute_mspct(), split2mspct(), subset2mspct()

Description

Return a copy of an R object with its class set to a given type of spectrum.

Usage

as.source_spct(x, ...)

## Default S3 method:
as.source_spct(
  x,
  time.unit = c("second", "day", "exposure"),
  bswf.used = c("none", "unknown"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  ...
)

Arguments

Value

A copy of x converted into a source_spct object.

Methods (by class)

• as.source_spct(default):

See Also

setGenericSpct

Other constructors of spectral objects: as.calibration_spct(), as.chroma_spct(), as.cps_spct(), as.filter_spct(), as.generic_spct(), as.object_spct(), as.raw_spct(), as.reflector_spct(), as.response_spct(), as.solute_spct(), source_spct()

Description

This function gives the result of integrating spectral data over wavelengths and dividing the result by the spread or span of the wavelengths.

Usage

average_spct(spct)

Arguments

Value

One or more numeric values with no change in scale factor: e.g. [W m-2 nm-1] -> [W m-2 nm-1]. Each value in the returned vector corresponds to a variable in the spectral object, except for wavelength.

Examples

average_spct(sun.spct)

Description

A dataset containing wavelengths at a 5 nm interval (300 nm to 700 nm) and the corresponding x, y, and z chromaticity coordinates. Original data from XXX.

A chroma_spct object with variables as follows:

Usage

beesxyzCMF.spct

Format

A data frame with 81 rows and 4 variables

Details

• w.length (nm)

• x

• y

• z

See Also

Other Visual response data examples: ciev10.spct, ciev2.spct, ciexyzCC10.spct, ciexyzCC2.spct, ciexyzCMF10.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Description

Datasets for a hypothetical objects with transmittance 0/1 (0%), reflectance 0/1 (0%), with transmittance 0/1 (0%), reflectance 1/1 (100%), and with with transmittance 1/1 (100%), reflectance 0/1 (0%).

Format

A object_spct object with 4 rows and 3 variables

Details

• w.length (nm)

• Tfr (0..1)

• Rfr (0..1)

See Also

Other Spectral data examples: A.illuminant.spct, D50.illuminant.spct, D65.illuminant.spct, Ler_leaf.spct, ccd.spct, clear.spct, filter_cps.mspct, green_leaf.spct, phenylalanine.spct, photodiode.spct, sun.spct, sun_daily.spct, sun_evening.spct, two_filters.spct, two_sensors.mspct, water.spct, white_led.source_spct

Description

Combine two or more generic_mspct objects into a single object.

Usage

## S3 method for class 'generic_mspct'
c(..., recursive = FALSE, ncol = 1, byrow = FALSE)

Arguments

Value

A collection of spectra object belonging to the most derived class shared among the combined objects.

Description

Calculate multipliers for selecting a range of wavelengths and optionally applying a biological spectral weighting function (BSWF) and wavelength normalization. This function returns numeric multipliers that can be used to select a waveband and apply a weight.

Usage

calc_multipliers(
  w.length,
  w.band,
  unit.out = "energy",
  unit.in = "energy",
  use.cached.mult = FALSE,
  fill = 0
)

Arguments

Value

a numeric vector of multipliers of the same length as w.length.

See Also

Other low-level functions operating on numeric vectors.: as_energy(), as_quantum_mol(), div_spectra(), energy_irradiance(), energy_ratio(), insert_hinges(), integrate_xy(), interpolate_spectrum(), irradiance(), l_insert_hinges(), oper_spectra(), photon_irradiance(), photon_ratio(), photons_energy_ratio(), prod_spectra(), s_e_irrad2rgb(), split_energy_irradiance(), split_photon_irradiance(), subt_spectra(), sum_spectra(), trim_tails(), v_insert_hinges(), v_replace_hinges()

Examples

with(sun.data,
     calc_multipliers(w.length = w.length,
                      w.band = new_waveband(400,700),
                      unit.out = "photon"))
with(sun.data,
     calc_multipliers(w.length = w.length,
                      w.band = new_waveband(400,700),
                      unit.out = "photon"),
                      use.cached.mult = TRUE)

Description

Values calculated by interpolation from user-supplied spectral emission data or by name for light source data included in the packages photobiologySun, photobiologyLamps, or photobiologyLEDs, optionally re-scaling the spectral data values.

Usage

calc_source_output(
  w.length.out,
  w.length.in,
  s.irrad.in,
  unit.in = "energy",
  scaled = NULL,
  fill = NA,
  ...
)

Arguments

Value

a source_spct with three numeric vectors with wavelength values (w.length), scaled and interpolated spectral energy irradiance (s.e.irrad), scaled and interpolated spectral photon irradiance values (s.q.irrad).

Note

This is a convenience function that adds no new functionality but makes it a little easier to plot lamp spectral emission data consistently. It automates interpolation, extrapolation/trimming and scaling.

Examples

with(sun.data,
     calc_source_output(290:1100,
                        w.length.in = w.length,
                        s.irrad.in = s.e.irrad)
    )

Description

A dataset containing wavelengths at a 1 nm interval and spectral response as quantum efficiency for CCD sensor type S11071/S10420 from Hamamatsu (measured without a quartz window). These vectors are frequently used as sensors in high-UV-sensitivity vector spectrometers. Data digitized from manufacturer's data sheet. The original data is expressed as percent quantum efficiency with a value of 77% at the peak. The data have been re-expressed as fractions of one.

Usage

ccd.spct

Format

A response_spct object with 186 rows and 2 variables

Details

• w.length (nm).

• s.q.response (fractional quantum efficiency)

References

Hamamatsu (2014) Datasheet: CCD Image Sensors S11071/S10420-01 Series. Hamamatsu Photonics KK, Hamamatsu, City. http://www.hamamatsu.com/jp/en/S11071-1004.html. Visited 2017-12-15.

See Also

Other Spectral data examples: A.illuminant.spct, D50.illuminant.spct, D65.illuminant.spct, Ler_leaf.spct, black_body.spct, clear.spct, filter_cps.mspct, green_leaf.spct, phenylalanine.spct, photodiode.spct, sun.spct, sun_daily.spct, sun_evening.spct, two_filters.spct, two_sensors.mspct, water.spct, white_led.source_spct

Examples

ccd.spct

Description

Check that an R object contains the expected data members and within range values in them. For wavelengths also check if ordered and if unique or not.

Usage

check_spct(x, byref, strict.range, force = FALSE, ...)

## Default S3 method:
check_spct(x, byref = FALSE, strict.range = NA, force = FALSE, ...)

## S3 method for class 'generic_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = NA,
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'calibration_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'raw_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'cps_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'filter_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'solute_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'reflector_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'object_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'response_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = NA,
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'source_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

## S3 method for class 'chroma_spct'
check_spct(
  x,
  byref = TRUE,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  force = FALSE,
  multiple.wl = getMultipleWl(x),
  ...
)

Arguments

Details

These methods are exported and can be called by user code if needed, for example, when the checks have been disabled by setting an R option with disable_check_spct.

Methods (by class)

• check_spct(default): Default for generic function.

• check_spct(generic_spct): Specialization for generic_spct.

• check_spct(calibration_spct): Specialization for calibration_spct.

• check_spct(raw_spct): Specialization for raw_spct.

• check_spct(cps_spct): Specialization for cps_spct.

• check_spct(filter_spct): Specialization for filter_spct.

• check_spct(solute_spct): Specialization for solute_spct.

• check_spct(reflector_spct): Specialization for reflector_spct.

• check_spct(object_spct): Specialization for object_spct.

• check_spct(response_spct): Specialization for response_spct.

• check_spct(source_spct): Specialization for source_spct.

• check_spct(chroma_spct): Specialization for chroma_spct.

See Also

Other data validity check functions: check_spectrum(), check_w.length(), enable_check_spct()

Examples

check_spct(sun.spct)

check_spct(sun.spct)
# try(check_spct(-sun.spct))
# try(check_spct((sun.spct[1, "w.length"] <- 1000)))

Description

Checks spectral irradiance data in numeric vectors for compliance with assumptions used in calculations.

Usage

check_spectrum(w.length, s.irrad)

Arguments

Value

A single logical value indicating whether test was passed or not

See Also

Other data validity check functions: check_spct(), check_w.length(), enable_check_spct()

Examples

with(sun.data, check_spectrum(w.length, s.e.irrad))

Description

This function checks a w.length vector for compliance with assumptions expected for valid calculations.

Usage

check_w.length(w.length)

Arguments

Value

a single logical value indicating whether test was passed or not

See Also

Other data validity check functions: check_spct(), check_spectrum(), enable_check_spct()

Examples

with(sun.data, photobiology:::check_w.length(w.length))

Description

Check the spread of wavelength step sizes in an ordered numeric vector, or in the "w.length" column of a spectral object containing a single spectrum.

Usage

check_wl_stepsize(x, span = Inf, na.rm = FALSE, min.stepsize = 1)

Arguments

Details

As the search for peaks uses a window based on a fixed number of observations at neighbouring wavelengths, if the wavelength step between observations varies drastically, the window expressed in nanometres of wavelength becomes very irregular. With the default span = 5 in peaks(), valleys(), and wls_at_target() the search in most cases still works for "thinned" spectra, and the check is skipped. With spikes() and despike() methods the check is always done as these methods do not override span = Inf.

The typical case when the step can vary strongly are spectra returned by thin_wl(). As when using default arguments, including span = 21, thin_wl() retains the original local maxima and global maximum, and a reasonably narrow wavelength maximum step a call to peaks with span = NULL or span = 5 tends to discover the original peaks missing at most a few.

Value

A logical TRUE is returned invisibly if check is passed and otherwise FALSE with a warning. A warning is issued on failure as a side effect.

Examples

check_wl_stepsize(sun.spct)
check_wl_stepsize(c(1:20, 25), span = 30)
check_wl_stepsize(1:20, span = 30, min.stepsize = 4)

Description

Function to read the "time.unit" attribute

Usage

checkTimeUnit(x)

Arguments

Value

x possibly with the time.unit attribute modified

Note

if x is not a source_spct or a response_spct object, NA is returned

See Also

Other time attribute functions: convertThickness(), convertTimeUnit(), getTimeUnit(), setTimeUnit()

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding response values for a 10 degrees target. Original data from http://www.cvrl.org/ downloaded on 2014-04-29 The variables are as follows:

• w.length (nm)

• s.e.response

Usage

ciev10.spct

Format

A chroma_spct object with 441 rows and 4 variables

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev2.spct, ciexyzCC10.spct, ciexyzCC2.spct, ciexyzCMF10.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Examples

ciev10.spct

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding response values for a 2 degrees target. Original data from http://www.cvrl.org/ downloaded on 2014-04-29 The variables are as follows:

Usage

ciev2.spct

Format

A chroma_spct object with 441 rows and 4 variables

Details

• w.length (nm)

• s.e.response

Note

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev10.spct, ciexyzCC10.spct, ciexyzCC2.spct, ciexyzCMF10.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Examples

ciev2.spct

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding x, y, and z chromaticity coordinates. Derived from proposed CIE 2006 standard. Original data from http://www.cvrl.org/ downloaded on 2014-04-29 The variables are as follows:

• w.length (nm)

• x

• y

• z

Usage

ciexyzCC10.spct

Format

A chroma_spct object with 441 rows and 4 variables

Note

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev10.spct, ciev2.spct, ciexyzCC2.spct, ciexyzCMF10.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Examples

ciexyzCC10.spct

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding x, y, and z chromaticity coordinates. According to proposed CIE 2006 standard. Original data from http://www.cvrl.org/ downloaded on 2014-04-28 The variables are as follows:

• w.length (nm)

• x

• y

• z

Usage

ciexyzCC2.spct

Format

A chroma_spct object with 441 rows and 4 variables

Note

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev10.spct, ciev2.spct, ciexyzCC10.spct, ciexyzCMF10.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Examples

ciexyzCC2.spct

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding x, y, and z 10 degrees CMF values. Derived from proposed CIE 2006 standard. Original data from http://www.cvrl.org/ downloaded on 2014-04-29 The variables are as follows:

• w.length (nm)

• x

• y

• z

Usage

ciexyzCMF10.spct

Format

A chroma_spct object with 441 rows and 4 variables

Note

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev10.spct, ciev2.spct, ciexyzCC10.spct, ciexyzCC2.spct, ciexyzCMF2.spct, cone_fundamentals10.spct

Examples

ciexyzCMF10.spct

Description

A dataset containing wavelengths at a 1 nm interval (390 nm to 830 nm) and the corresponding x, y, and z 2 degrees CMF values. Derived from proposed CIE 2006 standard. Original data from http://www.cvrl.org/ downloaded on 2014-04-29 The variables are as follows:

• w.length (nm)

• x

• y

• z

Usage

ciexyzCMF2.spct

Format

A chroma_spct object with 441 rows and 4 variables

Note

These data are not from the official CIE on-line distribution but are retained for backwards compatibility. It is recommended to download the latest version from https://cie.co.at/data-tables.

Author(s)

CIE

See Also

Other Visual response data examples: beesxyzCMF.spct, ciev10.spct, ciev2.spct, ciexyzCC10.spct, ciexyzCC2.spct, ciexyzCMF10.spct, cone_fundamentals10.spct

Examples

ciexyzCMF2.spct

Description

Extract class information from a generic spectrum.

Usage

class_spct(x)

Arguments

Details

The value returned is equivalent to the set intersection of the value returned by class(x) and the value returned by spct_classes, but preserving the order of the members of the character vector.

Value

A character vector containing all matching xxxx.spct S3 classes.

Examples

class_spct(sun.spct)
class(sun.spct)

Description

These functions implement the equivalent of replace() but for spectral objects instead of vectors.

Usage

clean(x, range, range.s.data, fill, ...)

## Default S3 method:
clean(x, range, range.s.data, fill, ...)

## S3 method for class 'source_spct'
clean(
  x,
  range = x,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'filter_spct'
clean(
  x,
  range = x,
  range.s.data = NULL,
  fill = range.s.data,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)

## S3 method for class 'reflector_spct'
clean(x, range = x, range.s.data = c(0, 1), fill = range.s.data, ...)

## S3 method for class 'solute_spct'
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)

## S3 method for class 'object_spct'
clean(
  x,
  range = x,
  range.s.data = c(0, 1),
  fill = range.s.data,
  min.Afr = NULL,
  ...
)

## S3 method for class 'response_spct'
clean(
  x,
  range = x,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'cps_spct'
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)

## S3 method for class 'raw_spct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  ...
)

## S3 method for class 'generic_spct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...
)

## S3 method for class 'source_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'filter_mspct'
clean(
  x,
  range = NULL,
  range.s.data = NULL,
  fill = range.s.data,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'reflector_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, 1),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'object_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, 1),
  fill = range.s.data,
  min.Afr = NULL,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'solute_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'response_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'cps_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'raw_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'generic_mspct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)