Nothing
# Tfr_ratio() -------------------------------------------------------------
#' transmittance:transmittance ratio
#'
#' This function returns the transmittance ratio for a given pair of wavebands of a
#' filter spectrum.
#'
#' @param spct an object of class "filter_spct".
#' @param w.band.num waveband object or a list of waveband objects used to
#' compute the numerator(s) and denominator(s) of the ratio(s).
#' @param w.band.denom waveband object or a list of waveband objects used to
#' compute the denominator(s) of the ratio(s).
#' @param scale.factor numeric vector of length 1, or length equal to that of
#' \code{w.band}. Numeric multiplier applied to returned values.
#' @param wb.trim logical if TRUE wavebands crossing spectral data boundaries
#' are trimmed, if FALSE, they are discarded
#' @param use.cached.mult logical indicating whether multiplier values should be
#' cached between calls
#' @param use.hinges logical Flag indicating whether to insert "hinges" into the
#' spectral data before integration so as to reduce interpolation errors at
#' the boundaries of the wavebands.
#' @param quantity character One of "total", "average" or "mean".
#' @param naming character one of "long", "default", "short" or "none". Used to
#' select the type of names to assign to returned value.
#' @param name.tag character Used to tag the name of the returned values.
#' @param ... other arguments (possibly ignored)
#'
#' @details With the default \code{quantity = "mean"} or \code{quantity =
#' "average"} the ratio is based on two \strong{mean spectral transmittance},
#' one computed for each waveband.
#'
#' \deqn{\frac{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{num})}{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{denom}))}}
#'
#' If the argument is set to \code{quantity = "total"} the ratio is based on
#' two \strong{integrated transmittance}, one computed for each waveband.
#'
#' \deqn{\frac{\mathrm{Tfr}(s, wb_\mathrm{num})}{\mathrm{Tfr}(s, wb_\mathrm{denom})}}
#'
#' Only if the wavelength expanse of the two wavebands is the same, these two
#' ratios are numerically identical.
#'
#' @return In the case of methods for individual spectra, a \code{numeric}
#' vector with name attribute set. The name is based on the name of the
#' wavebands unless a named list of wavebands is supplied in which case the
#' names of the list elements are used. "[Tfr:Tfr]" is appended if \code{quantity
#' = "total"} and "[Tfr(wl):Tfr(wl)]" if \code{quantity = "mean"} or
#' \code{quantity = "average"}.
#'
#' A \code{data.frame} is returned in the case of collections of spectra,
#' containing one column for each fraction definition, an index column with
#' the names of the spectra, and optionally additional columns with metadata
#' values retrieved from the attributes of the member spectra.
#'
#' Fraction definitions are "assembled" from the arguments passed to
#' \code{w.band.num} and \code{w.band.denom}. If both arguments are lists of
#' waveband definitions, with an equal number of members, then the wavebands
#' are paired to obtain as many fractions as the number of wavebands in each
#' list. Recycling for wavebands takes place when the number of denominator
#' and numerator wavebands differ.
#'
#' @export
#' @examples
#' Tfr_ratio(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"))
#' Tfr_ratio(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "total")
#' Tfr_ratio(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "mean")
#'
#' @note The last two parameters control speed
#' optimizations. The defaults should be suitable in most cases. If you will
#' use repeatedly the same SWFs on many spectra measured at exactly the same
#' wavelengths you may obtain some speed up by setting
#' \code{use.cached.mult=TRUE}. However, be aware that you are responsible for
#' ensuring that the wavelengths are the same in each call, as the only test
#' done is for the length of the \code{w.length} vector.
#'
#' @family transmittance ratio functions
#'
Tfr_ratio <- function(spct,
w.band.num,
w.band.denom,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) UseMethod("Tfr_ratio")
#' @describeIn Tfr_ratio Default for generic function
#'
#' @export
#'
Tfr_ratio.default <- function(spct,
w.band.num,
w.band.denom,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) {
warning("'Tfr_ratio' is not defined for objects of class ", class(spct)[1])
return(NA)
}
#' @describeIn Tfr_ratio Method for \code{filter_spct} objects
#'
#' @export
#'
Tfr_ratio.filter_spct <-
function(spct,
w.band.num = NULL,
w.band.denom = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
... ) {
# we look for multiple spectra in long form
if (getMultipleWl(spct) > 1) {
# convert to a collection of spectra
mspct <- subset2mspct(x = spct,
idx.var = getIdFactor(spct),
drop.idx = FALSE)
# call method on the collection
return(Tfr_ratio(spct = mspct,
w.band.num = w.band.num,
w.band.denom = w.band.denom,
scale.factor = scale.factor,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
... ))
}
if (is.null(name.tag) && naming != "none") {
if (quantity == "total") {
name.tag <- "[Tfr:Tfr]"
} else {
name.tag <- "[Tfr(wl):Tfr(wl)]"
}
}
transmittances <-
two_transmittances(spct = spct,
w.band.1 = w.band.num,
w.band.2 = w.band.denom,
quantity = quantity,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
naming = naming)
Tfr.num <- transmittances[["Tfr.1"]]
Tfr.denom <- transmittances[["Tfr.2"]]
ratio <- Tfr.num / Tfr.denom * scale.factor
names(ratio) <-
paste(names(Tfr.num), ":", names(Tfr.denom), name.tag, sep = "")
attr(ratio, "Tfr.type") <- getTfrType(spct)
if (quantity == "total") {
attr(ratio, "radiation.unit") <- "Tfr:Tfr ratio"
} else {
attr(ratio, "radiation.unit") <- "Tfr(wl):Tfr(wl) ratio"
}
return(ratio)
}
#' @describeIn Tfr_ratio Calculates Tfr:Tfr from a \code{filter_mspct}
#' object.
#'
#' @param attr2tb character vector, see \code{\link{add_attr2tb}} for the syntax
#' for \code{attr2tb} passed as is to formal parameter \code{col.names}.
#' @param idx character Name of the column with the names of the members of the
#' collection of spectra.
#' @param .parallel if TRUE, apply function in parallel, using parallel backend
#' provided by foreach
#' @param .paropts a list of additional options passed into the foreach function
#' when parallel computation is enabled. This is important if (for example)
#' your code relies on external data or packages: use the .export and
#' .packages arguments to supply them so that all cluster nodes have the
#' correct environment set up for computing.
#'
#' @export
#'
Tfr_ratio.filter_mspct <-
function(spct,
w.band.num = NULL,
w.band.denom = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
...,
attr2tb = NULL,
idx = "spct.idx",
.parallel = FALSE,
.paropts = NULL) {
if (naming == "none") {
# need names for columns
naming <- "short"
}
spct <- subset2mspct(spct) # expand long form spectra within collection
z <-
msdply(
mspct = spct,
.fun = Tfr_ratio,
w.band.num = w.band.num,
w.band.denom = w.band.denom,
wb.trim = wb.trim,
scale.factor = scale.factor,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
idx = idx,
.parallel = .parallel,
.paropts = .paropts
)
add_attr2tb(tb = z,
mspct = spct,
col.names = attr2tb,
idx = idx)
}
# Tfr_fraction() ----------------------------------------------------------
#' transmittance:transmittance fraction
#'
#' This function returns the transmittance fraction for a given pair of wavebands of a
#' filter spectrum.
#'
#' @param spct an object of class "filter_spct".
#' @param w.band.num waveband object or a list of waveband objects used to
#' compute the numerator(s) and denominator(s) of the fraction(s).
#' @param w.band.denom waveband object or a list of waveband objects used to
#' compute the denominator(s) of the fraction(s).
#' @param scale.factor numeric vector of length 1, or length equal to that of
#' \code{w.band}. Numeric multiplier applied to returned values.
#' @param wb.trim logical if TRUE wavebands crossing spectral data boundaries
#' are trimmed, if FALSE, they are discarded
#' @param use.cached.mult logical indicating whether multiplier values should be
#' cached between calls
#' @param use.hinges logical Flag indicating whether to insert "hinges" into the
#' spectral data before integration so as to reduce interpolation errors at
#' the boundaries of the wavebands.
#' @param quantity character One of "total", "average" or "mean".
#' @param naming character one of "long", "default", "short" or "none". Used to
#' select the type of names to assign to returned value.
#' @param name.tag character Used to tag the name of the returned values.
#' @param ... other arguments (possibly ignored)
#'
#' @details With the default \code{quantity = "mean"} or \code{quantity =
#' "average"} the ratio is based on two \strong{mean spectral transmittance},
#' one computed for each waveband.
#'
#' \deqn{\frac{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{num})}{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{denom}) + \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{num})}}
#'
#' If the argument is set to \code{quantity = "total"} the fraction is based on
#' two \strong{integrated transmittance}, one computed for each waveband.
#'
#' \deqn{\frac{\mathrm{Tfr}(s, wb_\mathrm{num})}{\mathrm{Tfr}(s, wb_\mathrm{denom}) + \mathrm{Tfr}(s, wb_\mathrm{num})}}
#'
#' Only if the wavelength expanse of the two wavebands is the same, these two
#' ratios are numerically identical.
#'
#' @return In the case of methods for individual spectra, a \code{numeric}
#' vector with name attribute set. The name is based on the name of the
#' wavebands unless a named list of wavebands is supplied in which case the
#' names of the list elements are used. "[Tfr:Tfr]" is appended if \code{quantity
#' = "total"} and "[Tfr(wl):Tfr(wl)]" if \code{quantity = "mean"} or
#' \code{quantity = "average"}.
#'
#' A \code{data.frame} is returned in the case of collections of spectra,
#' containing one column for each fraction definition, an index column with
#' the names of the spectra, and optionally additional columns with metadata
#' values retrieved from the attributes of the member spectra.
#'
#' Fraction definitions are "assembled" from the arguments passed to
#' \code{w.band.num} and \code{w.band.denom}. If both arguments are lists of
#' waveband definitions, with an equal number of members, then the wavebands
#' are paired to obtain as many fractions as the number of wavebands in each
#' list. Recycling for wavebands takes place when the number of denominator
#' and numerator wavebands differ.
#'
#' @export
#' @examples
#' Tfr_fraction(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"))
#' Tfr_fraction(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "total")
#' Tfr_fraction(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "mean")
#'
#' @note The last two parameters control speed
#' optimizations. The defaults should be suitable in most cases. If you will
#' use repeatedly the same SWFs on many spectra measured at exactly the same
#' wavelengths you may obtain some speed up by setting
#' \code{use.cached.mult=TRUE}. However, be aware that you are responsible for
#' ensuring that the wavelengths are the same in each call, as the only test
#' done is for the length of the \code{w.length} vector.
#'
#' @family transmittance ratio functions
#'
Tfr_fraction <- function(spct,
w.band.num,
w.band.denom,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) UseMethod("Tfr_fraction")
#' @describeIn Tfr_fraction Default for generic function
#'
#' @export
#'
Tfr_fraction.default <- function(spct,
w.band.num,
w.band.denom,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) {
warning("'Tfr_fraction' is not defined for objects of class ", class(spct)[1])
return(NA)
}
#' @describeIn Tfr_fraction Method for \code{filter_spct} objects
#'
#' @export
#'
Tfr_fraction.filter_spct <-
function(spct,
w.band.num = NULL,
w.band.denom = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
... ) {
# we look for multiple spectra in long form
if (getMultipleWl(spct) > 1) {
# convert to a collection of spectra
mspct <- subset2mspct(x = spct,
idx.var = getIdFactor(spct),
drop.idx = FALSE)
# call method on the collection
return(Tfr_fraction(spct = mspct,
w.band.num = w.band.num,
w.band.denom = w.band.denom,
scale.factor = scale.factor,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
... ))
}
if (is.null(name.tag) && naming != "none") {
if (quantity == "total") {
name.tag <- "[Tfr:Tfr]"
} else {
name.tag <- "[Tfr(wl):Tfr(wl)]"
}
}
transmittances <-
two_transmittances(spct = spct,
w.band.1 = w.band.num,
w.band.2 = w.band.denom,
quantity = quantity,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
naming = naming)
Tfr.num <- transmittances[["Tfr.1"]]
Tfr.denom <- transmittances[["Tfr.2"]]
fraction <- Tfr.num / (Tfr.denom + Tfr.num) * scale.factor
names(fraction) <- paste(names(Tfr.num), ":(",
names(Tfr.num), "+", names(Tfr.denom), ")",
name.tag, sep = "")
attr(fraction, "Tfr.type") <- getTfrType(spct)
if (quantity == "total") {
attr(fraction, "radiation.unit") <- "Tfr:Tfr fraction"
} else {
attr(fraction, "radiation.unit") <- "Tfr(wl):Tfr(wl) fraction"
}
return(fraction)
}
#' @describeIn Tfr_fraction Calculates Tfr:Tfr from a \code{filter_mspct}
#' object.
#'
#' @param attr2tb character vector, see \code{\link{add_attr2tb}} for the syntax
#' for \code{attr2tb} passed as is to formal parameter \code{col.names}.
#' @param idx character Name of the column with the names of the members of the
#' collection of spectra.
#' @param .parallel if TRUE, apply function in parallel, using parallel backend
#' provided by foreach
#' @param .paropts a list of additional options passed into the foreach function
#' when parallel computation is enabled. This is important if (for example)
#' your code relies on external data or packages: use the .export and
#' .packages arguments to supply them so that all cluster nodes have the
#' correct environment set up for computing.
#'
#' @export
#'
Tfr_fraction.filter_mspct <-
function(spct,
w.band.num = NULL,
w.band.denom = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
...,
attr2tb = NULL,
idx = "spct.idx",
.parallel = FALSE,
.paropts = NULL) {
if (naming == "none") {
# need names for columns
naming <- "short"
}
spct <- subset2mspct(spct) # expand long form spectra within collection
z <-
msdply(
mspct = spct,
.fun = Tfr_fraction,
w.band.num = w.band.num,
w.band.denom = w.band.denom,
wb.trim = wb.trim,
scale.factor = scale.factor,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
idx = idx,
.parallel = .parallel,
.paropts = .paropts
)
add_attr2tb(tb = z,
mspct = spct,
col.names = attr2tb,
idx = idx)
}
# Tfr_normdiff() ----------------------------------------------------------
#' transmittance:transmittance normalised difference
#'
#' This function returns the transmittance normalized difference index for a given
#' pair of wavebands of a filter spectrum.
#'
#' @param spct an object of class "filter_spct".
#' @param w.band.plus,w.band.minus waveband object(s) or a list(s) of waveband
#' objects used to compute the additive and subtractive transmittance terms of
#' the normalized difference index.
#' @param scale.factor numeric vector of length 1, or length equal to that of
#' \code{w.band}. Numeric multiplier applied to returned values.
#' @param wb.trim logical if TRUE wavebands crossing spectral data boundaries
#' are trimmed, if FALSE, they are discarded
#' @param use.cached.mult logical indicating whether multiplier values should be
#' cached between calls
#' @param use.hinges logical Flag indicating whether to insert "hinges" into the
#' spectral data before integration so as to reduce interpolation errors at
#' the boundaries of the wavebands.
#' @param quantity character One of "total", "average" or "mean".
#' @param naming character one of "long", "default", "short" or "none". Used to
#' select the type of names to assign to returned value.
#' @param name.tag character Used to tag the name of the returned values.
#' @param ... other arguments (possibly ignored)
#'
#' @details With the default \code{quantity = "mean"} or
#' \code{quantity = "average"} the ratio is based on
#' two \strong{mean spectral photon transmittances}, one computed for each waveband.
#'
#' \deqn{\frac{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{plus}) - \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{minus})}{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{plus}) + \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{minus})}}
#'
#' If the argument is set to \code{quantity = "total"} the fraction is based on
#' two \strong{photon transmittances}, one computed for each waveband.
#'
#' \deqn{\frac{\mathrm{Tfr}(s, wb_\mathrm{plus}) - \mathrm{Tfr}(s, wb_\mathrm{minus})}{\mathrm{Tfr}(s, wb_\mathrm{plus}) + \mathrm{Tfr}(s, wb_\mathrm{minus})}}
#'
#' Only if the wavelength expanse of the two wavebands is the same, these two
#' ratios are numerically identical.
#'
#' @return In the case of methods for individual spectra, a \code{numeric}
#' vector with name attribute set. The name is based on the name of the
#' wavebands unless a named list of wavebands is supplied in which case the
#' names of the list elements are used. "[Tfr:Tfr]" is appended if \code{quantity
#' = "total"} and "[Tfr(wl):Tfr(wl)]" if \code{quantity = "mean"} or
#' \code{quantity = "average"}.
#'
#' A \code{data.frame} is returned in the case of collections of spectra,
#' containing one column for each fraction definition, an index column with
#' the names of the spectra, and optionally additional columns with metadata
#' values retrieved from the attributes of the member spectra.
#'
#' Fraction definitions are "assembled" from the arguments passed to
#' \code{w.band.num} and \code{w.band.denom}. If both arguments are lists of
#' waveband definitions, with an equal number of members, then the wavebands
#' are paired to obtain as many fractions as the number of wavebands in each
#' list. Recycling for wavebands takes place when the number of denominator
#' and numerator wavebands differ.
#'
#' @export
#' @examples
#' Tfr_normdiff(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"))
#' Tfr_normdiff(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "total")
#' Tfr_normdiff(Ler_leaf_rflt.spct,
#' waveband(c(400,500), wb.name = "Blue"),
#' waveband(c(600,700), wb.name = "Red"),
#' quantity = "mean")
#'
#' @note The last two parameters control speed optimizations. The defaults
#' should be suitable in most cases. If you will use repeatedly the same SWFs
#' on many spectra measured at exactly the same wavelengths you may obtain
#' some speed up by setting \code{use.cached.mult =T RUE}. However, be aware
#' that you are responsible for ensuring that the wavelengths are the same in
#' each call, as the only test done is for the length of the \code{w.length}
#' vector.
#'
#' @family transmittance ratio functions
#' @seealso \code{\link{normalized_diff_ind}}, accepts different summary
#' functions.
#'
Tfr_normdiff <- function(spct,
w.band.plus,
w.band.minus,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) UseMethod("Tfr_normdiff")
#' @describeIn Tfr_normdiff Default for generic function
#'
#' @export
#'
Tfr_normdiff.default <- function(spct,
w.band.plus,
w.band.minus,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...) {
warning("'Tfr_fraction' is not defined for objects of class ", class(spct)[1])
return(NA)
}
#' @describeIn Tfr_normdiff Method for \code{filter_spct} objects
#'
#' @export
#'
Tfr_normdiff.filter_spct <-
function(spct,
w.band.plus = NULL,
w.band.minus = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
... ) {
# we look for multiple spectra in long form
if (getMultipleWl(spct) > 1) {
# convert to a collection of spectra
mspct <- subset2mspct(x = spct,
idx.var = getIdFactor(spct),
drop.idx = FALSE)
# call method on the collection
return(Tfr_normdiff(spct = mspct,
w.band.plus = w.band.plus,
w.band.minus = w.band.minus,
scale.factor = scale.factor,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
... ))
}
if (is.null(name.tag) && naming != "none") {
if (quantity == "total") {
name.tag <- "[Tfr:Tfr]"
} else {
name.tag <- "[Tfr(wl):Tfr(wl)]"
}
}
transmittances <-
two_transmittances(spct = spct,
w.band.1 = w.band.plus,
w.band.2 = w.band.minus,
quantity = quantity,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
naming = naming)
Tfr.plus <- transmittances[["Tfr.1"]]
Tfr.minus <- transmittances[["Tfr.2"]]
Tfr.normdiff <- (Tfr.plus - Tfr.minus) / (Tfr.plus + Tfr.minus) * scale.factor
names(Tfr.normdiff) <- paste("(",
names(Tfr.plus), "-", names(Tfr.minus),
"):(",
names(Tfr.plus), "+", names(Tfr.minus), ")",
name.tag, sep = "")
attr(Tfr.normdiff, "Tfr.type") <- getTfrType(spct)
if (quantity == "total") {
attr(Tfr.normdiff, "radiation.unit") <- "Tfr:Tfr normdiff"
} else {
attr(Tfr.normdiff, "radiation.unit") <- "Tfr(wl):Tfr(wl) normdiff"
}
return(Tfr.normdiff)
}
#' @describeIn Tfr_normdiff Calculates Tfr:Tfr from a \code{filter_mspct}
#' object.
#'
#' @param attr2tb character vector, see \code{\link{add_attr2tb}} for the syntax
#' for \code{attr2tb} passed as is to formal parameter \code{col.names}.
#' @param idx character Name of the column with the names of the members of the
#' collection of spectra.
#' @param .parallel if TRUE, apply function in parallel, using parallel backend
#' provided by foreach
#' @param .paropts a list of additional options passed into the foreach function
#' when parallel computation is enabled. This is important if (for example)
#' your code relies on external data or packages: use the .export and
#' .packages arguments to supply them so that all cluster nodes have the
#' correct environment set up for computing.
#'
#' @export
#'
Tfr_normdiff.filter_mspct <-
function(spct,
w.band.plus = NULL,
w.band.minus = NULL,
scale.factor = 1,
wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
use.cached.mult = FALSE,
use.hinges = NULL,
quantity = "mean",
naming = "short",
name.tag = NULL,
...,
attr2tb = NULL,
idx = "spct.idx",
.parallel = FALSE,
.paropts = NULL) {
if (naming == "none") {
# need names for columns
naming <- "short"
}
spct <- subset2mspct(spct) # expand long form spectra within collection
z <-
msdply(
mspct = spct,
.fun = Tfr_normdiff,
w.band.plus = w.band.plus,
w.band.minus = w.band.minus,
wb.trim = wb.trim,
scale.factor = scale.factor,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
quantity = quantity,
naming = naming,
name.tag = name.tag,
idx = idx,
.parallel = .parallel,
.paropts = .paropts
)
add_attr2tb(tb = z,
mspct = spct,
col.names = attr2tb,
idx = idx)
}
# internal utility function --------------------------------------------------
#' Compute two transmittances for ratio, fraction or normalised difference
#'
#' Internal function that computes the two transmittances needed to compute
#' various waveband ratios and fractions.
#'
#' @details See \code{\link{transmittance}} for details on the transmittance calculations.
#'
#' @param spct an object of class "filter_spct" or "object_spct".
#' @param w.band.1,w.band.2 waveband objects or lists of waveband objects
#' used to compute the numerator(s) and denominator(s) of the ratio(s). The
#' waveband(s) determine the region(s) of the spectrum that are summarized.
#' @param quantity character string One of "total", "average" or "mean".
#' @param wb.trim logical if TRUE wavebands crossing spectral data boundaries
#' are trimmed, if FALSE, they are discarded
#' @param use.cached.mult logical indicating whether multiplier values should be
#' cached between calls
#' @param use.hinges logical Flag indicating whether to insert "hinges" into the
#' spectral data before integration so as to reduce interpolation errors at
#' the boundaries of the wavebands.
#' @param naming character one of "long", "default", "short" or "none". Used to
#' select the type of names to assign to returned value.
#'
#' @keywords internal
#'
# This function is extremely simple but ensures consistency and avoids repetition
# It is used to define ratios, fractions and NDIs.
#
two_transmittances <- function(spct,
w.band.1,
w.band.2,
quantity,
wb.trim,
use.cached.mult,
use.hinges,
naming) {
stopifnot("Unsupported argument passed to 'quantity'" =
quantity %in% c("total", "average", "mean"))
Tfr.1 <- transmittance(spct,
w.band = w.band.1,
quantity = quantity,
scale.factor = 1,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
allow.scaled = TRUE,
naming = naming)
Tfr.2 <- transmittance(spct,
w.band = w.band.2,
quantity = quantity,
scale.factor = 1,
wb.trim = wb.trim,
use.cached.mult = use.cached.mult,
use.hinges = use.hinges,
allow.scaled = TRUE,
naming = naming)
list(Tfr.1 = Tfr.1, Tfr.2 = Tfr.2)
}
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