This function returns the transmittance normalized difference index for a given pair of wavebands of a filter spectrum.
Tfr_normdiff(
spct,
w.band.plus,
w.band.minus,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...
)# S3 method for default
Tfr_normdiff(
spct,
w.band.plus,
w.band.minus,
scale.factor,
wb.trim,
use.cached.mult,
use.hinges,
...
)
# S3 method for filter_spct
Tfr_normdiff(
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,
...
)
# S3 method for filter_mspct
Tfr_normdiff(
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
)
In the case of methods for individual spectra, a 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 quantity
= "total"
and "[Tfr(wl):Tfr(wl)]" if quantity = "mean"
or
quantity = "average"
.
A 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
w.band.num
and 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.
an object of class "filter_spct".
waveband object(s) or a list(s) of waveband objects used to compute the additive and subtractive transmittance terms of the normalized difference index.
numeric vector of length 1, or length equal to that of
w.band
. Numeric multiplier applied to returned values.
logical if TRUE wavebands crossing spectral data boundaries are trimmed, if FALSE, they are discarded
logical indicating whether multiplier values should be cached between calls
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.
other arguments (possibly ignored)
character One of "total", "average" or "mean".
character one of "long", "default", "short" or "none". Used to select the type of names to assign to returned value.
character Used to tag the name of the returned values.
character vector, see add_attr2tb
for the syntax
for attr2tb
passed as is to formal parameter col.names
.
character Name of the column with the names of the members of the collection of spectra.
if TRUE, apply function in parallel, using parallel backend provided by foreach
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.
Tfr_normdiff(default)
: Default for generic function
Tfr_normdiff(filter_spct)
: Method for filter_spct
objects
Tfr_normdiff(filter_mspct)
: Calculates Tfr:Tfr from a filter_mspct
object.
With the default quantity = "mean"
or
quantity = "average"
the ratio is based on
two mean spectral photon transmittances, one computed for each waveband.
$$\frac{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{plus}) - \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{minus})}{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{plus}) + \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{minus})}$$
If the argument is set to quantity = "total"
the fraction is based on
two photon transmittances, one computed for each waveband.
$$\frac{\mathrm{Tfr}(s, wb_\mathrm{plus}) - \mathrm{Tfr}(s, wb_\mathrm{minus})}{\mathrm{Tfr}(s, wb_\mathrm{plus}) + \mathrm{Tfr}(s, wb_\mathrm{minus})}$$
Only if the wavelength expanse of the two wavebands is the same, these two ratios are numerically identical.
normalized_diff_ind
, accepts different summary
functions.
Other transmittance ratio functions:
Tfr_fraction()
,
Tfr_ratio()
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")
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