---
title: "User Guide: 1 Radiation"
subtitle: "Package 'photobiology' `r packageVersion('photobiology')` "
author: "Pedro J. Aphalo"
date: "`r packageDate('photobiology')`"
output: 
  rmarkdown::html_vignette:
    toc: yes
vignette: >
  %\VignetteEncoding{UTF-8}
  %\VignetteIndexEntry{User Guide: 1 Radiation}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  markdown: 
    wrap: 72
---

## Radiation, astronomy and atmosphere

The User Guide is divided into two volumes: *1. Radiation* and *2.
Astronomy*. The second volume also describes functions related to water
vapour in the atmosphere.

## Naming conventions

I have developed package '**photobiology**' over several years, and even
though I have tried to remain consistent, some inconsistencies have
crept in. I have attempted to correct inconsistencies without breaking
old code by providing synonyms for some functions.

In general I have used names in *snake case* for methods and functions,
such as `source_spct()` and *dot case* for their arguments. There are
two exceptions to this: the `as.` and `is.` methods which for
consistency with base R, retain the dot: `as.source_spct()` and
`ìs.source_spct()`. There are still some functions and methods whose
names are in *camel case*: these are mostly accessors and setters of
metadata attributes such as `setWhatMeasured()` and `getWhatMeasured()`,
in which case synonyms `what_measured<-()` and `what_measured()` are now
provided with a syntax that parallels that of R's `comment<-()`,
`comment()`, and similar methods for other attributes. Names of
attributes themselves use dots, while classes use snake case as
functions do, allowing consistency between class names and their
constructor functions. There is an additional twist: functions named
like `clip_wl()` are "verbs" that act on the wavelengths ("wl")
modifying them, while those named like `wl_range()` are "nouns" for the
properties of the wavelengths.

In examples we use variable names ending in `.spct` for spectra, ending
in `.mspct` for collections of spectra and ending in `.tb` for tibbles.
In most cases the root of the variable names use "snake case" and may
have a tag at the end separated with a dot. In the case of variable
names used in examples I have been less strict about conventions than
for the objects exported by the package.

None of these naming conventions are enforced for user defined objects
and classes; these conventions are simply those I have tried to follow
while developing this package as well as other packages in the
r4photobiology suite.

## High and low level functions

The package exports two sets of functions for many operations: low-level
functions programmed following a functional paradigm, and higher-level
functions using an object-oriented paradigm. The former functions take
as arguments numeric vectors and are sometimes faster. The later ones
take *spectra* objects as arguments, are easier to use, and at least at
the moment, to some extent slower. For everyday use, methods for
*spectra* objects are recommended, but when maximum performance or
flexibility in scripts is desired, the use of the functions taking
numeric vectors as arguments may allow optimizations that are not
possible with the object-oriented functions. The differences in
performance becomes relevant only in extreme cases such as processing in
a single script tenths of thousands of spectra. In the vignettes we
emphasize the use of the object-oriented classes and methods.

## Example data

Data for several spectra are included for use in examples and vignettes,
and in testing (Tables 1 and 2). Other packages in the '**r4photobiology
suite**' provide many additional data sets.

------------------------------------------------------------------------

**Table 1. Data sets included in the package: spectra.** The CIE
standard illuminant data in this package are normalized to one at
$\lambda = 560\,$nm, while in the CIE standard they are normalized to
100 at the same wavelength. See documentation for each data object for
details and data sources.

| Object                  | class            | units                        | data description                 |
|:-------------|:-------------|:-------------|:------------------------------|
| `sun.spct`              | `source_spct`    | $W\,m^{-2}\,nm^{-1}$         | solar spectral irradiance        |
| `sun_daily.spct`        | `source_spct`    | $J\,m^{-2}\,d^{-1}\,nm^{-1}$ | solar spectral exposure          |
| `sun.data`              | `data.frame`     | $W\,m^{-2}\,nm^{-1}$         | solar spectral irradiance        |
| `sun_daily.data`        | `data.frame`     | $J\,m^{-2}\,d^{-1}\,nm^{-1}$ | solar spectral exposure          |
| `D65.illuminant.spct`   | `source_spct`    | (norm. 560 nm)               | CIE standard                     |
| `A.illuminant.spct`     | `source_spct`    | (norm. 560 nm)               | CIE standard                     |
| `clear.spct`            | `filter_spct`    | fraction                     | ideal transparent filter         |
| `opaque.spct`           | `filter_spct`    | fraction                     | ideal opaque filter              |
| `polyester.spct`        | `filter_spct`    | fraction                     | plastic film                     |
| `yellow_gel.spct`       | `filter_spct`    | fraction                     | theatrical *gel* filter          |
| `green_leaf.spct`       | `reflector_spct` | fraction                     | a birch leaf                     |
| `clear_body.spct`       | `object_spct`    | fraction                     | ideal transparent body           |
| `black_body.spct`       | `object_spct`    | fraction                     | ideal black body                 |
| `white_body.spct`       | `object_spct`    | fraction                     | ideal white body                 |
| `Ler_leaf.spct`         | `object_spct`    | fraction                     | Arabidopsis leaf                 |
| `Ler_leaf_trns.spct`    | `filter_spct`    | fraction                     | Arabidopsis leaf (T total)       |
| `Ler_leaf_trns_i.spct`  | `filter_spct`    | fraction                     | Arabidopsis leaf (T internal)    |
| `Ler_leaf_rflt.spct`    | `reflector_spct` | fraction                     | Arabidopsis leaf (R total)       |
| `water.spct`            | `solute_spct`    | $m^{-1}$                     | pure water molar att. coef.      |
| `phenylalanine`         | `solute_spct`    | $m^{-1}$                     | phenylalanine molar att. coef.   |
| `photodiode.spct`       | `response_spct`  | $A / W$                      | typical Si photodiode            |
| `ccd.spct`              | `response_spct`  | $A / W$                      | typical CCD array                |
| `white_led.raw_spct`    | `raw_spct`       | counts                       | example raw detector counts data |
| `white_led.cps_spct`    | `cps_spct`       | counts / s                   | example detector counts data     |
| `white_led.source_spct` | `source_spct`    | $W\,m^{-2}\,nm^{-1}$         | spectral irradiance              |
| `filter_cps.mspct`      | `cps_mspct`      | $\mathrm{counts} / s$        | example detector counts data     |

------------------------------------------------------------------------

------------------------------------------------------------------------

**Table 2. Data sets included in the package: chromaticity data.** See
documentation for each data object for details and data sources.

| Object             | class         | data description                          |
|:--------------|:--------------|:-----------------------------------------|
| `ciexyzCC2.spct`   | `chroma_spct` | human chromaticity coordinates $2^\circ$  |
| `ciexyzCC10.spct`  | `chroma_spct` | human chromaticity coordinates $10^\circ$ |
| `ciexyzCMF2.spct`  | `chroma_spct` | human colour matching function $2^\circ$  |
| `ciexyzCMF10.spct` | `chroma_spct` | human colour matching function $10^\circ$ |
| `ciev2.spct`       | `chroma_spct` | human luminous efficiency $2^\circ$       |
| `beesxyzCMF.spct`  | `chroma_spct` | bee colour matching function              |

------------------------------------------------------------------------

```{r, include=FALSE, echo=FALSE}
knitr::opts_chunk$set(fig.width=7.2, fig.height=4.3)
```

```{r, printing-spectra, eval=TRUE, include=FALSE}
# library(tibble)
options(tibble.print_max = 6, tibble.print_min = 4)
```

## Spectra

Package '**photobiology**' defines a family of classes based on the
`tibble` class, mostly compatible with R's data frames. The present
package by imposing some restrictions on the naming of the member
vectors, allows methods to *find* the data when passed one of these
objects as argument. In addition, as the data are checked when the
object is built or modified, there is no need to test for their validity
each time a calculation is carried out. Another advantage of using
spectrum objects, is that specialized versions of generic functions like
`print` and operators like `+` are defined for spectra. Objects of all
the `..._spct` classes are also `tibble` and `data.frame` objects, as a
result of how classes have been derived.

In this package we define a *generic* or *base* spectrum class, derived
from `tibble`, which in turn has been derived from `data.frame`. Classes
for specialized types of spectra are derived from `generic_spct`. This
*parenthood* hierarchy means that spectral objects can be used almost
anywhere where a `data.frame` is expected (and also converted into data
frames with R's function `as.data.frame()`). Specializations of many
methods including extraction (indexing) methods and partial assignment
methods are defined to ensure that the expectations on the variables
contained in objects of these classes remain valid in most situations.
Other specializations of methods and functions are related to achieving
a convenient and concise syntax tailored for spectral data as in the
case of mathematical operators and functions.

Another important aspect is that when spectral data are stored in
objects of these classes, the physical quantities and units of
expression are also stored as metadata. Furthermore, attributes are used
to keep track of both metadata related to the origin of the data and of
later transformations that affect their interpretation, such as
normalization or re-scaling. **Although sanity tests are applied at the
time of object creation, to a large extent the responsibility of
ensuring that the numbers provided as argument to object constructors
comply with expectations remains with the users of the package.**

In addition to the classes for storing individual spectra, classes for
storing collections of these spectral objects are defined. These classes
are derived from class `list` and can contain member spectra of
different lengths and measured at different wavelength values.

We give in this vignette brief descriptions and examples of the use of
different classes, methods, functions and operators. We start with the
simplest and most frequently used methods.

### Getting started

We load two packages in addition to '**photobiology**', '**lubridate**'
and '**dplyr**', as they will be used in the examples.

```{r, pkg-load, eval=TRUE, message = FALSE}
library(photobiology)
library(lubridate)
library(dplyr)
```

### Classes

Package '**photobiology**' defines several classes intended to be used
to store different types of spectral data. They are all derived from
`generic_spct`, which in turn is derived from `tibble::tibble`. Table 1
lists these classes. Attributes are used to store *metadata* such as
information about units of expression.

------------------------------------------------------------------------

**Table 1. Classes for spectral data.** In addition to the required
variables listed in the table, additional arbitrary variables are partly
supported---some operations will not include them in returned values to
avoid ambiguity and other possible conflicts. In addition to the
attributes listed in the table, all spectral objects support attributes
`multiple.wl`, `idfactor`, `normalized`, `scaled`, `when.measured`,
`where.measured`, `what.measured`, `how.measured` plus the normal
attributes of `tibble` (and `data.frame`) objects including `comment`.
All these attributes plus attributes `instrument.descriptor` and
`instrument.settings` are retained across operations on spectra as long
as they remain valid.

| Class name          | Required variables         | Attributes                                          |
|:----------------|:------------------|:-----------------------------------|
| `generic_spct`      | `w.length`                 |                                                     |
| `calib ration_spct` | `w.length`, `irrad.mult`   | `instr.desc`                                        |
| `raw_spct`          | `w.length`, `counts`       | `instr.desc`, `instr.settings`, `linearized`        |
| `cps_spct`          | `w.length`, `cps`          | `instr.desc`, `instr.settings`, `linearized`        |
| `source_spct`       | `w.length`, `s.e.irrad`    | `instr.desc`, `instr.settings`, `time.unit`, `bswf` |
|                     | `w.length`, `s.q.irrad`    | `time.unit`, `bswf`                                 |
| `filter_spct`       | `w.length`, `Tfr`          | `Tfr.type`, `filter.properties`                     |
|                     | `w.length`, `A`            | `Tfr.type`, `filter.roperties`                      |
| `ref lector_spct`   | `w.length`, `Rfr`          | `Rfr.type`                                          |
| `object_spct`       | `w.length`, `Tfr`, `Rfr`   | `Tfr.type`, `Rfr.type`                              |
| `re sponse_spct`    | `w.length`, `s.e.response` | `time.unit`                                         |
|                     | `w.length`, `s.q.response` | `time.unit`                                         |
| `chroma_spct`       | `w.length`, `x`, `y`, `z`  |                                                     |
| `solute_spct`       | `w.length`, `K.mole`       | `K.type`, `solute.properties`                       |
|                     | `w.length`, `K.mass`       | `K.type`, `solute.properties`                       |

------------------------------------------------------------------------

The *design* imposes the restriction that data from different
observations are never present as different *data columns*, if present,
additional data columns represent different properties from the same
observation event. In other words, the storage format is *tidy* as
nicknamed by Hadley Wickham. In most cases, one spectral object correspond to 
one spectral observation, but most functions and methods are
compatible or can be used to create spectral objects where the spectral
data from different observations are stored "longitudinally" and
"tagged" with a factor with a level for each observation event. These
observations must use consistent units of expression. This long format is 
useful, for example, when producing plots with package 'ggplot2' or when
acquiring or storing time series of spectra. If spectra are stored in 
*long form*, e.g. for plotting with 'ggplot2', attributes are stored as named 
lists or enforced to be the same across spectra. This allows to reconstruct a
collection of spectra from a long-form spectral object and *vice versa*
preserving nearly all of the metadata. In 'photobiology' (<= 0.11.0) the
support for these conversions was limited and spectral objects with multiple
spectra in long form created with these versions lack complete metadata
or have the metadata stored in a way that cannot be easily retrieved, leading
to metadata loss on conversion to collections of spectra.

------------------------------------------------------------------------

*Collections of spectra are to be in general preferred to multiple
spectra stored in a single spectral object.* This is because collections are the
"native" storage approach in the 'photobiology' package, supporting all
operations efficiently, while operations on spectra stored in long form are
implemented by means of two way on-the-fly conversions into collections of
spectra. Two-way conversions can be expected to depend on memory allocation and
thus to decrease performance.

------------------------------------------------------------------------

### Data assumptions

A key assumption of the package is that wavelengths are always expressed
in manometers ($1~\mathrm{nm} = 1 \cdot 10^{-9}\,\mathrm{m}$). If the
data to be analysed use different units for wavelengths, e.g. Ångstrom
($1~\textrm{Å} = 1 \cdot 10^{-10}\,\mathrm{m}$), the values need to be
re-expressed before creating objects of the spectral classes. The same
applies to all spectral quantities, as there is an expectation in every
case, of using base SI units for expression. Table 2 lists the units of
expression for the different variables and the metadata attributes that
may determine variations in the expression of the quantities.

------------------------------------------------------------------------

**Table 2. Variables used for spectral data and their units of
expression.** **A:** as stored in objects of the spectral classes,
**B:** also recognized by the `set` family of functions for spectra and
automatically converted. `time.unit` accepts in addition to the
character strings listed in the table, objects of classes
`lubridate::duration` and `period`, in addition `numeric` values are
interpreted as seconds. `exposure.time` accepts these same values, but
not the character strings.

| Variables                   | Unit of expression                      | Attribute value        |
|:---------------------|:------------------------------|:------------------|
| **A: stored**               |                                         |                        |
| w.length                    | nm                                      |                        |
| counts                      | $n$                                     |                        |
| cps                         | $n\,s^{-1}$                             |                        |
| irrad.mult                  | $J\,m^{-2}\,nm^{-1}\,n^{-1}$            |                        |
| s.e.irrad                   | $W\,m^{-2}\,nm^{-1}$                    | time.unit = "second"   |
| s.e.irrad                   | $J\,m^{-2}\,d^{-1}\,nm^{-1}$            | time.unit = "day"      |
| s.e.irrad                   | $J\,m^{-2}\,nm^{-1}$                    | time.unit = "exposure" |
| s.e.irrad                   | varies                                  | time.unit = *duration* |
| s.q.irrad                   | $mol\,m^{-2}\,s^{-1}\,nm^{-1}$          | time.unit = "second"   |
| s.q.irrad                   | $mol\,m^{-2}\,d^{-1}\,nm^{-1}$          | time.unit = "day"      |
| s.q.irrad                   | $mol\,m^{-2}\,nm^{-1}$                  | time.unit = "exposure" |
| s.q.irrad                   | varies                                  | time.unit = *duration* |
| Tfr                         | [0..1]                                  | Tfr.type = "total"     |
| Tfr                         | [0..1]                                  | Tfr.type = "internal"  |
| A                           | a.u.                                    |                        |
| Afr                         | [0..1]                                  |                        |
| Rfr                         | [0..1]                                  | Rfr.type = "total"     |
| Rfr                         | [0..1]                                  | Rfr.type = "specular"  |
| s.e.response                | $\mathit{x}\,J^{-1}\,s^{-1}\,nm^{-1}$   | time.unit = "second"   |
| s.e.response                | $\mathit{x}\,mol^{-1}\,d^{-1}\,nm^{-1}$ | time.unit = "day"      |
| s.e.response                | $\mathit{x}\,J^{-1}\,nm^{-1}$           | time.unit = "exposure" |
| s.e.response                | varies                                  | time.unit = *duration* |
| s.q.response                | $\mathit{x}\,mol^{-1}\,s^{-1}\,nm^{-1}$ | time.unit = "second"   |
| s.q.response                | $\mathit{x}\,mol^{-1}\,d^{-1}\,nm^{-1}$ | time.unit = "day"      |
| s.q.response                | $\mathit{x}\,mol^{-1}\,nm^{-1}$         | time.unit = "exposure" |
| s.q.response                | varies                                  | time.unit = *duration* |
| x, y, z                     | [0,1]                                   |                        |
| K.mole                      | $m^{2}\,mol^{-1}, \log_{10}$ based      | K.type = "attenuation" |
| K.mole                      | $m^{2}\,mol^{-1}, \log_{10}$ based      | K.type = "absorption"  |
| K.mole                      | $m^{2}\,mol^{-1}, \log_{10}$ based      | K.type = "scattering"  |
| K.mass                      | $m^{2}\,g^{-1}, \log_{10}$ based        | K.type = "attenuation" |
| K.mass                      | $m^{2}\,g^{-1}, \log_{10}$ based        | K.type = "absorption"  |
| K.mass                      | $m^{2}\,g^{-1}, \log_{10}$ based        | K.type = "scattering"  |
| **B: converted**            |                                         |                        |
| wl $\to$ w.length           | nm                                      |                        |
| wavelength $\to$ w.length   | nm                                      |                        |
| Tpc $\to$ Tfr               | [0..100]                                | Tfr.type = "total"     |
| Tpc $\to$ Tfr               | [0..100]                                | Tfr.type = "internal"  |
| Rpc $\to$ Rfr               | [0..100]                                | Rfr.type = "total"     |
| Rpc $\to$ Rfr               | [0..100]                                | Rfr.type = "specular"  |
| counts.per.second $\to$ cps | $n\,s^{-1}$                             |                        |
| K.mole $log_e \to log_{10}$ | $m^{-1}\,mol^{-1}, \log_{e}$ based      | K.type = "attenuation" |
| K.mole $log_e \to log_{10}$ | $m^{-1}\,mol^{-1}, \log_{e}$ based      | K.type = "absorption"  |
| K.mole $log_e \to log_{10}$ | $m^{-1}\,mol^{-1}, \log_{e}$ based      | K.type = "scattering"  |
| K.mass $log_e \to log_{10}$ | $m^{-1}\,g^{-1}, \log_{e}$ based        | K.type = "attenuation" |
| K.mass $log_e \to log_{10}$ | $m^{-1}\,g^{-1}, \log_{e}$ based        | K.type = "absorption"  |
| K.mass $log_e \to log_{10}$ | $m^{-1}\,g^{-1}, \log_{e}$ based        | K.type = "scattering"  |

------------------------------------------------------------------------

Energy irradiance is assumed to be expressed in $W\,m^{-2}$ and photon
irradiance in $mol^{-1}\,m^{-2}\,s^{-1}$, that is to say using second
as unit for time and no SI scale factors for the measured variables.
With respect to time, second is the default, but it is possible to set
the unit for time to an arbitrary time duration such as day. Obviously,
this applies only to rate variables like irradiance and response rates,
but not to time-invariant intensive properties like transmittance of
filters.

The default time unit used is *second*, but *minute*, *hour*, *day* and
*exposure* can be used by supplying as arguments `"minute"`, `"hour"`,
`"day"`, or `"exposure"`---The meaning of `"exposure"` is the total
exposure time, in other words, fluence instead of irradiance---to the
constructor `source_spct()`. In addition to these character constants
objects of class `lubridate:duration` are also accepted. In other words
irradiance is a flux rate while exposure is a flux, as both are
expressed per unit of illuminated area.

In the case of spectra of the molar attenuation coefficient we use
$\log_{10}$ as a base for the stored values but the constructor accepts
data expressed in other log bases. The expected units are always in
metres ($m^{-1}$) rather than the frequently used centimetres
($cm^{-1}$).

Transmittance, reflectance and absorptance are stored as fractions of
one. The constructors also accept these quantities expressed as
percentages, and convert them.

Most attributes are set when a spectral object is created, either using
default values or with values supplied as arguments to the constructor.
In many cases the default is `NA` used to indicate missing information.

Methods for querying and setting these attributes in already constructed
objects are also available.

------------------------------------------------------------------------

Not respecting the expectations about data inputs or setting erroneous
values in the metadata attributes will yield completely wrong results if
calculations are attempted! It is extremely important to make sure that
the wavelengths are in nanometres as this is what all functions expect.
If wavelength values are in the wrong units, the action-spectra weights
and quantum to/from energy units conversions will be wrongly calculated,
and the values returned by most functions wrong, without warning. Errors
in some cases will be triggered at the time of object creation as the
data input to constructors is tested to be within the expected range of
values, which in the case of some quantities frequently allows detection
of mistakes in the use unit scaling factors.

------------------------------------------------------------------------

If spectral irradiance data is in $W\,m^{-2}\,nm^{-1}$, and the
wavelength in $nm$, as is the case for many Macam spectroradiometers, the
data can be used directly and functions in the package will return
irradiances in $W\,m^{-2}$.

If, for example, the spectral irradiance data output by a
spectroradiometer is expressed in $mW\,m^{-2}\,nm^{-1}$, and the
wavelengths are in Ångstrom then to obtain correct results when using
any of the packages in the suite, we need to rescale the data when
creating a new object.

```{r, example-1, eval=FALSE}
# not run
my.spct <- source_spct(w.length = wavelength/10, s.e.irrad = irrad/1000)
```

In the example above, we take advantage of the behaviour of the R
language: an operation between a scalar and a vector, is equivalent to
applying this operation to each element of the vector. Consequently, in
the code above, each value from the vector of wavelengths is divided by
10, and each value in the vector of spectral irradiances is divided by
1000.

### Querying the class

Before giving examples of how to construct objects to store spectral
data we show how to query the class of an object, and how to query the
class of a spectrum. Consistently with R, the package provides *is*
functions for querying the type of spectra objects. The only *unusual*
function name, defined as a *synonym* for `is.generic_spct`:
`is.any_spct()`.

```{r, query-class-1}
is.any_spct(sun.spct)
is.generic_spct(sun.spct)
is.source_spct(sun.spct)
is.data.frame(sun.spct)
```

In addition function `class_spct()` returns directly the
spectrum-related class attributes---i.e. it filters out from the output
of `class()` the underlying inherited classes.

```{r, query-class-2}
class_spct(sun.spct)
class(sun.spct)
```

### Construction

There are two different approaches to the creation of spectral objects
by users. The first group are constructors similar to the `data.frame()`
constructor, which take vectors as arguments. The second group are
constructors that convert `list` objects, and because of class
derivation also `data.frame` objects, into spectral objects.
Constructors in this second group are similar to `as.data.frame` from
base R. In contrast to the data frame constructors, spectral object
constructors require the variables or the vector arguments to be
suitably named so that they can be recognized.

Here we briefly describe the *as* constructor functions for spectra. In
the first example we create an object to store spectral irradiance data
for a *fictitious light source*, by first creating a data frame, and
creating the spectral object as a copy of it. In the example below we
supply a single value, 1, for the spectral irradiance. This value gets
recycled as is normal in R, but of course in real use it is more usual
to supply a vector of the same length as the `w.length` vector.

```{r, construction-1}
my.df <- data.frame(w.length = 400:410, s.e.irrad = 1)
my.spct <- as.source_spct(my.df)
class(my.spct)
class(my.df)
my.spct
```

We can copy and convert any spectrum object into any of its base clases,
such as `generic_spct` or `data.frame`. This can result in the immediate
and surely in the delayed loss of metadata when modified. In addition,
objects *downgraded* to a base class support fewer operations and those
still available may behave differently.

```{r, construction-2}
my.g.spct <- as.generic_spct(my.spct)
class(my.g.spct)
```

When constructing spectral objects from numeric vectors the names of the
arguments are meaningful and convey information on the nature of the
spectral data and basis of expression.

```{r, construction-3}
source_spct(w.length = 300:305, s.e.irrad = 1)
```

```{r, construction-4}
z <- 300:305
y <- 2
source_spct(w.length = z, s.e.irrad = y)
```

When argument names are not supplied explicitly as above, the names of
the variables are used to identify the data vectors.

```{r, construction-5}
w.length <- 300:305
s.e.irrad <- 1
source_spct(w.length, s.e.irrad)
```

The different constructors have additional arguments to be used in
setting non-default values for the attributes. These arguments have the
same name as the attributes. Here we used the data frame created in the
first code chunk of this section.

```{r, construction-6}
my.d.spct <- as.source_spct(my.df, time.unit = "day")
```

Argument `strict.range` can be used to override or make more strict the
validation of the data values.

```{r, construction-7}
source_spct(w.length = 300:305, s.e.irrad = -1)
source_spct(w.length = 300:305, s.e.irrad = -1, strict.range = NULL)
```

Argument `comment` can be used to add a comment to the data at the time
of construction.

```{r, construction-8}
my.cm.spct <- source_spct(w.length = 300:305, s.e.irrad = 1,
                          comment = "This is a comment")
comment(my.cm.spct)
```

The constructors treat unrecognized named arguments as data to create
aditional columns in the spectral objects.

### Metadata attributes

Metadata attributes are used in the spectral objects to store metadata
in a consistently. These metadata are in some cases required for
conversion among related physical quantities, while in other cases allow
printing of ancillary information needed for interpretation, like units
of expression. These metadata are also used in other packages in the
suite, for example in 'ggspectra' to automatically produce axis labels,
titles and annotations. A few attributes are simply a way or organizing
the storage of information which is not used in any calculations,
functioning as a kind of specialized comments. The metadata described in
this section are stored in spectral objects using attributes, which are
a normal feature of the R language. An example, is attribute `time.unit`
used to indicate if spectral irradiance is expressed per second or
integrated over some other time duration.

#### Attributes supported by all spectral objects

Some attributes are meaningful for all the classes of spectra defined in
the package, while most others a specific to individual classes (Table
1). Those that apply to all spectral objects and their summaries are
*time of measurement* using attribute `"when.measured"`, *place of
measurement* using attribute `"where.measured"`, a *user supplied label*
using attribute `"what.measured"`, a label describing origin of the data
using attribute `"how.measured"` and free-text *comments*. One can set
and get comments stored in spectra by means of base R's `comment()` and
`comment() <-` functions and the other attributes listed above with
functions following the same syntax and named after the attributes but
replacing any `.` by `_`. Functions in this package may set additional
attributes to keep track of the actions. For example when a spectrum is
normalized or scaled a record of these action is kept in attributes.
When spectra are are operated upon the metadata that is not invalidated
will be merged when possible---e.g., comments of operands are
concatenated comments and set as comment to the returned object.

Functions `when_measured()` and `when_measured<-()` are used for
retrieving and setting the `"when.measured"` attribute to a date
supplied as a `POSIXct` value. Note: we use `POSIXct` objects which
describes instants in time in absolute terms as they include time zone
information. Package `lubridate` makes entering and operating on
`POSIXct` objects rather easy.

```{r, attr-1}
my.spct <- sun.spct
when_measured(my.spct) <-  NULL
when_measured(my.spct)
when_measured(my.spct) <- lubridate::ymd_hms("2015-10-31 22:55:00", tz = "EET")
when_measured(my.spct)
```

Functions `where_measured()` and `where_measured<-()` are used for
retrieving and setting a geocode stored in a `data.frame`. This format
is compatible with function `geocode()` from package `ggmap`. We pass
latitude and longitude coordinates, as shown below. The returned value
is always a data frame with columns `"lon"`, `"lat"` and `"address"`.

```{r, attr-2}
where_measured(my.spct) <- NULL
where_measured(my.spct)
where_measured(my.spct) <- data.frame(lat = 60, lon = -10)
where_measured(my.spct)
where_measured(my.spct) <- data.frame(lat = 60, lon = -10, address = "Somewhere")
where_measured(my.spct)
my.spct
```

Functions `what_measured()` and `where_measured<-()`, and
`how_measured()` and `how_measured<-()` are used for retrieving or
setting a text value containing information about what was measured to
obtain the data.

```{r, attr-2a}
what_measured(my.spct) <- "something"
what_measured(my.spct)
my.spct
```

Functions using a different syntax are also available, for these and
other attributes which are not likely to be set by users. Many of these
additional attributes are meaningful only for some types of spectra.

#### Attributes supported by `source_spct` objects

One example is the time unit used to express spectral irradiance.
Functions are available for querying and setting the state if these
attributes. `is_` functions return a logical value, and `get` functions
return the values of the attributes themselves. In addition `set`
functions can be used to set the value stored in the attributes. Several
of the `set` functions are very rarely needed in user code, as these
attributes are set during construction or as a side effect of applying
other functions and/or operators to the objects. Function
`setBSWFUsed()` and other *set* functions are mainly useful to
programmers extending the package, but only exceptionally to users. One
exception is the case when a wrong value has been assigned by mistake
and needs to be overwritten.

We can see in the printout that the time unit is reported in the header.

```{r}
sun.spct
```

For example function `is_effective()` returns `TRUE` if the spectral
data has been weighted with a BSWF. The corresponding `getBSWFUsed()`
function can be used, in this case to retrieve the name of the BSWF that
was used. Here we demonstrate with one example, where we use a
`waveband` object---constructed on-the-fly with a constructor
function---, defining a range of wavelengths.

```{r, attr-3}
is_effective(sun.spct)
is_effective(sun.spct * waveband(c(400, 700)))
```

Sometimes it may be desired to change the time unit used for expressing
spectral irradiance or spectral response, and this can be achieved with
the *conversion* function `convertTimeUnit`. This function both converts
spectral data to the new unit of expression and sets the `time.unit`
attribute, preserving the validity of the data object.

```{r, attr-4}
ten.minutes.spct <-
  convertTimeUnit(sun.spct, time.unit = duration(10, "minutes"))
ten.minutes.spct
getTimeUnit(ten.minutes.spct)
```

#### Attributes supported by `filter_spct` objects

A crucial information is whether transmittance (`Tfr`) is expressed as
internal or total, stored in attribute `Tfr.type`, as this affects how
absorptances and absorbances are computed. The key step is when a
`filter_spct` object is created, when the user has to be careful to set
this attribute correctly.

The objects from which transmittance can differ in additional properties
that affect possible calculations. Attribute `filter.properties` is used
to store these in an object with fields `Rfr.constant`, `thickness` and
`attenuation.mode`. When these metadata are available, in many cases we
can use function `convertTfrType()` to convert internal transmittance
into total transmittance and *vice versa* and function
`convertThickness()` to compute the spectral transmittance of a filter
of the same material but different thickness.

These attributes are also allowed in the case of `object_spct` and
`reflector_spct` and retained during class conversions between them and
`filter_spct` objects.

They are included in the printout of `filter.spct` objects.

```{r}
polyester.spct
```

We estimate the spectral transmittance of 2 mm-thick PET film.

```{r}
convertThickness(polyester.spct, thickness = 2e-3)
```

------------------------------------------------------------------------

Attributes `instr_desc` and `instr_settings` are used to store
measurement-related metadata, describing the instrument used and its
settings. These attributes are lists, with a few default fields and
possibly unlimited *special* attributes. The present package provides
functions for operating on them and print-outs include some of the
default fields if the attribute is set. The expectation is that these
attributes are set by other packages such as 'ooacquire' used for direct
data acquisition or raw instrument data import.

These instrument-specific attributes can contain lots of information and bloat
the size of spectral objects. Two methods, `trimInstrDesc()` and
`trimInstrSettings()` can be used to discard parts of these metadata, such as
instrument calibration information, once the raw-counts data have been converted
into physical units.

------------------------------------------------------------------------

------------------------------------------------------------------------

Spectral objects created with earlier versions (from before the first CRAN
release in 2016) of this package are missing some metadata attributes. For this
reason *summary* methods from this package and `autoplot()` and `ggplot()`
methods from package 'ggspectra' may print warnings. These *very old* objects
can be updated by adding the missing attributes using functions `setTimeUnit`,
`setBSWFUsed`, `setTfrType` and `setRfrType`. However, in many cases function
`update_spct` can be used to set the missing attributes to default values, or
user scripts re-run to rebuild the data objects from raw data.

------------------------------------------------------------------------

## Collections of spectra

### Classes

The package defines several classes intended to be used to store
*collections* of different types of spectral data. They are all derived
from `generic_mspct`, which in turn is derived from `list`. Table 3
lists them.

------------------------------------------------------------------------

**Table 3. Classes for collections of spectral objects.** Objects of
class `generic_mspct` can have member objects of any class derived from
`generic_spct` and can be heterogeneous, while the other classes support
homogeneous collections of spectral objects. Attributes of these objects
can be queried and set with the normal R methods `attr` and `attributes`
as well as with functions defined in this package. See table 1 for the
attributes used in individual member spectra of collections.

| Class name          | Class of member objects | Attributes                |
|:--------------------|:------------------------|---------------------------|
| `generic_mspct`     | `generic_spct`          | `names`, `dim`, `comment` |
| `calibration_mspct` | `calibration_spct`      | `names`, `dim`, `comment` |
| `raw_mspct`         | `raw_spct`              | `names`, `dim`, `comment` |
| `cps_mspct`         | `cps_spct`              | `names`, `dim`, `comment` |
| `source_mspct`      | `source_spct`           | `names`, `dim`, `comment` |
| `filter_mspct`      | `filter_spct`           | `names`, `dim`, `comment` |
| `reflector_mspct`   | `reflector_spct`        | `names`, `dim`, `comment` |
| `object_mspct`      | `object_spct`           | `names`, `dim`, `comment` |
| `response_mspct`    | `response_spct`         | `names`, `dim`, `comment` |
| `chroma_mspct`      | `chroma_spct`           | `names`, `dim`, `comment` |
| `solute_mspct`      | `solute_spct`           | `names`, `dim`, `comment` |

------------------------------------------------------------------------

Objects of these classes, except for class `generic_mspct`, can only contain
members belonging the matching class of spectra. As all other spectral object
classes are derived from `generic_spct`, `generic_mspct` objects can contain
heterogeneous collections of spectra. In all cases, there are no restrictions on
the lengths, wavelength range and/or wavelength step size, or attributes other
than `class` of the contained spectra. Mimicking R's arrays and matrices, a
`dim` attribute is always present and `dim` methods are provided. This approach
is expected to allow the storage of time series of spectral data, or
(hyper)spectral image data, or even higher dimensional spectral data. The
handling of 1D and 2D spectral collections is already implemented in the summary
methods. Handling of 3D and higher dimensional data can be implemented in the
future without changing the class definitions. By having implemented `dim`, also
methods `ncol` and `nrow` are available as they use `dim` internally. Array-like
subscripting collections of spectra is **not** implemented.

### Construction

#### Constructors

We can construct a collection using a list of spectral objects as a
starting point, in this case the spectral irradiance for sunlight.

```{r, col-construction-1}
two_suns.mspct <- source_mspct(list(sun1 = sun.spct, sun2 = sun.spct))
two_suns.mspct
```

We can also create heterogeneous collections, but this drastically
limits the methods that are applicable to the resulting collection.

```{r, col-construction-2}
mixed.mspct <- generic_mspct(list(filter = polyester.spct, source = sun.spct))
class(mixed.mspct)
lapply(mixed.mspct, class_spct)
```

#### Using *as.* conversion functions

The `as.` coercion methods for collections of spectra, not only change
the class of the collection object, but can also optionally apply the
corresponding `as.` functions to the member objects. A copy of the
original object is made and then class-converted and returned.

```{r, col-construction-3}
two_gen.mspct <- as.generic_mspct(two_suns.mspct)
class(two_gen.mspct)
str(two_gen.mspct, max.level = 1, give.attr = FALSE)
```

In addition to coercion methods for lists of spectra objects, coercion
methods are available for lists of data frames (or tibbles) and from
matrix objects.

One additional feature is that if a single spectrum object or data frame
are coerced into a collection of spectra, the behaviour is equivalent to
having passed as argument a list containing such object as its only
member.

```{r, col-construction-4}
one_sun.mspct <- as.source_mspct(sun.spct)
class(one_sun.mspct)
str(one_sun.mspct, max.level = 1, give.attr = FALSE)
```

Sometimes spectral data stored in a matrix need to be coerced into a
collection of spectra. Coercion methods are defined also for this cases.
Several spectra may be stored in a matrix either by row or by column,
but this can be deduced automatically in the case of rectangular
matrices. Wavelengths values are not expected to be part of the matrix,
and need to be supplied as a separate numeric vector sorted in ascending
order. As in a spectrum wavelength values never repeat, the vector of
wavelengths is never recycled and uniqueness of values is enforced.

We here use artificial data, in this first example with spectra saved by
column. We assume that the values in the matrix are spectral
transmittance stored as percentages (hence "Tpc").

```{r, col-construction-5}
x <- matrix(1:100, ncol = 2)
wl <- 501:550 # wavelengths in nanometres
as.filter_mspct(x, wl, "Tpc")
```

In a second example we supply explicit names for the spectra.

```{r, col-construction-6}
as.filter_mspct(x, wl, "Tpc", spct.names = c("A", "B"))
```

There is no change in the call for data stored by row. We create a new
matrix, with the same data as above, but stored by row, as some R
packages do.

```{r, col-construction-7}
xrow <- matrix(1:100, nrow = 2, byrow = TRUE)
as.filter_mspct(xrow, wl, "Tpc")
```

There is only one case when an explicit argument for `byrow` is needed:
square matrices (same number of spectra as of wavelength values in each
spectrum).

When coercing collections of spectra into matrices, the metadata
contained in the individual spectral objects is discarded, and only the
`"comment"` attribute of the collection of spectra copied to the
returned object. The wavelength values are preserved in an attribute
named "w.length", but are not included as part of the matrix.

```{r, col-construction-8}
two_suns.mat <- as.matrix(two_suns.mspct, "s.e.irrad")
class(two_suns.mat)
dim(two_suns.mat)
head(dimnames(two_suns.mat)$spct)
head(dimnames(two_suns.mat)$w.length)
head(attr(two_suns.mat, "w.length"))
```

The argument `byrow` in the coercion into matrix methods has the same
meaning as in the `matrix` constructor function.

```{r, col-construction-9}
two_suns.row_mat <- as.matrix(two_suns.mat, "s.e.irrad", byrow = TRUE)
class(two_suns.row_mat)
dim(two_suns.row_mat)
head(dimnames(two_suns.row_mat)$spct)
head(attr(two_suns.row_mat, "w.length"))
```

Collections of spectra have a `dim` attribute but it is discarded as it
describes dimensions that could require spectral data to be stored in a
three dimensional array and cannot be mapped to the two dimensions of a
matrix.

These functions are not fully automatic, the user needs to provide the
name of the variable to extract from each spectrum. If the wavelength
values are not consistent among spectra, only those with the same values
as the first spectrum in the collection are retained and the remaining
ones dropped with a warning.

#### Converting *tidy* data

Spectral objects containing multiple spectra identified by a factor can
be created by row-binding compatible spectral objects. For for binding
to succeed, the list of spectra passed as argument must be homogeneous
with respect to member class, as well as for certain attributes such as
`time.unit`. Other metadata attributes are retained as named lists or
multi-row data frames. We use a time series of sunlight spectra. The
default name `spct.idx` is used for the `idfactor` unless an argument is
passed to parameter `idfactor`.

```{r, bind-1}
sun_evening_12.spct <- rbindspct(sun_evening.mspct[1:2])
sun_evening_12.spct
```

The reverse operation, separating the individual spectra from a spectrum
object containing multiple spectra in *long form* and storing them as a
collection, is implemented in method `subset2mspct`. In this case,
metadata is set for the individual spectra if it is available in the
object being subset. What metadata is automatically stored depends on
the version of this package used when creating the long form spectrum
object by means of `rbindspct()`. Versions 0.9.14 and later preserve
most of the metadata.

```{r, bind-1a}
subset2mspct(sun_evening_12.spct)
```

If multiple spectra are stored in long form (as *tidy* data) in an
ordinary `data.frame` or a `tibble` object with columns with suitable
names, the same `subset2mspct` method can be used. In these case,
arguments indicating the target class for conversion and supplying the
name of the index variable encoding the grouping into multiple spectra
need to be supplied. A call as in the example below, adds only default
metadata to spectral objects.

```{r, bind-2}
test1.df <- data.frame(w.length = rep(200:210, 2),
                       s.e.irrad = rep(c(1, 2), c(11, 11)),
                       spectrum = factor(rep(c("A", "B"), c(11,11))))
subset2mspct(test1.df, member.class = "source_spct", idx.var = "spectrum")
```

If all member spectra share the same metadata, and the constructor has a
parameter allowing it to be set, it can be passed as a named argument. Here
we set the time base of expression of the spectral data to a whole day instead
of the default of using seconds as is usual for irradiance.

```{r, bind-3}
subset2mspct(test1.df, member.class = "source_spct", idx.var = "spectrum",
             time.unit = "day")
```

To directly convert a *tidy* data frame into a long form spectral object
we need to pass the number of spectra through parameter `multiple.wl` to
change the target value of the check for unique wavelength values (default is
`multiple.wl = 1L`). The data should be anyway ordered by increasing wavelength 
and the name of the factor distinguishing the spectra also passed as an 
argument.

```{r, set-class-1}
test2.df <- test1.df
setSourceSpct(test2.df, multiple.wl = 2L, idfactor = "spectrum")
getMultipleWl(test2.df)
getIdFactor(test2.df)
```

If `multiple.wl = NULL` a suitable value is guessed from the data frame
passed as first argument. This should work in most cases, but is more
time consuming. Using this approach in addition disables the check for a
fixed number of spectra.

```{r, set-class-2}
test3.df <- test1.df
setSourceSpct(test3.df, multiple.wl = NULL, idfactor = "spectrum")
getMultipleWl(test3.df)
getIdFactor(test3.df)
```

#### Converting *untidy* data frames

In a *broad form* (or *untidy*) data.frame the spectral values for
different spectra are stored side-by-side as columns, and a single
additional column used to store the shared wavelength values. To create
a collection of spectral objects, with each member containing a single
spectrum, we use function `split2source_mspct` and its equivalents for
the remaining classes of spectral objects (class is determined by the
function used, and columns which are not `numeric` are skipped). The
column containing wavelength values in nanometres is recognized by means
of its name. The names used for the spectra in the collection are
derived from the names of the columns containing numeric (assumed spectral data) 
values.

Using defaults when variables have the names expected by default.

```{r, split-1a}
test2.df <- data.frame(w.length = 200:210, A = 1, B = 2)
split2source_mspct(x = test2.df)
```

If variable names differ from the default expectation, they can be named in the call.

```{r, split-1b}
test3.df <- data.frame(w = 200:210, A = 1, B = 2, z = "Z")
split2source_mspct(x = test3.df, w.length.var = "w", idx.var = "z")
```

The interpretation of the data in the numeric columns other than the wavelengths
can be changed.

```{r}
split2source_mspct(test2.df, spct.data.var = "s.q.irrad")
```

Also in this case, it is possible to pass additional named arguments to
the constructor of spectral objects.

```{r, split-2}
split2source_mspct(test2.df, spct.data.var = "s.q.irrad", time.unit = "day")
```

An additional way of storing spectral data is with one spectrum per row and
one wavelength per coulmn. In such a case, we can transpose the data frame
with function `t()` before pasing it as argument to `split2source_mspct()`,
taking care to copy wavelength values into a column and that the column
names of the transposed data frame match the expected ones.

### Conversion into a "wide" data frame

Sometimes, when exporting spectral data we may need to convert a
collection of spectra into an *untidy* or *wide form* data frame. In the
example below we use a collection with only two member spectra, but
`join_mspct()` can handle collections of any length.

```{r, join-mspct-01}
my.df <- join_mspct(sun_evening.mspct)
head(my.df)
```

### Querying the class

`is.` functions are defined for all the new classes. R's `class` method
can also be used.

```{r, col-query-class-1}
is.source_mspct(sun_evening.mspct)
class(sun_evening.mspct)
```

In addition to using `class` to query the class of the collection, we
can use base R's `lapply` together with `class` or `class_spct` to query
the class of each of the members of the collection.

```{r, col-query-class-2}
is.filter_mspct(sun_evening.mspct)
is.any_mspct(sun_evening.mspct)
class(sun_evening.mspct)
lapply(sun_evening.mspct, class_spct)
lapply(sun_evening.mspct, class)
```

### Extract, replace and combine

R's extraction and replacement methods have specializations for
collections of spectra and can be used with the same syntax and
functionality as for R lists. However they test the class and validity
of the returned objects and replacement members.

------------------------------------------------------------------------

Methods `[`, and `[<-`, extract and replace *parts* of the collection,
respectively. Even when only one member is extracted, the returned value
is a collection of spectra. The expected replacement value is also,
always a collection of spectra.

------------------------------------------------------------------------

```{r, extract-1}
sun_evening.mspct[1]
```

```{r, extract-1a}
sun_evening.mspct[1:3]
```

**Code like that in the chunk below, may be counterintuitive. Collections of
spectra are named lists, consequently assigning by position as shown here swaps
the values without swapping the names of the slots!**

Using summary to check the names and time stamps we can demonstrate this
behaviour.

```{r, extract-2}
# warning: this does not swap the names, even if it swaps the spectra
my.mspct <- sun_evening.mspct
summary(my.mspct, which.metadata = "when.measured")$summary[ , -(2:6)]

# member spectr swapped positions, but not the slot names
my.mspct[1:2] <- my.mspct[2:1]
summary(my.mspct, which.metadata = "when.measured")$summary[ , -(2:6)]

# of course, we can also swap the names if needed
names(my.mspct)[1:2] <- names(my.mspct)[2:1]
summary(my.mspct, which.metadata = "when.measured")$summary[ , -(2:6)]
```

------------------------------------------------------------------------

Methods `[[`, `$` and `[[<-`, extract and replace individual members of
the collection, respectively. They always return or expect objects of
one of the spectral classes.

------------------------------------------------------------------------

```{r, extract-3}
sun_evening.mspct[[1]]
sun_evening.mspct$time.01
sun_evening.mspct[["time.01"]]
```

```{r, extract-4}
# local copy
my.mspct <- sun_evening.mspct
names(my.mspct)
# add computed member
my.mspct[["time.01x2"]] <- my.mspct[["time.01"]] * 2
names(my.mspct)
# delete a member
my.mspct[["time.01x2"]] <- NULL
names(my.mspct)
```

As with R's `list` objects, can combine collections of spectra with
method `c()` but we can not create new collections from individual
spectra using this method. Extraction plus concatenation, moves names 
together with spectra.

```{r, extract-5}
new.spct <- c(my.mspct[5:4], my.mspct[3])
summary(new.spct, which.metadata = "when.measured")$summary[ , -(2:6)]
```

### Random sampling

With large collections of spectra it can be useful to extract a random subset of
spectra. Method `pull_sample()` make this easy for multiple spectra, stored
either in long form or in collections of spectra. (We can set the seed of the
pseudo-random number generator to ensure repeatability).

```{r}
set.seed(1234564)
sampled.mspct <- pull_sample(sun_evening.mspct, size = 2)
summary(sampled.mspct, which.metadata = "when.measured")$summary[ , -(2:6)]
```

```{r}
set.seed(1234564)
sampled.spct <- pull_sample(sun_evening.spct, size = 2)
summary(sampled.spct)
```

### Transform or *apply* functions

For our *apply* functions we follow the naming convention used in
package `plyr`, but using `ms` as prefix for `_mspct` objects. The
*apply* functions implemented in the '**photobiology**' package are
`msmsply`, `msdply`, `mslply` and `msaply` which both accept a
collection of spectra as first argument and return a collection of
spectra, a data frame, a list, or an array respectively (see Table 4).

------------------------------------------------------------------------

**Table 4. Apply functions for collections of spectra.** Key: v., value
returned by *apply* function; f.v., value returned by the applied
function (argument `.fun`). In the table `generic_mspct` and
`generic_spct` indicate objects of these classes or any class derived
from them. The exact class of the collection of spectra object returned
will be determined by the class(es) of the values returned by the
applied function.

| *apply* function | first arg. class | v\. class       | f.v. class     | f.v. length | f.v. dims   |
|:-----------|:-----------|:-----------|:-----------|:-----------|:-----------|
| `msmsply`        | `generic_mspct`  | `generic_mspct` | `generic_spct` | 1           | any         |
| `msdply`         | `generic_mspct`  | `data.frame`    | `numeric`      | $1\ldots n$ | 1           |
| `mslply`         | `generic_mspct`  | `list`          | any            | any         | any         |
| `msaply`         | `generic_mspct`  | `vector`        | any simple     | 1           | 0           |
| `msaply`         | `generic_mspct`  | `matrix`        | any simple     | $2\ldots n$ | $2\ldots n$ |
| `concolve_each`  | `generic_mspct`  | `generic_mspct` | `generic_spct` | 1           | any         |

------------------------------------------------------------------------

Functions `msmsply()`, `msdply` and `mslply` can be used to apply a
function to each member spectrum in a collection. The *apply* function
to use depends on the return value of the applied function.

In the case of `msmsply()` the applied function is expected to return a
*transformed* spectrum as another object of class `generic_spct` or a
class derived from it. The value returned by `msmsply` is a collection
of spectra, of a type determined by the class(es) of the member spectra
in the new collection.

We start with a simple example in which we add a constant to each
spectrum in the collection

```{r, apply-1}
two.mspct <- sun_evening.mspct[1:2]
msmsply(two.mspct, `+`, 0.1)
```

and continue with a more complex example in which we trim each spectrum, and
fill the added values with `NA` values.

```{r, apply-2}
msmsply(two.mspct, trim_wl, range = c(285, 500), fill = NA)
```

In the second example we pass two arguments by name to the applied
function. The number of arguments is not fixed, but the spectrum will be
always passed as the first argument to the function.

In the case of `msdply()` the applied function is expected to return an
R object of the same length for each of the member spectra.

```{r, apply-3}
msdply(two.mspct, max)
```

```{r, apply-4}
ranges.df <- msdply(two.mspct, range)
ranges.df
cat(comment(ranges.df))
```

```{r, apply-5}
msdply(two.mspct, range, na.rm = TRUE)
```

In the case of `mslply()` the applied function is expected to return an
R object of any length, possibly variable among members.

```{r, apply-6}
str(mslply(two.mspct, colnames))
```

In the case of `msaply()` the applied function is expected to return an
R object of length 1, although a list with dimensions will be returned
for longer return values.

```{r, apply-7}
str(msaply(two.mspct, max))
```

```{r, apply-8}
msaply(two.mspct, range)
```

For the most common cases for which one would use the *apply* functions
described in the previous section methods and functions for operations
on collections of spectra are defined in the package. These methods are
described in a later section and listed in Table 9.

### Summary spectra

Starting from a collection of spectra we may want to obtain a single
spectrum containing a summary of them. The current implementation of the
methods described in this section expects that all spectra in a
collection are of the same class, and data is available for each of them
at exactly the same set of wavelengths.

| functions                 | class of argument   | class of returned spectrum | variables in spectrum                |
|:------------------|:---------------|:---------------|:---------------------|
| `s_sum`                   | `source_mspct`      | `source_spct`              | same as input                        |
| `s_sum`                   | `response_mspct`    | `response_spct`            | same as input                        |
| `s_sum`                   | `filter_mspct`      | `generic_spct`             | input tagged `.sum`                  |
| `s_sum`                   | `reflector_mspct`   | `generic_spct`             | input tagged `.sum`                  |
| `s_sum`                   | `calibration_mspct` | `generic_spct`             | input tagged `.sum`                  |
| `s_prod`                  | `source_mspct`      | `source_spct`              | input tagged `.prod`                 |
| `s_prod`                  | `response_mspct`    | `response_spct`            | input tagged `.prod`                 |
| `s_prod`                  | `filter_mspct`      | `filter_spct`              | same as input                        |
| `s_prod`                  | `reflector_mspct`   | `reflector_spct`           | same as input                        |
| `s_prod`                  | `calibration_mspct` | `generic_spct`             | input tagged `.prod`                 |
| `s_mean` or `s_median`    | `source_mspct`      | `source_spct`              | same as input                        |
| `s_mean` or `s_median`    | `response_mspct`    | `response_spct`            | same as input                        |
| `s_mean` or `s_median`    | `filter_mspct`      | `filter_spct`              | same as input                        |
| `s_mean` or `s_median`    | `reflector_mspct`   | `reflector_spct`           | same as input                        |
| `s_mean` or `s_median`    | `calibration_mspct` | `calibration_spct`         | same as input                        |
| `s_var`, `s_se` or `s_sd` | `source_mspct`      | `generic_spct`             | input tagged `.var`, `.se` or `.sd`  |
| `s_var`, `s_se` or `s_sd` | `response_mspct`    | `generic_spct`             | input tagged `.var`, `.se` or `.sd`  |
| `s_var`, `s_se` or `s_sd` | `filter_mspct`      | `generic_spct`             | input tagged `.var`, `.se` or `.sd`  |
| `s_var`, `s_se` or `s_sd` | `reflector_mspct`   | `generic_spct`             | input tagged `.var`, `.se` or `.sd`  |
| `s_var`, `s_se` or `s_sd` | `calibration_mspct` | `generic_spct`             | input tagged `.var`, `.se` or `.sd`  |
| `s_mean_se`               | `source_mspct`      | `source_spct`              | same as input plus col. tagged `.se` |
| `s_mean_se`               | `response_mspct`    | `response_spct`            | same as input plus col. tagged `.se` |
| `s_mean_se`               | `filter_mspct`      | `filter_spct`              | same as input plus col. tagged `.se` |
| `s_mean_se`               | `reflector_mspct`   | `reflector_spct`           | same as input plus col. tagged `.se` |
| `s_mean_se`               | `calibration_mspct` | `calibration_spct`         | same as input plus col. tagged `.se` |
| `s_range`                 | `source_mspct`      | `generic_spct`             | input tagged `.min` and `.max`       |
| `s_range`                 | `response_mspct`    | `generic_spct`             | input tagged `.min` and `.max`       |
| `s_range`                 | `filter_mspct`      | `generic_spct`             | input tagged `.min` and `.max`       |
| `s_range`                 | `reflector_mspct`   | `generic_spct`             | input tagged `.min` and `.max`       |
| `s_range`                 | `calibration_mspct` | `generic_spct`             | input tagged `.min` and `.max`       |

The calculations are done wavelength by wavelength yielding a spectrum
at the same wavelengths than those in the input. Removal of `NA` values
is done wavelength by wavelength. As shown in the table above, depending
on the operation the returned quantity may be equivalent or not to the
quantity in the input. When the quantity changes, even if units of
expression remain the same, the name of the variable and class of the
returned spectrum are different to those in the input.

Methods in this "family" are fast and are specially useful for large
collections of spectra containing even thousands of individual spectra.
Nonetheless, for the example below we use a collection of two spectra.
As computing the mean returns values of the same quantity as in the
input the returned value is a `source_spct` object, in other words of
the same class as the members of `two.mspct`.

```{r}
s_mean(sun_evening.mspct)
```

When we compute the standard error, the quantity returned is not the
same. Consequently, the object returned is in this case a `generic_spct`
instead of `source_spc` as it does not contain spectral irradiance data
as the input did. The variable name is in addition tagged with `.se` to
*advertise* the change in the quantity.

```{r}
s_se(sun_evening.mspct)
```

We can also compute both the mean and standard error simultaneously.

```{r}
s_mean_se(sun_evening.mspct)
```

The other functions in this family work in a similar way to those
described here.

### Convolution

By convolution we normally mean the multiplication value by value at
matching wavelengths of two spectra. The function described in this
section facilitates this and similar operations among collections of
spectra. An example use case could be the convolution of spectral
irradiance by spectral transmittance for all combinations of light
sources and filters in a collection of source spectra and a collection
of filter spectra.

Default operator (or function) is that for multiplication, either one or
both of the two first arguments must be a collection of spectra. When
only one argument is a collection of spectra, the other one can be a
spectrum, or even a numeric vector. For multiplication the order of the
operands does not affect the returned value. With operators or functions
for non-transitive operations the order does, obviously, matter.

Convolution can be used, for example to simulate the effect of an optical
filter on the irradiance from a light source.

```{r, convolve-1}
convolve_each(two.mspct, yellow_gel.spct)
```

```{r, convolve-2}
convolve_each(yellow_gel.spct, two.mspct)
```

```{r, convolve-3}
another_two.mspct <- two.mspct
names(another_two.mspct) <- c("a", "b")
convolve_each(another_two.mspct, two.mspct)
```

The function `convolve_each` will use other operators or functions and
even pass additional named arguments when these are supplied as
arguments.

```{r}
convolve_each(two.mspct, sun.spct, oper = `+`)
```

------------------------------------------------------------------------

There are cases where functions `convolve_each()` and `msmsply()` can be
both used, but there are also cases where their differences matter. An
example is convolving two collections of spectra, a case where only
`convolve_each()` can be used. In contrast, when one of the arguments is
not a spectrum or a collection of spectra, `msmsply()` should be used
instead.

------------------------------------------------------------------------

### Metadata attributes

Some of the `set` and `get` functions used with attributes have method
definitions for collections of spectra. Some examples follow.

```{r, col-attr-1}
when_measured(two.mspct)
when_measured(two.mspct) <- ymd("2015-10-31", tz = "EET")
when_measured(two.mspct)
when_measured(two.mspct) <- list(ymd_hm("2015-10-31 10:00", tz = "EET"),
                                 ymd_hm("2015-10-31 11:00", tz = "EET"))
when_measured(two.mspct) # UTC shown!
two.mspct
```

Other methods available are `getWhereMeasured` and `setWhereMeasured`,
and `getWhatMeasured` and `setWhatMeasured`.

Functions `when.measured2tb()`, `geocode2tb()`, `lon2tb()`, `lat2tb()`
and `what.measured2tb()` extract these same attributes from collection
members into a tibble or data frame. In contrast to the "get" methods
described above, if an existing data frame or tibble with a matching
number of rows is passed as second argument, the values for the
attribute are saved into a new column appended at the right edge of the
tibble or data frame.

```{r}
when_measured2tb(sun_evening.mspct)
```

By default the new column is named after the name of the attribute, but
this default can be overridden by the user.

```{r}
when_measured2tb(sun_evening.mspct, col.names = c(when.measured = "acquisition.time"))
```

Function `spct_metadata()` returns the metadata in a tibble. Unless the
user supplies a list of names of attributes, all applicable metadata
values are returned. A single spectrum or a collection of spectra can be
passed. By default columns containing only missing data are dropped.

```{r}
spct_metadata(two.mspct)
```

```{r}
spct_metadata(two.mspct, 
              col.names = c("when.measured" = "time", 
                            "where.measured" = "geocode"),
              unnest = FALSE)
```

Function `add_attr2tb()` adds one or more columns with attributes to a
tibble or data frame. We here also demonstrate that because the data
frame object is passed to the first positional argument, we can use a
*pipe*. This difference in interface is the main difference between this
function and `spct_metadata()`.

```{r}
q_irrad(two.mspct) %>%
  add_attr2tb(two.mspct, 
              col.names = c("lon", "lat", "when.measured"))
```

We can set the desired names for the columns if we wish them to be
something else than the default.

```{r}
q_irrad(two.mspct) %>%
  add_attr2tb(two.mspct, 
              col.names = c(lon = "longitude", 
                            lat = "latitude", 
                            when.measured = "time"))
```

## Wavebands

When a range of wavelengths or a range of wavelengths plus a spectral
weighting function (SWF) is needed for radiation summaries or
transformations, methods, operators and functions defined in package
'**photobiology**' use `waveband` objects to store these data. A few
other bits of information can be included to fine-tune calculations. The
waveband definitions do NOT describe whether input spectral irradiances
are photon or energy based, nor whether the output irradiance will be
based on photon or energy units. All waveband objects belong to the S3
class `waveband`.

A waveband stores the boundaries of a range of wavelengths, $\lambda_1$
and $\lambda_2$, so that wavelengths within
$\lambda_1 \ge \lambda > \lambda_2$ belong to the waveband. If the
waveband describes a spectral weighting function, in addition to the
range, two formulations of the function used to compute the weights as a
function of wavelength are also stored, $w_E(\lambda)$ and
$w_Q(\lambda)$ to be used with energy- or photon based irradiances.

Spectral weighting functions are normally used to compute effective
irradiances. In the current implementation their use is limited to this
case, while for other summaries only the wavelength range is made use
of, even when weighting functions are available.

### Construction

To create a waveband object we use constructor function `waveband`, and
optionally giving a name to it. **We will use these objects in many of
the examples below, so you will need to run the code chunk bellow to be
able to reproduce those examples.** It should be noted that waveband
constructors for the most frequently used wavelength-range definitions
are provided by package '**photobiologyWavebands**'.

```{r, wb-1}
PAR.wb <- waveband(c(400, 700), wb.name = "PAR")
UVA.wb <- waveband(c(315, 400), wb.name = "UVA")
UVB.wb <- waveband(c(280, 315), wb.name = "UVB")
UVC.wb <- waveband(c(100, 280), wb.name = "UVC")
UV.wb  <- waveband(c(100, 400), wb.name =  "UV")
UV_bands.lst <- list(UVC.wb, UVB.wb, UVA.wb)
```

When including a BSWF, we can supply, one or two versions of functions
returning the weights as a function of wavelength. Several such
functions are defined in package '**photobiologyWavebands**' as well as
waveband constructors using them. Here we show how a waveband can be
defined based on a SWF, using the CIE definition for the erythemal
spectral weighting function. Although the constructor is smart enough to
derive the missing function when only one function is supplied,
performance may suffer unless two performance-optimized function are
provided, one for energy-based effect and a second one for photon-based
effect.

```{r, wb-2}
CIE_e_fun <-
function(w.length){
    CIE.energy <- numeric(length(w.length))
    CIE.energy[w.length <= 298] <- 1
    CIE.energy[(w.length > 298) & (w.length <= 328)] <-
      10^(0.094*(298-w.length[(w.length > 298) & (w.length <= 328)]))
    CIE.energy[(w.length > 328) & (w.length <= 400)] <-
      10^(0.015*(139-w.length[(w.length > 328) & (w.length <= 400)]))
    CIE.energy[w.length > 400] <- 0
    return(CIE.energy)
}
```

```{r, wb-3}
CIE.wb <- waveband(c(250, 400), weight = "SWF",
                   SWF.e.fun = CIE_e_fun, SWF.norm = 298)
```

Another case where you might want to enter the same function twice, is
if you are using an absorptance spectrum as SWF, as the percent of
radiation absorbed will be independent of whether photon or energy units
are used for the spectral irradiance.

The first argument to `waveband()` does not need to be a numeric vector
of length two. Any R object of a class that supplies a `range()` method
definition that can be interpreted as a range of wavelengths in
nanometres can be used. As a consequence, when wanting to construct a
waveband covering the whole range of a spectrum one can simply supply
the spectrum as argument, or to construct an non-weighed waveband which
covers exactly the same range of wavelengths as an existing effective
(weighted) waveband, one can supply a waveband object as an argument.

```{r, wb-4}
waveband(sun.spct)
```

An "empty" waveband is returned by some functions as a "null" value.

```{r}
waveband()
```

### Querying the class

The function `is.waveband` can the used to query any R object. This
function returns a logical value.

```{r, wb-5}
is.waveband(PAR.wb)
```

Above, we demonstrate that `PAR.wb` is a waveband object, the function
`photobiologyWavebands::PAR()` is a waveband constructor returning a
waveband object. See package '**photobiologyWavebands**' for details on
pre-defined waveband constructors for frequently used wavelength ranges
and biological spectral weighting functions (BSWFs).

### Retrieving properties

The function `is_effective` can the used to query any R object.

```{r, wb-6}
is_effective(waveband(c(400,500)))
```

## Collections of wavebands

In the current implementation there is no special class used for storing
collections of `waveband` objects. We simply use base R's `list` class.

### Construction

#### List constructor

Just base R's functions used to create a list object.

```{r, wb-list-1}
wavebands <- list(waveband(c(300,400)), waveband(c(400,500)))
wavebands
```

#### Special constructor

The function `split_bands` can be used to generate lists of non-weighed
wavebands in two different ways: a) it can be used to split a range of
wavelengths given by an R object into a series of adjacent wavebands, or
b) with a list of objects returning ranges, it can be used to create
non-adjacent and even overlapping wavebands.

The code chunk bellow shows an example of two variations of case a).
With the default value for `length.out` of `NULL` each numerical value
in the input is taken as a wavelength (nm) at the boundary between
adjacent wavebands. If a numerical value is supplied to `length.out`,
then the whole wavelength range of the input is split into this number
of equally spaced adjacent wavebands.

```{r, wb-split-1}
split_bands(c(200, 225, 300))
split_bands(c(200, 225, 300), length.out = 2)
```

In both examples above, the output is a list of two wavebands, but the
*split* boundaries are at a different wavelength. The chunk bellow gives
a few more examples of the use of case a).

```{r, wb-split-2}
split_bands(sun.spct, length.out = 2)
split_bands(PAR.wb, length.out = 2)
split_bands(c(200, 800), length.out = 3)
```

Now we demonstrate case b). This case is handled by recursion, so each
list element can be anything that is a valid input to the function,
including a nested list. However, the returned value is always a flat
list of wavebands.

```{r, wb-split-3}
split_bands(list(A = c(200, 300), B = c(400, 500), C = c(250, 350)))
split_bands(list(c(100, 150, 200), c(800, 825)))
```

In case b) if we supply a numeric value to `length.out`, this value is
used recursively for each element of the list.

```{r, wb-split-4}
split_bands(UV_bands.lst, length.out  =  2)
split_bands(list(c(100, 150, 200), c(800, 825)), length.out = 1)
```

## Object *inspection* methods

### Printing

The `print()` method for spectra is based on the method defined in
package '**tibble**', consequently, it is possible to use the options
from this package to control printing. In the code chunk below,
`tibble.print_max`, the number of rows in the spectral object above
which only `tibble.print_min` rows are printed, are both set to 5,
instead of the default 20 and 10, to avoid excessive clutter in our
examples.

```{r, set-up-printing, eval=FALSE}
options(tibble.print_max = 4)
options(tibble.print_min = 4)
```

For explicit calls to `print()` its argument `n` can be used to control
the number of lines printed. If `n` is set to `Inf` the whole spectrum
is always printed. The output differs from that of the `print()` method
from package 'dplyr' in that additional metadata specific to spectra are
shown.

```{r, print-1, eval=FALSE}
print(sun.spct, n = 3)
```

Specialized `print()` methods for collections of spectra and for
`waveband` objects are also defined.

### Summary

The `summary()` method for spectra is based on base R's `summary()`
method for data frames, and accepts the same arguments. The main
difference is that the attributes containing metadata and dimensions of
the original spectrum object are copied to the summary object.

```{r, print-2, eval=FALSE}
summary(sun.spct)
```

Specialized `print()` methods for summaries of spectra are defined. The
output differs from that of the `print()` method from base R in that
additional metadata specific to spectra are shown.

### Handling `NA`s

Functions `na.omit()` and `na.exclude` are implemented for all spectral
classes. These methods test for `NA`s only the spectral data, not
wavelength. They set the `"na.action"` attribute in the same way as the
corresponding methods for data frames. In the case of `na.fail()`,
`na.pass()` and `na.action()`, the methods from base R, can be used with
spectra.

```{r}
na.omit(sun.spct)
na.exclude(sun.spct)
```

## Transformations: using operators

### Binary operators

All of R's built-in maths operators have definitions for spectra. It is
possible to sum, subtract, multiply and divide spectra. These operators
can be used even if the spectral data is on different arbitrary sets of
wavelengths. Operators by default return values expressed in energy
units. Only certain operations are meaningful for a given combination of
objects belonging to different classes, and meaningless combinations
return `NA` also issuing a warning (see Table 5). By default operations
are carried out on spectral energy irradiance for `source_spct` objects
and transmittance for `filter_spct` objects.

------------------------------------------------------------------------

**Table 5. Binary operators and their operands.** Validity and class of
result. All operations marked `\Y' are allowed, those marked`\N' are
forbidden and return `NA` and issue a warning. Operators `%/%` and `%%`
follow `/`.

| e1                 | `+` | `-` | `*` | `/` | `^` | e2                   | value                     |
|:--------|:-------:|:-------:|:-------:|:-------:|:-------:|:--------|:----------|
| `raw_spct`         |  Y  |  Y  |  Y  |  Y  |  Y  | `raw_spct`           | `raw_spct`                |
| `cps_spct`         |  Y  |  Y  |  Y  |  Y  |  Y  | `cps_spct`           | `cps_spct`                |
| `source_spct`      |  Y  |  Y  |  Y  |  Y  |  Y  | `source_spct`        | `source_spct`             |
| `filter_spct` (T)  |  N  |  N  |  Y  |  Y  |  N  | `filter_spct`        | `filter_spct`             |
| `filter_spct` (A)  |  Y  |  Y  |  N  |  N  |  N  | `filter_spct`        | `filter_spct`             |
| `reflector_spct`   |  N  |  N  |  Y  |  Y  |  N  | `reflector_spct`     | `reflector_spct`          |
| `object_spct`      |  N  |  N  |  N  |  N  |  N  | `object_spct`        | --                        |
| `response_spct`    |  Y  |  Y  |  Y  |  Y  |  N  | `response_spct`      | `response_spct`           |
| `chroma_spct`      |  Y  |  Y  |  Y  |  Y  |  Y  | `chroma_spct`        | `chroma_spct`             |
| `raw_spct`         |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `raw_spct`                |
| `cps_spct`         |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `cps_spct`                |
| `calibration_spct` |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `calibration_spct`        |
| `source_spct`      |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `source_spct`             |
| `filter_spct`      |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `filter_spct`             |
| `reflector_spct`   |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `reflector_spct`          |
| `object_spct`      |  N  |  N  |  N  |  N  |  N  | `numeric`            | --                        |
| `response_spct`    |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `response_spct`           |
| `chroma_spct`      |  Y  |  Y  |  Y  |  Y  |  Y  | `numeric`            | `chroma_spct`             |
| `cps_spct`         |  N  |  N  |  Y  |  N  |  N  | `calibration_spct`   | `source_spct`             |
| `source_spct`      |  N  |  N  |  Y  |  Y  |  N  | `response_spct`      | `response_spct`           |
| `source_spct`      |  N  |  N  |  Y  |  Y  |  N  | `filter_spct` (T)    | `source_spct`             |
| `source_spct`      |  N  |  N  |  Y  |  Y  |  N  | `filter_spct` (A)    | `source_spct`             |
| `source_spct`      |  N  |  N  |  Y  |  Y  |  N  | `reflector_spct`     | `source_spct`             |
| `source_spct`      |  N  |  N  |  N  |  N  |  N  | `object_spct`        | --                        |
| `source_spct`      |  N  |  N  |  Y  |  N  |  N  | `waveband` (no BSWF) | `source_spct`             |
| `source_spct`      |  N  |  N  |  Y  |  N  |  N  | `waveband` (BSWF)    | `source_spct` (effective) |

------------------------------------------------------------------------

```{r, bin-oper-1}
sun.spct * sun.spct
```

When meaningful, operations between different spectra are also allowed.
For example, it is possible to simulate the effect of a filter on a
light source by multiplying (or convolving) the two spectra.

```{r, bin-oper-2}
sun.spct * polyester.spct
```

If we have two layers of the filter, this can be approximated using
either of these two statements.

```{r, bin-oper-3}
sun.spct * polyester.spct * polyester.spct
sun.spct * polyester.spct^2
```

Operators are also defined for operations between a spectrum and a
numeric vector (with normal recycling).

```{r, bin-oper-4}
sun.spct * 2
2 * sun.spct
sun.spct * c(0,1)
```

There is one special case, for `chroma_spct`: if the numeric operand has
length three, containing three *named* values *x*, *y* and *z*, the
corresponding value is used for each of the chromaticity *columns* in
the `chroma_spct`. Un-named values or differently named values are not
treated specially.

Operators are also defined for operations between an spectrum and a
`waveband` object. The next to code chunks demonstrate how the class of
the result depends on whether the `waveband` object describes a range of
wavelengths or a range of wavelengths plus a BSWF.

```{r, bin-oper-5}
sun.spct * UVB.wb
```

```{r, bin-oper-6, eval=FALSE}
sun.spct * CIE.wb
```

And of course these operations can be combined into more complex
statements, including parentheses, when needed. The example below
estimates the difference in effective spectral irradiance according to
the CIE98 definition, between sunlight and sunlight filtered with a
polyester film. Of course, the result is valid only for the solar
spectral data used, which corresponds to Southern Finland.

```{r, bin-oper-7, warning=TRUE, purl=FALSE}
sun.spct * CIE.wb - sun.spct * polyester.spct * CIE.wb
```

### Unary operators and maths functions

Many common maths functions, as well as unary minus and plus, are
implemented for spectral objects (see Table 6).

------------------------------------------------------------------------

**Table 6. Unary operators and maths functions for spectra.** Classes
for which they are implemented and class of the result. All operations
marked Y are allowed, those marked N are not implemented and return `NA`
and issue a warning. Additional supported functions:
`log2, log10, sin, cos, tan, asin, acos, atan, sinpi, cospi, tanpi, signif, floor, ceiling, trunc, sign, abs`.

| e1                 | `+, -` | `log, exp` | trig. | `round` | `sqrt` | value              |
|:----------|:---------:|:---------:|:---------:|:---------:|:---------:|:----------|
| `raw_spct`         |   Y    |     Y      |   Y   |    Y    |   Y    | `raw_spct`         |
| `cps_spct`         |   Y    |     Y      |   Y   |    Y    |   Y    | `cps_spct`         |
| `calibration_spct` |   Y    |     Y      |   Y   |    Y    |   Y    | `calibration_spct` |
| `source_spct`      |   Y    |     Y      |   Y   |    Y    |   Y    | `source_spct`      |
| `filter_spct`      |   Y    |     Y      |   Y   |    Y    |   Y    | `filter_spct`      |
| `reflector_spct`   |   Y    |     Y      |   Y   |    Y    |   Y    | `reflector_spct`   |
| `object_spct`      |   N    |     N      |   N   |    N    |   N    | --                 |
| `response_spct`    |   Y    |     Y      |   Y   |    Y    |   Y    | `response_spct`    |
| `chroma_spct`      |   Y    |     Y      |   Y   |    Y    |   Y    | `chroma_spct`      |

------------------------------------------------------------------------

```{r, unary-oper-1}
-sun.spct
sqrt(sun.spct)
```

### Options

Table 7 lists all the recognized options affecting maths operators and
functions, and their default values. Within the suite all functions have
a default value which is used when the options are undefined. Options
are set using base R's function `options`, and queried with functions
`options` and `getOption`.

------------------------------------------------------------------------

**Table 7. Options used in the 'r4photobiology suite' and recognized by
methods, operators and functions in the 'photobiology' package.** Option
names, accepted and default values, and the purpose of the options are
given. Option `photobiology.verbose` is set to the value of R's own
`verbose` option at the time the 'photobiology' package is attached to
the session.

| Option                       | `values`, **default** | purpose, *unit*                                            | *convenience function*                  |
|:--------------|:---------------|:---------------------------|---------------|
| **Base R**                   |                       |                                                            |                                         |
| `digits`                     | 7                     | $d - 3$ used by `summary`                                  |                                         |
| **tibble**                   |                       |                                                            |                                         |
| tibble.print_max             | **20**                | Maximum number of rows printed                             |                                         |
| tibble.print_min             | **10**                | Number of rows printed if row number threshold is exceeded |                                         |
| tibble.width                 | **NULL**              | Output width                                               |                                         |
| **r4photobiology**           |                       |                                                            |                                         |
| photobiology.radiation.unit  | **"energy"**          | $W\,m^{-2}\,nm^{-1}$                                       | `using_energy()`, `energy_as_default()` |
|                              | `"photon"`            | $\mu mol\,m^{-2}\,nm^{-1}$                                 | `using_photon()`, `photon_as_default()` |
| photobiology.filter.qty      | **"transmittance"**   | $/1$                                                       | `using_Tfr()`, `Tfr_as_default()`       |
|                              | `"absorptance"`       | $/1$                                                       | `using_Afr()`, `Afr_as_default()`       |
|                              | `"absorbance"`        | a.u. $\log_{10}$ base                                      | `using_A()`, `A_as_default()`           |
| photobiology.strict.range    | `NA`                  | skip range test                                            | `strict_range_as_default(NA)`           |
|                              | `TRUE`                | trigger an error                                           | `strict_range_as_default(TRUE)`         |
|                              | **FALSE**             | trigger a warning                                          | `strict_range_as_default(FALSE)`        |
| photobiology.check.spct      | **TRUE**              | enable `check_spct()`                                      | `enable_check_spct()`                   |
|                              | `FALSE`               | disable `check_spct()`                                     | `disable_check_spct()`                  |
| photobiology.waveband.trim   | `FALSE`               | exclude                                                    | `wb_trim_as_default(FALSE)`             |
|                              | **TRUE**              | trim or exclude                                            | `wb_trim_as_default(TRUE)`              |
| photobiology.use.cached.mult | **FALSE**             | do not cache intermediate results                          | `use_cached_mult_as_default(FALSE)`     |
|                              | `TRUE`                | cache intermediate results                                 | `use_cached_mult_as_default(TRUE)`      |
| photobiology.verbose         | `FALSE`               | minimal warnings and messages                              | `verbose_as_default(FALSE)`             |
|                              | `TRUE`                | all warnings and messages                                  | `verbose_as_default(TRUE)`              |

The behaviour of the operators defined in this package depends on the
value of two global options. For example, if we would like the operators
to operate on spectral photon irradiance and return spectral photon
irradiance instead of spectral energy irradiance, this behaviour can be
set, and will remain active until unset or reset. It is possible to
change options using base R's function `options()` as shown in the next
code chunk. The other options listed in the Table above can be set
similarly, while to unset any option, they can be given a `NULL` value.

```{r, options-1}
options(photobiology.radiation.unit = "photon")
sun.spct * UVB.wb
options(photobiology.radiation.unit = "energy")
sun.spct * UVB.wb
```

However using convenience functions is easier. The chunk above can be
rewritten as below.

```{r, options-2}
photon_as_default()
sun.spct * UVB.wb
energy_as_default()
sun.spct * UVB.wb
unset_radiation_unit_default()
```

Furthermore, it is possible to temporarily change the options for the
evaluation of a single, possibly compound, R expression using a
different syntax, reminiscent of that of R's `with()`.

```{r, options-3}
using_photon(sun.spct * UVB.wb)
using_energy(sun.spct * UVB.wb)
```

## Transformations: methods and functions

In this section we describe methods and functions that take one or more
spectral objects, and in some cases also waveband objects, as arguments
and return another spectral object (see Tables 8 and 9) or that take a
collection of spectral objects, and in some cases also waveband objects,
as arguments and return a collection of spectral objects.

------------------------------------------------------------------------

**Table 8. Transformation methods for spectra.** Key: + available, --
not available.

| methods               | raw/cps | source | response | filter | reflector | object | chroma |
|:---------|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|
| merge                 |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| rbindspct             |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| e2q, q2e              |   --    |   \+   |    \+    |   --   |    --     |   --   |   --   |
| A2T, T2A              |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| Afr2T, T2Afr          |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| any2T, any2A, any2Afr |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| convertTfrType        |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| convertThickness      |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| subset                |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| clip_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| trim_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| (trim_spct)           |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| thin_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| interpolate_wl        |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| (interpolate_spct)    |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| fscale                |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| fshift                |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| normalize             |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| clean                 |   --    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| despike               |   --    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| *maths operators*     |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| *maths functions*     |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| tag                   |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| untag                 |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |

------------------------------------------------------------------------

------------------------------------------------------------------------

**Table 9. Transformation methods for collections of spectra.** Key: +
available, -- not available, **ms** use `msmsply()` or `convolve_each()`
to apply function or operator to collection members.

| methods               | raw/cps | source | response | filter | reflector | object | chroma |
|:---------|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|
| convolve_each         |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| msmsply               |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| msdply                |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| mslply                |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| msaply                |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| rbindspct             |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| c                     |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| *maths operators*     |   ms    |   ms   |    ms    |   ms   |    ms     |   ms   |   ms   |
| *maths functions*     |   ms    |   ms   |    ms    |   ms   |    ms     |   ms   |   ms   |
| e2q, q2e              |   --    |   \+   |    \+    |   --   |    --     |   --   |   --   |
| A2T, T2A              |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| Afr2T, T2Afr          |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| any2T, any2A, any2Afr |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| convertTfrType        |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| convertThickness      |   --    |   --   |    --    |   \+   |    --     |   --   |   --   |
| clip_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| trim_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| trim2overlap          |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| extend2extremes       |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| (trim_mspct)          |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| thin_wl               |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| interpolate_wl        |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| (interpolate_mspct)   |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| fscale                |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| fshift                |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| normalize             |   \+    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| clean                 |   --    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| despike               |   --    |   \+   |    \+    |   \+   |    \+     |   --   |   --   |
| tag                   |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| untag                 |   --    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |

------------------------------------------------------------------------

### Manipulating spectra

Sometimes, especially for plotting, we may want to row-bind spectra.
When the aim is that the returned object retains its class and other
attributes like the time unit. Package '**photobiology**' provides
function `rbinspct` for row-binding spectra, with the necessary checks
for consistency of the bound spectra.

```{r, manip-1}
# STOPGAP
shade.spct <- sun.spct
```

By default an ID factor named `spct.idx` is added allow to identify the
source of the observations after the binding. If the supplied list has
named members, then these names are used as factor levels. If a
character value is supplied to as `idfactor` argument, this is used as
name for the factor.

```{r, manip-2}
rbindspct(list(sun.spct, shade.spct))
rbindspct(list(A = sun.spct, B = shade.spct), idfactor = "site")
```

The name of the ID factor is stored as metadata in attribute
`"idfactor"` of the spectral data object.

Special *Extract* methods for spectral objects have been implemented.
These are used by default and preserve the attributes used by this
package, except when the returned value is a single column from the
spectral object.

```{r, manip-3}
sun.spct[1:10, ]
sun.spct[1:10, 1]
sun.spct[1:10, 1, drop = TRUE]
sun.spct[1:10, "w.length", drop = TRUE]
```

In contrast to `trim_spct`, `subset` never interpolates or inserts
*hinges*. On the other hand, the `subset` argument accepts any logical
expression and can be consequently used to do subsetting, for example,
based on factors. Both `subset()` and `trim()` methods preserve
attributes.

```{r, manip-4}
subset(sun.spct, s.e.irrad > 0.2)
subset(sun.spct, w.length > 600)
subset(sun.spct, c(TRUE, rep(FALSE, 99)))
```

R's Extract methods `$` and `[[` can be used to extract whole columns.
Replace methods `$<-` and `[<-` have definitions for spectral objects,
which allow their safe use. They work identically to those for data
frames but check the validity of the spectra after the replacement.

### Conversions between radiation units

The functions `e2q` and `q2e` can be used on source spectra to convert spectral
energy irradiance into spectral photon irradiance and vice versa. They can be
also used with response spectra. A second optional argument sets the action with
`"add"` and `"replace"` as possible values. By default these functions use
normal copy semantics but also support reference semantics.

```{r, manip-5}
e2q(sun.spct, "add")
e2q(sun.spct, "replace")
```

When a normalized spectrum is converted, the normalization is reapplied to
the converted data.

### Conversions among transmission quantities

For `filter_spct` objects functions `any2T()`, `any2A()`, and
`any2Afr()` allow conversion among spectral transmittance, spectral
absorptance and spectral absorbance. Although some conversions require a
known reflectance, either as an `Rfr` column in the data or an
`Rfr.constant` in the attribute `filter.properties`.

```{r}
polyester.spct
```

```{r}
any2Afr(polyester.spct, "add")
```

```{r}
any2Afr(polyester.spct, "replace")
```

When a normalized spectrum is converted, the normalization is not reapplied to
the converted data. _This will change in the future._

### Normalizing a spectrum

Normalization is a way rescaling a spectrum so that the spectral
quantity takes a fixed value, in most cases exactly 1, at a specific
wavelength. Frequently this wavelength corresponds to the maximum value
of the spectral quantity.

$$Q_\mathrm{norm}(\lambda) = \frac{Q(\lambda)}{\max{Q(\lambda)}}$$ When
normalizing to a specific wavelength, say 300 nm, the equation becomes
$$Q_\mathrm{norm}(\lambda) = \frac{Q(\lambda)}{{Q(\lambda = 300)}}$$
Function `normalize` permits normalizing a spectrum to a value of one at
an arbitrary wavelength (nm) or to the wavelength of either the maximum
or the minimum spectral value. It supports all the different spectral
classes. In the example we use a `source_spct` object. (Equivalent
functions with names spelled with "s" instead of "z" are available.)

```{r, manip-6}
normalize(sun.spct)
```

Which is equivalent to supplying `"max"` as argument to `norm`, it is
also possible to give a range within which the maximum should be
searched.

```{r, manip-7}
normalize(sun.spct, range = PAR.wb, norm = "max")
```

It is also possible to normalize to an arbitrary wavelength within the
range of the data, even if it is not one of the wavelength values
present in the spectral object, as interpolation is used when needed.

```{r, manip-8}
normalize(sun.spct, norm = 600.3)
```

The normalization status of a spectral object can be tested with method
`is_normalized()` and the normalization used can be recalled with method
`getNormalized()`.

```{r}
my.spct <- normalize(sun.spct)
is_normalized(my.spct)
getNormalized(my.spct)
```

Once a spectrum is normalized, summary methods that return values in
absolute units such as `irrad()`, will trigger an error if applied.
Ratios and similar summaries that are invariant with respect to
normalization can be calculated. Already normalized spectra can be normalized
again.

Applying method `fscale()` removes the normalization and clears the
corresponding attribute where the normalization information is stored.
This attribute also can be cleared with method `setNormalized()`, but
this is rarely valid or of any use.

### Rescaling a spectrum

While normalization is done with respect to a single wavelength,
rescaling as implemented in this package is more flexible. The scaling
factor is computed as a summary over a range of wavelengths. This allows
us, among other things to rescale spectral irradiance so that irradiance
in a specific waveband is equal to one, or to some other user supplied
target value.

$$Q^\prime(\lambda) = \frac{Q(\lambda)}{f(Q(\lambda))_{\ \mathrm{for}\ \ \lambda_1\geq\lambda>\lambda_2}}\times \alpha$$
where $\alpha$ is the target value for $f(Q(\lambda))$.

In other words, function `fscale()` rescales a spectrum by dividing each
spectral data value by a value calculated with a function (f) selected
by a character string ("total" or "mean"), or an actual R function which
can accept the spectrum object supplied as its first argument.
Additional named arguments can be also passed.

How metadata is set in the returned object is controlled by a logical
argument to parameter `set.scaled`. If `TRUE`, the data are labelled as
being expressed in relative units and if `FALSE` this attribute is not
set. The default argument depends on the value passed as argument to
`target`. If this value is one, then the data are marked as no longer
being expressed in absolute units. If the `target` is any other numeric
value then it is assumed that the intention is to re-scale the data and
that absolute physical units remain meaningful. It is important that the
metadata matches the actual use as printing of summaries and plot
labelling depends on them.

```{r, manip-9}
fscale(sun.spct)
fscale(sun.spct, set.scaled = FALSE)
fscale(sun.spct, target = 100)
fscale(sun.spct, target = 100, set.scaled = TRUE)
```

The default for `f` can be overridden. R functions passed as argument
should be suitable for summarizing spectral objects as they will receive
as first argument a spectrum rather than a numeric vector. Behind this
requirement is the need to take into account wavelength steps for
integration to be meaningful. In the example below we compute energy and
photon irradiances. (The character arguments `"mean"` and `"total"` call
functions specific to spectral data.)

```{r, manip-9a}
fscale(sun.spct, f = "integral")
fscale(sun.spct, range = PAR.wb, f = e_irrad)
fscale(sun.spct, range = PAR.wb, f = q_irrad, target = 800e-6)
```

In the third example, the spectral data is rescaled so that the
corresponding photosynthetically-active irradiance is equal to one.

The normalization status of a spectral object can be tested with method
`is_normalized()` and the normalization used can be recalled with method
`getNormalized()`.

```{r, manip-9b}
my.spct <- fscale(sun.spct)
is_scaled(my.spct)
getScaled(my.spct)
```

Once a spectrum is scaled, summary methods that return values in
absolute units such as `irrad()`, will trigger a warning if applied.
Ratios and similar summaries that are invariant with respect to
normalization do not trigger warnings.

Applying method `normalize()` removes the scaling and clears the
corresponding attribute where the scaling information is stored. This
attribute also can be cleared with method `setScaled()`, and this can be
useful is some cases such as when irradiance has been measured
separately from the emission spectrum.

### Shifting the zero of the spectral data scale

While re-scaling relies on a multiplicative factor shifting of the scale
is done by addition (or subtraction) or constant. This allows us, among
other things to remove a baseline computed from a region known to be
equal to zero.

$$Q^\prime(\lambda) = Q(\lambda) - f(Q(\lambda))_{\ \mathrm{for}\ \ \lambda_1\geq\lambda>\lambda_2}$$
Function `fshift()` shifts the zero of the scale of a spectrum by
subtracting from each spectral data value a value calculated with a
function (f) selected by a character string ("mean", "min" or "max"), or
an actual R function which can accept the spectrum object supplied as
its first argument. The range argument selects a region of the spectrum
to be used as *reference* in the calculation of the summary.

```{r, manip-10}
fshift(white_led.source_spct, range = UVB.wb, f = "mean")
fshift(sun.spct, range = c(280,290), f = "min")
```

In the first example, the spectral data shifted so that the mean
spectral irradiance becomes zero for the UV-B region. In the second
example the minimum value in the range of wavelengths between 280\~nm
and 290\~nm is used as zero reference for the scale.

### Replacing off-range spectral data values

Method `clean()` should be used with care as off-range values stem
almost always from calibration errors or measuring noise. This function
allows one to replace such values, but in many cases a zero shift or
rescaling could be a better option. Even when the off-range values are
the result of random noise, replacing them with the boundary values can
cause bias, by censoring the data. In such cases smoothing may be
applied first to reduce the possible bias caused by `clean()`. Here we
create *artificial* off-range values by subtracting a constant from each
spectrum.

```{r, manip-11}
clean(polyester.spct - 0.053)
```

It is possible to restrict the *cleaning* to a range of wavelengths and
to provide a value to be used as replacement for the off-range data.

```{r, manip-11a}
clean(sun.spct - 0.01, range = c(280.5, 282), fill = NA)
```

### Removing spikes

Method `despike()` replaces spikes (very narrow peaks, or valleys) by
values estimated from neighbouring pixels. This method should be also
used carefully and the results inspected as it can remove features of
interest from the data. Usually one knows from theory or experience if
spikes can be real features or not.

```{r, manip-12}
spikes(sun.spct)
```

```{r, manip-12a}
my_sun.spct <- despike(sun.spct)
spikes(my_sun.spct)
```

### Smoothing of spectra

We can use smoothing both to average out random variation among nearby
pixels caused by measuring noise, or to filter out the real fine
structure of a spectrum to better assess the larger features. The
methods described here work by averaging the spectral data from
neighbouring wavelengths. The simplest methods are running medians and
running means (or "boxcar smoothing" in the terminology used in some
software). There are several methods for smoothing available in R based
on different algorithms. Some of these methods also automatically set
the degree of smoothing based on the data being smoothed. Package
'photobiology' defines function `smooth_spct`, which at the moment
supports three different methods. Two are wrappers on R's own methods
and a third one, `"custom"`, is designed to use stronger smoothing for
values close to zero, where noise in spectral irradiance measurements is
proportionally more. The strength of the smoothing and the range of
wavelengths operated upon can be adjusted through arguments to
parameters. The `comment` attribute is updated.

```{r}
smooth_spct(sun.spct)
```

```{r}
smooth_spct(polyester.spct, method = "supsmu", strength = 2)
```

### Wavelength interpolation

Converting spectra available at a given set of wavelengths values to a
different one, is frequently needed when operating with several spectra
of different origin. One can increase the *apparent* resolution by
interpolation, and reduce it by local averaging or smoothing and
resampling. The same function works on all `spct` objects, interpolating
every numeric column except `w.length` which is set to the new
wavelength values supplied as argument. The optional argument
`fill.value` controls what value is assigned to the "interpolated" data
columns at wavelengths in the new data that are outside the range of
wavelengths in the original spectrum being interpolated.

```{r, manip-13}
interpolate_wl(sun.spct, seq(400, 500, by = 0.1))
```

### Trimming, clipping and thining

#### Method `clip_wl()`

Sometimes it is desirable to change the range of wavelengths included in
a spectrum. If we are interested in a given part of the spectrum, there
is no need to do calculations or plotting the whole spectrum. To select
part of a spectrum based on a range of wavelengths we may use the
`clip_wl()` method. Method `clip_wl()` simply selects a range from the
existing spectrum, and unless the range exactly matches the wavelength
values present in the spectrum, the range of wavelengths in the returned
clipped spectrum will be slightly narrower than the requested by
`range`.

The range of wavelengths expressed in nanometres can be given as numeric
vector of length two.

```{r, trim-1}
clip_wl(sun.spct, range = c(400, 402))
clip_wl(sun.spct, range = c(400, NA))
```

As for other methods in the package, the range can be also supplied as a
`waveband` object, or any other object for which `range()` returns a
numeric range. Even a different spectrum object is acceptable, and in
many cases useful.

```{r, trim-2}
clip_wl(sun.spct, range = UVA.wb)
```

The result can be a spectrum of length zero.

```{r, trim-3}
clip_wl(sun.spct, range = c(100, 200))
```

#### Method `trim_wl()`

Sometimes, we need more flexibility. We may want to replace the observed
values outside a certain range or expand the range of wavelengths,
filling the expansion of all other variables with a certain value (i.e.
a number, or NA.). In contrast to *clipping* (or functionally
equivalent, indexing, or subsetting), *trimming* ensures that there will
be spectral data returned at the boundaries of the trimmed region. These
values are obtained by interpolation when they are not already present
in the data.

More flexibility is available in method `trim_wl()`, to which we can
supply arguments `range`, `use.hinges`, and `fill`. By default
interpolation is used at the boundaries of the `range`, in which case
the range of wavelengths in the returned spectrum is that passed as
argument to `range`.

```{r, trim-4}
trim_wl(sun.spct, c(282.5, NA))
clip_wl(sun.spct, c(282.5, NA))
```

As for `clip_wl()` the range can be also supplied as a `waveband`
object, or any other object for which `range()` returns a numeric range.
Even a different spectrum object is acceptable.

```{r, trim-5}
trim_wl(sun.spct, PAR.wb)
```

The default for `fill` is `NULL` which results in deletion values
outside the trimmed region. However, it is possible to supply a
different argument, to be used to replace the off-range data values.

```{r, trim-6}
trim_wl(sun.spct, c(281.5, NA), fill = NA)
```

Furthermore, when fill is not `NULL`, expansion is possible.

```{r, trim-7}
trim_wl(sun.spct, c(275, NA), fill = 0)
```

By default interpolation at the boundaries is used, but setting
`use.hinges` to `FALSE` results in clipping, a behaviour similar to that
of `clip_wl` only if `fill == NULL`.

```{r, trim-8}
trim_wl(sun.spct, c(281.5, NA), fill = NA)
trim_wl(sun.spct, c(281.5, NA), fill = NA, use.hinges = FALSE)
```

When `use.hinges == TRUE` and expansion or replacement is done, two
observations are inserted at each boundary, differing in wavelength by
$1 \times 10^{-12}$,nm to prevent rounding errors in later calculations.

#### Functions `trim2ovelap()` and `extend2extremes()`

Functions `trim2ovelap()` and `extend2extremes()` are defined only for
collections of spectra. They are convenience functions, as they handle
special use cases of `trim_wl()` with a simplified syntax. They can be
used to make the wavelength range of the different members of a
collection of spectra consistent, either by trimming all spectra to the
range of overlapping wavelengths, or by extending the wavelength ranges
as needed and filling the added spectral values with a constant value.

```{r}
trim2overlap(two.mspct)
```

```{r}
extend2extremes(two.mspct, fill = 0)
```

#### Method `thin_wl()`

One possible way of decreasing the storage space occupied by spectral
data is to vary the density of wavelength values stored based on the
local change in slope (second derivative) of the plot a spectrum. Method
`thin_wl()` can be used to remove or "thin" down the wavelength values
stored in those regions of the spectrum where this would result in
minimal loss of information. The algorithm currently in use is
suboptimal in the removal of wavelength values but fast and easy to
implement. **Which wavelength values are retained or not could change
with future implementations.**

```{r}
nrow(yellow_gel.spct)
wl_stepsize(yellow_gel.spct)
thinned.spct <- thin_wl(yellow_gel.spct)
nrow(thinned.spct)
wl_stepsize(thinned.spct)
```

The strength of the thinning can be adjusted by passing arguments to
parameters `max.wl.step` and `max.slope.delta`. This method is
implemented for objects of all spectral classes that a single default
data column in addition to wavelengths and also for collections of those
objects.

**NOTE:** Thinning, obviously, almost always changes spectra originally
expressed at the same set of wavelength values into spectra expressed at two
different sets of wavelengths values. This forbid some operations among
them, like _parallel_ operations in collections of spectra or combining
them into a wide data frame. Most of these restrictions have been removed
by implementing on-the-fly interpolation in version 0.10.15.

### Convolving weights

It is very instructive to look at weighted spectral data to understand
how effective irradiances are calculated. Plotting effective spectral
irradiance data can be very informative when analysing interactions
among photoreceptors and ambient radiation. It can also illustrate the
large effect that small measuring errors can have on the estimated
effective irradiances or exposures when SWFs have a steep slope.

For biologically effective energy irradiance $E_\mathrm{BE}$ the
following equation describes the convolution, wavelength by wavelength,
between spectral energy irradiance and a biological spectral weighting
function

$$E_\mathrm{BE}(\lambda) = E(\lambda) \times w_E(\lambda)$$ or for
biologically effective photon irradiance $Q_\mathrm{BE}$
$$Q_\mathrm{BE}(\lambda) = Q(\lambda) \times w_Q(\lambda)$$ For the
convolution to be possible, both spectral irradiance and spectral
weights should be available for the same basis of expression and at the
same discrete wavelength values.

#### Individual spectra

The multiplication operator is defined for operations between a
`source_spct` and a `waveband`, so this is the easiest way of doing the
calculations.

```{r, weights-1}
sun.spct * CIE.wb
```

### Tagging with bands and colours

We call tagging, to the process of adding reference information to
spectral data. For example we can add a factor indicating regions or
bands in the spectrum. We can add also information on the colour, as
seen by humans, for each observed value, or for individual regions or
bands of the spectrum. In most cases this additional information is used
for annotations when plotting the spectral data.

#### Individual spectra

The function `tag` can be used to tag different parts of a spectrum
according to wavebands.

```{r, tag-1}
tag(sun.spct, PAR.wb)
tag(sun.spct, UV_bands.lst)
```

The added factor and colour data can be used for further processing or
for plotting. Information about the tagging and wavebands is stored in
an attribute `tag.attr` in every tagged spectrum, this yields a more
compact output and keeps a *trace* of the tagging.

```{r, tag-2}
tg.sun.spct <- tag(sun.spct, PAR.wb)
attr(tg.sun.spct, "spct.tags")
```

Additional functions are available which return a tagged spectrum and
take as input a list of wavebands, but no spectral data. They *build* a
spectrum from the data in the wavebands, and are useful for plotting the
boundaries of wavebands.

```{r, tag-3}
wb2tagged_spct(UV_bands.lst)
wb2rect_spct(UV_bands.lst)
```

Function `wb2tagged_spct` returns a tagged spectrum, with two rows for
each waveband, corresponding to the low and high wavelength boundaries,
while function `wb2rect_spct` returns a spectrum with only one row per
waveband, with `w.length` set to its midpoint but with additional
columns `xmin` and `xmax` corresponding to the low and high wavelength
boundaries of the wavebands.

Function `is_tagged` can be used to query if an spectrum is tagged or
not, and function `untag` removes the tags.

```{r, tag-4}
tg.sun.spct
is_tagged(tg.sun.spct)
untg.sun.spct <- untag(tg.sun.spct)
is_tagged(untg.sun.spct)
```

In the chuck above, we can see how this works, using in this case the
default `byref = FALSE` which adds the tags to a copy of the spectrum
object. In contrast, setting `byref = TRUE` adds the tags in place, or
"by reference"", to the spct object supplied as argument. Passing
arguments by reference is unusual for R and is best avoided.

```{r}
is_tagged(untg.sun.spct)
untag(tg.sun.spct, byref = TRUE)
is_tagged(untg.sun.spct)

```

## Summaries

Summaries can be calculated both from individual spectral objects (Table
10) and from collections of spectral objects (Table 11). They return a
*simpler* object than the spectral data in their arguments. For example
a vector of numeric values, possibly of length one, in the case of
individual spectra, or a data frame containing one row of summary data
for each spectrum in a collection of spectra.

------------------------------------------------------------------------

**Table 10. Summary methods for spectra.** Key: + available, - not
available, (+) object_spct objects can be converted into filter_spct or
reflector_spct objects before applying these methods.

| methods        | raw/cps | source | response | filter | reflector | object | chroma |
|:---------------|:-------:|:------:|:--------:|:------:|:---------:|:------:|:------:|
| irrad          |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| e_irrad        |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| q_irrad        |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| fluence        |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| e_fluence      |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| q_fluence      |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| ratio          |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| e_ratio        |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| q_ratio        |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| qe_ratio       |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| eq_ratio       |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |
| response       |   --    |   --   |    \+    |   --   |    --     |   --   |   --   |
| e_response     |   --    |   --   |    \+    |   --   |    --     |   --   |   --   |
| q_response     |   --    |   --   |    \+    |   --   |    --     |   --   |   --   |
| transmittance  |   --    |   --   |    --    |   \+   |    --     |   \+   |   --   |
| absorptance    |   --    |   --   |    --    |   \+   |    --     |   \+   |   --   |
| absorbance     |   --    |   --   |    --    |   \+   |    --     |   \+   |   --   |
| reflectance    |   --    |   --   |    --    |   --   |    \+     |   \+   |   --   |
| wl_range       |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| wl_min         |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| wl_max         |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| wl_stepsize    |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| wl_expanse     |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| wl_midpoint    |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| labels         |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| summary        |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| peaks          |   --    |   \+   |    \+    |   \+   |    \+     |  (+)   |   \-   |
| spikes         |   --    |   \+   |    \+    |   \+   |    \+     |  (+)   |   \-   |
| valleys        |   --    |   \+   |    \+    |   \+   |    \+     |  (+)   |   \-   |
| wls_at_target  |   --    |   \+   |    \+    |   \+   |    \+     |  (+)   |   \-   |
| integrate_spct |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| average_spct   |   \+    |   \+   |    \+    |   \+   |    \+     |   \+   |   \+   |
| color_of       |   --    |   \+   |    --    |   --   |    --     |   --   |   --   |

------------------------------------------------------------------------

As mentioned above, summary methods for collections of spectra return
data frame objects. In many cases preserving the attributes from the
different members of the collection in the returned value is important,
and can be achieved easily by passing a suitable character vector as
argument to parameter `attr2tb`, using the same syntax as described for
function `add_attr2tb`.

------------------------------------------------------------------------

**Table 11. Summary methods for collections of spectra.** Key: +
available, \* `attr2tb` supported, -- not available, **ms** use
`msmsply()` to apply function to collection members, **d** use
`msdply()`, **l** use `mslply` to apply function to collection members,
**a** use `msaply` to apply function to collection members.

| methods        |   raw/cps   |   source    |  response   |   filter    |  reflector  |   object    |   chroma    |
|:--------|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|:-------:|
| irrad          |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| e_irrad        |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| q_irrad        |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| fluence        |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| e_fluence      |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| q_fluence      |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| ratio          |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| e_ratio        |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| q_ratio        |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| qe_ratio       |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| eq_ratio       |     --      |     \*      |     --      |     --      |     --      |     --      |     --      |
| response       |     --      |     --      |     \*      |     --      |     --      |     --      |     --      |
| e_response     |     --      |     --      |     \*      |     --      |     --      |     --      |     --      |
| q_response     |     --      |     --      |     \*      |     --      |     --      |     --      |     --      |
| transmittance  |     --      |     --      |     --      |     \*      |     --      |     \*      |     --      |
| absorptance    |     --      |     --      |     --      |     \*      |     --      |     \*      |     --      |
| absorbance     |     --      |     --      |     --      |     \*      |     --      |     \*      |     --      |
| reflectance    |     --      |     --      |     --      |     --      |     \*      |     \*      |     --      |
| color_of       |     --      |     \+      |     --      |     --      |     --      |     --      |     --      |
| wl_range       |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| wl_min         |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| wl_max         |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| wl_stepsize    |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| wl_spread      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| wl_midpoint    |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |     \+      |
| labels         |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |
| summary        |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |    **l**    |
| peaks          |     --      |     \+      |     \+      |     \+      |     \+      |     (+)     |     \-      |
| valleys        |     --      |     \+      |     \+      |     \+      |     \+      |     (+)     |     \-      |
| spikes         |     --      |     \+      |     \+      |     \+      |     \+      |     (+)     |     \-      |
| wls_at_target  |     --      |     \+      |     \+      |     \+      |     \+      |     (+)     |     \-      |
| integrate_spct | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** |
| average_spct   | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** | **a, d, l** |

------------------------------------------------------------------------

### Summary

Specialized definitions of `summary` and the corresponding `print`
methods are available for spectral objects. Attributes
`"what.measured"`, `"when.measured"` and `"where.measured"` are included
in the summary print out only if set in the spectral object summarized.

```{r, summary-1}
summary(sun.spct)
```

```{r, summary-2}
summary(sun_evening.spct)
```

```{r, summary-2a}
summary(sun_evening.mspct)
```

### Wavelength

#### Individual spectra

The *usual* and three new summary methods are available for spectra, but
redefined to return wavelength-based summaries in nanometres (nm). For
clarity synonyms with clearer names are provided. The three new generic
methods `midpoint()`, `expanse()` and `stepsize()` are also defined for
`numeric`.

```{r, summary-3}
wl_range(sun.spct)
wl_min(sun.spct)
wl_max(sun.spct)
wl_midpoint(sun.spct)
wl_expanse(sun.spct)
wl_stepsize(sun.spct)
```

#### Collections of spectra

------------------------------------------------------------------------

Most frequently used summary methods are implemented for collections of
spectra. See the Table 11 for those methods that need to be applied with
functions `msaply`, `msdply` or `mslply` to members in a collection
returning the results in an array (vector, or matrix), a data frame or a
list object. In many cases depending of the class desired for the
result, one can chose a suitable *apply* function, and sometimes it is
best to use such a function, even when the corresponding method is
implemented for collections of spectra.

------------------------------------------------------------------------

Collections of spectra can be useful not only for time-series of spectra
or spectral images, but also when dealing with a small group of related
spectra. In the example below we show how to use a collection of spectra
for calculating summaries. The spectra in a collection do **not** need
to have been measured at the same wavelength values, or have the same
number of rows or even of columns. Consequently, in many cases applying
the wavelength summary functions described above to collections of
spectra can be useful. The value returned is a data frame, with a number
of data columns equal to the length of the returned value by the
corresponding method for individual spectra.

```{r, summary-4}
filters.mspct <- filter_mspct(list(none = clear.spct,
                                   pet = polyester.spct,
                                   yellow = yellow_gel.spct))
wl_range(filters.mspct)
```

### Peaks, valleys and spikes

Peaks and valleys in spectra are usually features of interest, while in
most cases spikes (very narrow peaks or valleys) are undesired "noise".
Of course, there are exceptions and for this reason methods used for
extract any of these features have a similar interface.

Peaks and valleys can be identified simply as local maxima and minima,
or their actual location better estimated by fitted a model to the local
maximum or minimum and its neighbours.

#### Individual spectra

Methods `peaks` and `valleys` take spectra as first argument and return
a subset of the spectral object data corresponding to local maxima and
local minima of the measured variable. `span` defines the width of the
*window* used as a number of observations.

```{r, summary-5}
peaks(sun.spct, span = 51)
valleys(sun.spct, span = 51)
```

In the case of `source_spct` and `response_spct` methods `unit.out` can
be used to force peaks to be searched using either energy or photon
based spectral irradiance. The default is energy, or the option
`"photobiology.radiation.unit"` if set.

```{r, summary-6}
peaks(white_led.source_spct, 
      span = 101, 
      unit.out = "photon")$w.length
```

By passing `refine.wl = TRUE` we request that location of the peaks is
*refined* by fitting a model to describe the peak.

```{r, summary-6a}
peaks(white_led.source_spct, 
      span = 101, 
      unit.out = "photon", 
      refine.wl = TRUE)$w.length
```

It is possible to approximately set the width in nanometres of the
moving window within which a maximum is searched by passing an odd
number as argument to `span`. However, even numbers if passed are
increased with a warning.

```{r, summary-7}
peaks(sun.spct, span = 21)
```

A value of `NULL` as argument to `span` searches for a single maximum
for the whole spectrum.

```{r, summary-8}
peaks(sun.spct, span = NULL)
```

The position of peaks can be refined by spline interpolation. This is
still an experimental feature, that may fail, especially in the estimate
of the value of the spectral quantity at the peak.

```{r, summary-9}
peaks(sun.spct, span = NULL, refine.wl = TRUE)
```

Method `spikes` differs from `peaks` in that it uses a different
algorithm that detects only very narrow peaks, usually called by the
name of spikes. The value returned is as in the case of `peaks` a subset
of the original spectrum. The parameters controlling the sensitivity
also differ.

```{r, summary-10}
spikes(sun.spct)
```

Low level functions `find_peaks`, `get_peaks`, `get_valleys`,
`fit_peaks`, `fit_valleys`, and `find_spikes` take numeric vectors as
first argument.

#### Collections of spectra

The methods are also implemented for collections of spectra.

```{r, col-summary-1}
msmsply(filters.mspct, peaks, span = 21)
```

Two of the filters in the collection do not have peaks, and a spectrum
object of length zero is returned for them.

### Wavelengths at target value

Method `wls_at_target` takes a spectrum as first argument and returns a
subset of the spectral object data or a new object corresponding to
wavelengths at which the spectrum is at the target value. Geometrically
is equivalent to finding the wavelengths at which a horizontal *target*
line intercepts the curve depicting the spectrum.

```{r, find-wls-1}
wls_at_target(Ler_leaf_trns.spct, target = "half.maximum")
wls_at_target(Ler_leaf_trns.spct, target = "half.maximum", interpolate = TRUE)
```

This function can be used with all spectral classes defined in the
package. In the case of `source_spct` and `response_spct` methods
parameter `unit.out` allows to switch between energy and photon units
for the search and returned value, while in the case of `filter_spct`
methods filter.qty\` allows to switch between transmittance, absorptance
and absorbance.

#### Collections of spectra

The method is also implemented for collections of spectra.

```{r, find-wls-2}
wls_at_target(filters.mspct, target = "half.maximum")
```

### Irradiance

Energy irradiance is the integral over wavelengths of spectral energy
irradiance

$$E = \int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda)\ \mathrm{d}\lambda$$
where $\lambda_1 \geq \lambda > \lambda_2$ defines a waveband, or range
of wavelengths.

Photon (=quantum) irradiance is the integral over wavelengths of
spectral photon irradiance.

$$Q = \int_{\lambda = \lambda_1}^{\lambda = \lambda_2} Q(\lambda)\ \mathrm{d}\lambda$$
Spectrally weighted (or biologically effective) energy irradiance is the
integral of the result of the convolution of spectral energy irradiance
by a spectral weighting function $w(\lambda)$.

$$E_{BE} = \int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda) \cdot w_E(\lambda)\ \mathrm{d}\lambda$$
Spectrally weighted (or effective) photon irradiance can be computed
similarly with the corresponding weighting function $w_Q(\lambda)$.

#### Individual spectra

The code using `spct` objects is simple; to integrate the whole spectrum
we can use `irrad()` that returns by default energy irradiance, unless
an R option is set to make photon-based units the default. When this
flexibility is not needed, `e_irrad()` and `q_irrad()` should be
preferred. For most examples we use energy-based units and `e_irrad()`,
but they also apply unchanged to `q_irrad()` and photon-based units, and
*vice-versa* for those examples using `q_irrad()`.

The abbreviations *E* and *Q* are used to denote these two quantities,
usually with the waveband as a subscript. In what follows "Total" as
subscript denotes the whole range of wavelengths in the spectrum. This
is the default.

```{r, irrad-1}
e_irrad(sun.spct)
```

To integrate one restricted range of wavelengths from a spectrum, we can
provide a wavelength definition. In this example, waveband `PAR.wb`
giving the definition of *photosynthetically active radiation*.
(`PAR.wb` was defined above.)

```{r, irrad-2}
e_irrad(sun.spct, PAR.wb)
```

It is also valid to pass as argument for `w.band` a numeric range
representing wavelengths in manometers (nm), which is converted into a
waveband definition on-the-fly. Note, however, that the automatically
assigned name gives only the range.

```{r, irrad-3}
e_irrad(sun.spct, c(400, 700))
```

The 'photobiology' package uses base SI units, so by default photon
irradiance (= quantum irradiance) is expressed in $mol\,s^{-1}\,m^{-2}$.
We can pass a scaling factor as shown below if needed.

```{r, irrad-4a}
q_irrad(sun.spct, PAR.wb, scale.factor = 1e6) # umol s-1 m-2
```

It is possible to supply a time unit to use, instead of the default of
seconds, as basis of expression for the returned value. However, be
aware that conversion into a different time unit than that used during
measurement, is only valid for sources like lamps, which have an output
the remains constant in time.

```{r, irrad-5}
q_irrad(white_led.source_spct, PAR.wb, time.unit = "hour")
```

Using a shorter time unit than the original, yields an average value
re-expressed on a new time unit base.

```{r, irrad-6}
e_irrad(sun_daily.spct, PAR.wb, time.unit = "second")
```

Lists of wavebands are also accepted as argument for parameter `w.band`
in which case a named numeric vector of summary values is returned by
default.

```{r, irrad-7}
e_irrad(sun.spct, UV_bands.lst) # W m-2
```

```{r, irrad-7a}
q_irrad(sun.spct, UV_bands.lst) # mol s-1 m-2
```

```{r, irrad-7b}
q_irrad(sun.spct, UV_bands.lst, scale.factor = 1e6) # umol s-1 m-2
```

These functions have an additional argument `quantity`, with default
`"total"`, which can take values controlling the output. The value
"total" yields **irradiance** in $W\,m^{-2}$, integrated over
wavelengths for each waveband, while "average" yields the mean
**spectral irradiance** within each waveband in $W\,m^{-2}\,nm^{-1}$.

```{r, irrad-8a}
e_irrad(sun.spct, UV_bands.lst, quantity = "total") # watt m-2
```

```{r, irrad-8b}
e_irrad(sun.spct, UV_bands.lst, quantity = "average") # watt m-2 nm-1
```

When `quantity = "contribution"` irradiances for individual wavebands
are expressed relative to the irradiance computed for the whole
spectrum, while for `quantity = "relative"` they are expressed relative
to the sum of the irradiances for all the wavebands. In both cases
values are expressed as fractions of one.

```{r, irrad-8c}
e_irrad(sun.spct, UV_bands.lst, quantity = "contribution")
```

```{r, irrad-8cc}
e_irrad(sun.spct, UV_bands.lst, quantity = "relative")
```

When setting `"contribution.pc"` or `"relative.pc"` as `quantity` the
same values as in the examples above, are expressed as percentages
instead of fractions.

```{r, irrad-8d}
e_irrad(sun.spct, UV_bands.lst, quantity = "contribution.pc")
```

```{r, irrad-8dd}
e_irrad(sun.spct, UV_bands.lst, quantity = "relative.pc")
```

The total radiation received on a surface during an exposure event can
be also calculated with methods `irrad()`, `e_irrad()` and `q_irrad()`,
but the values returned are irradiances expressed on a very unusual time
basis. These are no longer W m-2 (J s-1 m-2), but instead J per 8 hours
per square meter.

```{r}
e_irrad(sun.spct, PAR.wb, time.unit = duration(8, "hours"))
```

When the intention is to calculate a total fluence or exposure for an
event, function `fluence()`, `e_fluence()` or `q_fluence()` should be
used as this will add the correct metadata attributes to the returned
value: expressed as energy or photons per unit area per event. See later
sections for details.

```{r}
e_fluence(sun.spct, PAR.wb, exposure.time = duration(8, "hours"))
```

In all earlier examples in this section, the default naming of returned
values was active. The default naming of the values is an abbreviation
of the physical quantity plus the name of the wavelength. Alternatively
`"short"` naming uses only the name of the wavebands as shown below,
obtained from the label stored in the waveband definitions.

```{r}
q_irrad(sun.spct, UV_bands.lst, naming = "short")
```

Naming can also be completely suppressed.

```{r}
q_irrad(sun.spct, UV_bands.lst, naming = "none")
```

Names of members of a list of wavebands, override the labels in waveband
definitions.

```{r}
names(UV_bands.lst) <- c("UV-C", "UV-B", "UV-A")
q_irrad(sun.spct, UV_bands.lst, naming = "short", scale.factor = 1e6)
```

#### Collections of spectra

Collections of spectra can be useful not only for time-series of spectra
or spectral images, but also when dealing with a small group of related
spectra. In the example below we show how to use a collection of spectra
to estimate irradiances under different filters set up in sunlight.

We create a collection of two spectra, for use in our examples.

```{r}
two_suns.mspct <- source_mspct(list(sun1 = sun.spct, sun2 = sun.spct * 2))
```

Methods `irrad()`, `e_irrad()` and `q_irrad()` can be used for
collections of spectra exactly as for a single spectrum (as described
above). We here only show the additional features that apply to
collections. In this first example, we can see that the returned object
is a data frame instead of a named numeric vector.

```{r}
e_irrad(two_suns.mspct, w.band = PAR.wb)
```

Spectral objects can contain metadata as attributes. When summarizing a
collection of spectra it is frequently very useful to copy some of these
metadata, extracted from each member of the collection, to columns in
the returned data frame. This can be done as follows.

```{r}
q_irrad(two_suns.mspct, 
        w.band = PAR.wb,
        scale.factor = 1e6, # umol m-2 s-1
        attr2tb = c(when.measured = "time", lon = "lon", lat = "lat"))
```

For a more advanced example, we reuse the collection of filter spectra
`filters.mspct` from an earlier section. We convolve each filter's
spectral transmittance by the spectral irradiance of the light source so
as to predict the irradiances under the filters. We specify the name of
the column where the names of the spectra (their index) is stored.

```{r, col-convolve-1}
filtered_sun <- convolve_each(filters.mspct, sun.spct)
q_irrad(filtered_sun,
        list(UVA.wb, PAR.wb),
        scale.factor = 1e6,
        idx = "Filter")
```

The code above example can also be written as a single statement. Here
we also tweak column names, delete one column, and swap the position of
the remaining columns.

```{r, col-convolve-2}
q_irrad(convolve_each(filters.mspct, sun.spct), 
        list("UV-A" = UVA.wb, PAR.wb),
        scale.factor = 1e6,  # umol m-2 s-1
        naming = "short",
        attr2tb = c(what.measured = "Filter type"))[ , c(4, 2, 3)]
```

It is also possible to use an *apply* function. See sections *apply*
functions and `convolve` for more details, as in certain cases only one
or the other can be used.

### Fluence

Energy fluence is energy irradiance integrated over a lapse of time or
event, and is expressed as energy per area.

Energy fluence is the integral over wavelengths and time of spectral
energy irradiance

$$F_E = \int_{\lambda = \lambda_1}^{\lambda = \lambda_2} \int_{t = t_1}^{t = t_2} E(\lambda)\ \mathrm{d}\lambda\,\mathrm{d}t$$
where $\lambda_1 \geq \lambda > \lambda_2$ defines a waveband, or range
of wavelengths, and $t_1 \geq t > t_2$.

However, if we assume that irradiance does not vary in time it
simplifies to
$$F_E =  \Delta t\times\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda)\ \mathrm{d}\lambda$$
where $\Delta t = t_2 - t_1$.

The equivalent equation for photon fluence is
$$F_Q =  \Delta t\times\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} Q(\lambda)\ \mathrm{d}\lambda$$

Spectrally weighted (or effective) energy fluence is the integral over
wavelengths and time of the result of the convolution of spectral energy
irradiance by a spectral weight function $w(\lambda)$. Assuming that
spectral irradiance does not vary with time the corresponding equation
is

$$F_{E_{BE}} = \Delta t\times\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda) \times w_E(\lambda)\ \mathrm{d}\lambda$$

Spectrally weighted (or effective) photon fluence can be computed
similarly with the corresponding weighting function $w_Q(\lambda)$.

#### Individual spectra

The calculation of fluence values (time-integrated irradiance) is
identical to that for irradiance, except that a `exposure.time` argument
needs to be supplied. The exposure time must be a `lubridate::duration`,
but any argument accepted by `as.duration` can also be used. Functions
`fluence`, `e_fluence` and `q_fluence` correspond to `irrad`, `e_irrad`
and `q_irrad`,

```{r, fluence-1}
fluence(sun.spct, exposure.time = duration(1, "hours"))
```

or

```{r, fluence-1a}
fluence(sun.spct, exposure.time = 3600) # seconds
```

and, to obtain the photon fluence for a range of wavelengths, in the
example, photosynthetically active radiation, we use the `PAR.wb`
waveband object earlier defined, and integrate for 25 minutes of
exposure.

```{r, fluence-2}
q_fluence(sun.spct, PAR.wb, exposure.time = duration(25, "minutes"))
```

### Photon and energy ratios

A way to summarize the "colour" of light is to compute a ratio between
irradiances computed for two different wavebands of the same spectrum.
They can be computed either on an energy or photon (quantum) basis, and
although not a requirement, use of two wavelength bands with the same
expanse is usually most informative. Photon ratios are usually preferred
compared to energy ratios in work related to photobiology and
photochemistry.

$$Q_1 : Q_2 = \frac{\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} Q(\lambda)\ \mathrm{d}\lambda}
{\int_{\lambda = \lambda_3}^{\lambda = \lambda_4} Q(\lambda)\ \mathrm{d}\lambda}$$

where $\lambda_1 \geq \lambda > \lambda_2$ defines the waveband for the
numerator and $\lambda_3 \geq \lambda > \lambda_4$ defines the waveband
for the denominator, i.e., two ranges of wavelengths.

Energy ratios are computed similarly

$$E_1 : E_2 = \frac{\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda)\ \mathrm{d}\lambda}
{\int_{\lambda = \lambda_3}^{\lambda = \lambda_4} E(\lambda)\ \mathrm{d}\lambda}$$

where $\lambda_1 \geq \lambda > \lambda_2$ defines the waveband for the
numerator and $\lambda_3 \geq \lambda > \lambda_4$ defines the waveband
for the denominator, i.e., two ranges of wavelengths.

An energy irradiance to photon irradiance ratio describes the average
energy per mol of photon for a waveband or range of wavelengths.

$$E : Q = \frac{\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} E(\lambda)\ \mathrm{d}\lambda}
{\int_{\lambda = \lambda_1}^{\lambda = \lambda_2} Q(\lambda)\ \mathrm{d}\lambda}$$

where $\lambda_1 \geq \lambda > \lambda_2$ defines a waveband, or range
of wavelengths.

We can compute the photon to energy ratio ($Q : E$) similarly.

Although all these ratios are usually computed without use of spectral
weighting functions, their computation can be easily done by including
in the equations above a weighting functions ($w(\lambda)$) as described
in the section on irradiance.

#### Individual spectra

The functions described here, in there simplest use, calculate a ratio
between two wavebands. The function `q_ratio` returning photon ratios.
However both waveband parameters can take lists of wavebands as
arguments, with normal recycling rules in effect. The corresponding
function `e_ratio` returns energy ratios.

A single ratio.

```{r}
q_ratio(sun.spct, UVB.wb, PAR.wb)
```

If no waveband is passed as numerator, the whole spectrum is used. The
waveband fully outside the wavelength range of the spectrum is dropped
silently.

```{r}
q_ratio(sun.spct, list(UVC.wb, UVB.wb, UVA.wb))
```

Three denominators (one skipped) and a single denominator.

```{r}
q_ratio(sun.spct, list(UVC.wb, UVB.wb, UVA.wb), PAR.wb)
```

Function `qe_ratio`, has only one waveband parameter, and returns the
*photon* to *energy* ratio, while its complement `eq_ratio` returns the
*energy* to *photon* ratio. Here we show how parameters `scale.factor`
and `name.tag` make scaling the returned value easy.

```{r, ratios-2}
qe_ratio(sun.spct,
         list("UV-B" = UVB.wb, PAR.wb), 
         scale.factor = 1e6,
         name.tag = " (umol/J)")
```

#### Collections of spectra

As other summary methods, `q_ratio()`, `e_ratio()`, `qe_ratio()` and
`eq_ratio()` when applied to a collection of spectra, they return a data
frame.

```{r, ratios-3}
q_ratio(filtered_sun, 
        list(UVB.wb, UVA.wb),
        PAR.wb)
```

Additional parameters allow the scaling and customized column names
possible.

```{r, ratios-3a}
q_ratio(filtered_sun, 
        list(UVB.wb, UVA.wb),
        PAR.wb, 
        scale.factor = 100, 
        name.tag = " (% photons)", 
        idx = "Filter")
```

### Transmittance, reflectance, absorptance and absorbance

Given the laws of conservation of energy, transmittance, reflectance and
absorptance, expressed as fractions, always add up to one.

$$1 = R_\mathrm{fr,total} + A_\mathrm{fr,total} + T_\mathrm{fr,total}$$
Transmittance can be defined either as the fraction of the radiation
"entering" an object that is transmitted, called internal transmittance
($T_\mathrm{fr,internal}$) or as the fraction of the ration incident on
an object that is transmitted ($T_\mathrm{fr,total}$).

$$1 \times R_\mathrm{fr,total} =  A_\mathrm{fr,internal} + T_\mathrm{fr,internal}$$
giving

$$T_\mathrm{fr,internal} = T_\mathrm{fr,total} / R_\mathrm{fr,total}$$
and
$$A_\mathrm{fr,internal} = T_\mathrm{fr,total} / R_\mathrm{fr,total}$$
In the case of reflectance, "total" has a different meaning, and refers
to whether all reflected light or that an specific angle in considered.

In practice, both definitions of transmittance and absorptance are in
use, while as it is easier to measure total- than internal
transmittance, internal transmittance allows the computation of
transmittance for different thickness of a material.

Consequently, absorptance can be computed as:

$$A_\mathrm{fr,internal} = 1 - T_\mathrm{fr,internal}$$ or as

$$A_\mathrm{fr,total} = 1 - T_\mathrm{fr,total} - R_\mathrm{fr,total}$$
Absorbance, is a log transformed quantity that tends to be used when the
range of values spans several orders of magnitude. It is frequently
based on internal absorptance, but can be also based on total
absorptance.

$$A_\mathrm{internal} = -\log_{10}(1 -A_\mathrm{fr,internal}) = -\log_{10}(T_\mathrm{fr,internal}) $$
and

$$A_\mathrm{total} = -\log_{10}(1 - A_\mathrm{fr,total}) = -\log_{10}(T_\mathrm{fr,total} + R_\mathrm{fr,total})$$
When using a spectrophotometer, if our reference is a cuvette with pure
solvent and the sample a solution of a compound in the same solvent we
measure *internal* transmittance, absorptance or absorbance. If we
instead measure the transmittance of a piece of glass or plastic with
air as reference, we measure *total* transmittance, absorptance or
absorbance. This is so because in the first case the reference is the
light transmitted after the reflectance on the cuvette walls has taken
place while in the second case the reflections at the glass-air
interfaces are missing from the reference.

As a result of these different definitions, the implementation of the
class `filter_spct()` and `object_spct` and their methods, need to keep
track of whether quantities are expressed as internal or total. As in
many glasses reflectance varies very weakly with wavelength, storing a
constant value for $R_\mathrm{fr,total}$ is also supported. The
refractive index of a material can also be used to estimate
$R_\mathrm{fr,total}$ for a polished surface. Lack of a value for
$R_\mathrm{fr,total}$ can make some conversions and computations
impossible.

#### Individual spectra

The functions `transmittance`, `absorptance` and `absorbance` take
`filter_spct` as argument, while function `reflectance` takes
`reflector_spct` objects as argument. Functions `transmittance`,
`reflectance` and `absorptance` are also implemented for `object_spct`.
These functions return as default an average value for these quantities
**assuming** a light source with a flat spectral energy output, but this
can be changed as described above for `irrad()`.

```{r}
transmittance(polyester.spct, list(UVB.wb, UVA.wb, PAR.wb))
```

We can obtain numerical values without names if needed,

```{r}
transmittance(polyester.spct, 
              list(UVB.wb, UVA.wb, PAR.wb),
              naming = "none")
```

or named only according to the wavebands.

```{r}
transmittance(polyester.spct, 
              list(UVB.wb, UVA.wb, PAR.wb),
              naming = "short")
```

The reflectance of a leaf.

```{r}
reflectance(green_leaf.spct, waveband(c(600, 700)))
```

#### Collections of spectra

Here we calculate the transmittance of a collection of spectra for three
filters in two wavebands, obtaining the results as a data frame, with
one row per filter, and one column per waveband. We reuse once more
`filters.mspct` from an earlier section.

Column names formed from quantity abbreviation and label in waveband
definitions.

```{r}
transmittance(filters.mspct, 
              w.band = list(UVA.wb, PAR.wb))
```

With `naming = "short"` column names are the labels of waveband
definitions.

```{r}
transmittance(filters.mspct, 
              w.band = list(UVA.wb, PAR.wb),
              naming = "short")
```

If list members are named, column names are formed from quantity
abbreviation and name of list members, overriding the labels in the
waveband definitions.

```{r}
transmittance(filters.mspct, 
              w.band = list("UV-A" = UVA.wb, PAR = PAR.wb))
```

If list members are named, with `naming = "short"` column names are the
names of list members.

```{r}
transmittance(filters.mspct, 
              w.band = list(UVA = UVA.wb, PAR = PAR.wb),
              naming = "short")
```

We can add metadata attributes as columns, changing the name if desired.

```{r}
transmittance(filters.mspct, 
              w.band = UVA.wb,
              naming = "short",
              attr2tb = c("what.measured" = "Filter type"))
```

We can add metadata attributes as a column, and select and rearrange the
columns.

```{r}
transmittance(filters.mspct,
              w.band = UVA.wb,
              attr2tb = "what.measured")[ , c(3, 2)]
```

### Normalized difference indexes

Like the ratios discussed above normalized differences are a way of
summarizing or describing the colour of light sources or objects
independently of the overall irradiance. As their name tells, they are
defined as differences relative to a sum.

Normalized difference indexes are used to summarize the spectral
characteristics of light or objects. They are most frequently used in
the analysis of spectral reflectance data in remote sensing.

$$NDI_{a, b} = \frac{R_a - R_b}{R_a + R_b}$$

where $R_a$ and $R_b$ are reflectances computed from the same spectrum
using two different wavebands.

The most frequently used NDI is the NDVI or normalized difference
vegetation index, which compares reflectance in the red and far-red
regions as a way of assessing the presence of vegetation vs. bare land
in remote sensing imagery.

However, they can be computed based on energy or photon irradiances for
two wavebands as shown here, or for any other spectral quantity.

$$NDI_{a, b} = \frac{Q_a - Q_b}{Q_a + Q_b}$$

where $Q_a$ and $Q_b$ are irradiances computed from the same spectrum
using two different wavebands.

Although we here describe how to compute normalized difference indexes
from spectral data, they are most frequently generated from data from
broad-band sensors in satellite, air-borne or terrestrial imagers. To
reconstruct from spectral data indexes computed from these instruments
we need to use waveband definitions that mimic the spectral response of
the imager of interest. Package 'photobiologyWavebands' provides
pre-defined wavebands for several different satellite imagers as well as
for wavelength ranges in common use.

#### Individual spectra

Here we give an example of a possible definition of NDVI using function
`normalized_diff_ind()` can be used to calculate, or any index with a
similar formulation structure.

```{r}
normalized_diff_ind(Ler_leaf_rflt.spct,
                    waveband(c(740, 840)), waveband(c(590, 690)),
                    reflectance)
```

Here we give an *unusual* example to demonstrate that function
`normalized_diff_ind()` can be used to calculate any index with a
similar formulation structure and using other spectral quantities and
summary functions.

```{r}
normalized_diff_ind(sun.spct,
                    waveband(c(600, 700)), waveband(c(400, 500)),
                    q_irrad)
```

### Integrated response

As with other spectral quantities, we can integrate over wavelengths
spectral responsiveness. In response and action spectra the quantity is
a response measured in some arbitrary unit expressed per unit
wavelengths and per unit energy or quantum.

$$X_E = \int_{\lambda = \lambda_1}^{\lambda = \lambda_2} X_E(\lambda)\ \mathrm{d}\lambda$$
where $\lambda_1 \geq \lambda > \lambda_2$ defines a waveband, or range
of wavelengths.

The conversion between energy and photon (= quantum) basis of expression
is possible as it is for radiation spectra. Depending on the base of
expression the returned integrated value is computed **assuming** either
a light source with a flat spectral energy irradiance of 1 or spectral
photon irradiance of 1, respectively.

#### Individual spectra

The functions `response`, `e_response` and `q_response` take
`response_spct` objects as arguments. If no waveband is supplied as
argument, the whole spectrum is integrated.

```{r}
response(photodiode.spct)
```

When a waveband, or list of wavebands, is supplied the response is
calculated for the wavebands.

```{r}
e_response(photodiode.spct, list(UVB.wb, UVA.wb))
```

This function has an additional argument `quantity`, with default
`"total"`, as described for `irrad()`.

#### Collections of spectra

```{r}
sensors <- response_mspct(list(GaAsP = photodiode.spct,
                               CCD = ccd.spct))
response(sensors, list(UVB.wb, UVA.wb, PAR.wb), quantity = "contribution")
```

### Integration over wavelengths

When we need to integrate some \emph{non-standard} `numeric` variable
stored in a spectral object we can use functions `integrate_spct` or
`average_spct`.

#### Calculation from individual spectra

We can integrate the values of arbitrary `numeric` columns other than
`w.length` in an spectral object. All spectral classes are derived from
`generic_spct`, so the examples in this section apply to objects of any
of the derived spectral classes as well.

```{r}
integrate_spct(sun.spct)
```

The function `average_spct` integrates every column holding numeric
values from a spectrum object, except for `w.length`, and divides the
result by the *spread* or width of the wavelength range integrated,
returning a value expressed in the same units as the spectral data.

```{r}
average_spct(sun.spct)
```

## Comparison of spectra

Comparison of spectra for which data is expressed at different discrete
wavelength values can be easily affected by bias if interpolation is
used. Function `compare_spct()` does a coarse grained comparison by
first summarizing each spectrum over consecutive ranges of wavelengths,
and then applying a comparison function to these summary values.

The function can be used to compare pairs of spectra, stored as a
collection. In the next example we compare two `source_spct` objects
using defaults for most arguments.

```{r}
compare_spct(source_mspct(list(sun1 = sun.spct, sun2 = sun.spct * 2)))
```

The value returned by default is a `generic_spct` object containing the
computed summaries for each waveband plus the result of the comparison
between the summaries. The first three columns contain the wavelength at
the midpoint of the wavelength range of waveband plus its extremes.

In this example we compare two `filter_spct` objects, using summaries
over 50-nm-wide bands, and using an operator returning a logical value
for the comparison instead of the default division operator.

```{r}
compare_spct(filter_mspct(list(pet = polyester.spct,
                              yllw = yellow_gel.spct)),
             w.band = 50,
            .comparison.fun = `<`)
```

## Illumination and light as seen by humans

### Illuminance

Illuminance, or luminous flux incident on a surface, is relevant to
human vision. It is an approximate quantity as the spectral response
function of human vision varies among individuals, with their age and
the conditions during measurement. The SI unit for illuminance is lux
(lx) or lumnes per square meter.

When function `illuminance()` is applied to spectral (energy) irradiance
or spectral photon irradiance, illuminance can be directly computed
using the same time base of 1 s.

```{r}
illuminance(sun.spct)
```

The response of the human eye depends on the size of the target, and
response spectra have been defined by CIE for both 2 degrees and 10
degrees targets.

```{r}
illuminance(sun.spct, std = "CIE10deg")
```

If one attempts to compute illuminance from spectral fluence or
radiation spectra expressed as a flux of energy or photons over a period
of time different to 1 s, the average illuminance is returned, in lux.

```{r}
illuminance(sun_daily.spct)
```

### CCT and CRI

Colour temperature and colour rendition index can be computed from
spectral irradiance. Package 'colorSpec' implement these and other
calcualtions related to colour. Package 'photobiologyInOut' provides
wrappers to facilitate the computation of CCT and CRI directly from
`source_spct` objects by on-the-fly conversion and calling functions
from 'colorSpec'.

### RGB colours

Different `color_of()` methods allow calculation of RGB colour values
for light sources or objects. The returned values are R colour
definitions. Method `color_of()` works rather differently depending on
the object. The method for `numeric` vectors assumes the numbers are
wavelengths in nanometres, and returns a vector of colour definitions of
the same length assuming monochromatic light.

```{r}
color_of(550) # green
color_of(630) # red
color_of(c(550, 630, 380, 750)) # vectorized
```

The method for `source_spct` objects returns a single colour definition
corresponding to the whole spectrum of a light sources.

```{r}
color_of(sun.spct)
color_of(sun.spct * yellow_gel.spct)
```

There are no methods for `filter_spct` and `reflector_spct` objects so
as shown above we need to convolve them with spectral irradiance from a
`source_spct` object.

The method for `waveband` objects returns one colour definition per
waveband, corresponding to their central wavelength.

```{r}
color_of(waveband(c(400, 500), wb.name = "my_BL"))
```

By default CIE coordinates for *typical* human vision are used, but the
functions have a parameter that can be used for supplying a different
chromaticity definition as a `chroma_spct` object.

```{r}
color_of(sun.spct, chroma.type = "CC")
color_of(sun.spct, chroma.type = "CMF")
color_of(sun.spct, chroma.type = beesxyzCMF.spct)
```

In the case of bees, the RGB values represent a shift towards longer
wavelengths compared to the true sensitivity. In other words, they are
translated into colours that humans can see and monitors and printers
can generate.
