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Calculate default values inside methods of as.hyperSpec() #298

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Dec 24, 2020
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Calculate default values inside methods of as.hyperSpec() #298

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26f1f20
Calculate default values inside methods of as.hyperSpec()
GegznaV Dec 23, 2020
c2b501c
Update documentation and messeges in as_hyperSpec.R
GegznaV Dec 23, 2020
76ebb03
Update NEWS.md
GegznaV Dec 23, 2020
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5 changes: 4 additions & 1 deletion hyperSpec/NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,10 @@
* Column names in spectra matrix (`$spc` column of `hyperSpec` object) are now returned correctly by functions `spc.bin()` (#237), and `spc.loess()` (#245).
* New function `hy_list_available_hySpc_packages()` lists packages, that are available in GitHub organization `r-hyperSpec`.
* New function `hy_browse_homepage()` opens the homepage of *R hyperSpec* in a web browser.
* New method `as.hyperSpec(<hyperSpec>)` (#282).
* Changes related to function `as.hyperSpec()`:
- New method `as.hyperSpec(<hyperSpec>)` was created (#282).
- The default value of argument `wl` is now set to `wl = NULL` (#297).
- `wl = NULL` now means that the default values of wavelengths should be calculated inside the methods of `as.hyperSpec()` (#297).
* Possibility to initialize `hyperSpec` object by providing wavelengths only (#288).
* Function `wl.eval()` is converted into S3 generic. Methods `wl.eval(<hyperSpec>)` and `wl.eval(<numeric>)` for numeric vectors were added (#287).
* New function `new_hyperSpec()` that initializes `hyperSpec` object in a similar way as `new("hyperSpec")` does but has autocompletion possibilities in RStudio (#283).
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37 changes: 21 additions & 16 deletions hyperSpec/R/as_hyperSpec.R
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@@ -1,13 +1,16 @@

#' `as.hyperSpec`: Convenience Conversion Functions
#'
#' These functions are shortcuts to convert other objects into hypeSpec objects.
#' These functions are shortcuts to convert other objects into `hypeSpec`
#' objects.
#'
#' @param X the object to convert. If `X` is:
#'
#' - a `matrix`, it is assumed to contain the spectra matrix,
#' - a `data.frame`, it is assumed to contain extra data.
#'
#' @param X the object to convert.
#' A matrix is assumed to contain the spectra matrix,
#' a data.frame is assumed to contain extra data.
#' @param ... additional parameters that should be handed over to
#' `new("hyperSpec")` (initialize)
#' `new("hyperSpec")` (initialize).
#'
#' @return hyperSpec object
#' @seealso [hyperSpec::initialize()]
Expand All @@ -23,14 +26,15 @@ setGeneric(
)

#' @include guess_wavelength.R
.as.hyperSpec.matrix <- function(X, wl = guess.wavelength(colnames(X)), ...) {
.as.hyperSpec.matrix <- function(X, wl = NULL, ...) {
if (is.null(wl)) wl <- guess.wavelength(colnames(X))
new("hyperSpec", spc = X, wavelength = wl, ...)
}

#' @rdname as.hyperSpec
#' @param wl wavelength vector. Defaults to guessing from the column names in `X`
#' @param spc spectra matrix
#' @param labels list with labels
#' @param wl wavelength vector. Defaults to guessing from the column names in `X`.
#' @param spc spectra matrix.
#' @param labels list with labels.
#' @export
#'
#' @concept hyperSpec conversion
Expand All @@ -41,12 +45,14 @@ setGeneric(
#' guess.wavelength(wl)
setMethod("as.hyperSpec", "matrix", .as.hyperSpec.matrix)

.as.hyperSpec.data.frame <- function(X, spc = NULL, wl = guess.wavelength(spc),
.as.hyperSpec.data.frame <- function(X, spc = NULL, wl = NULL,
labels = attr(X, "labels"), ...) {

if (is.null(wl)) wl <- guess.wavelength(X)
# TODO: remove after 31.12.2020
if (!all(!is.na(guess.wavelength(colnames(X))))) {
warning(
"as.hyperSpec.data.frame has changed its behaviour. ",
"Method as.hyperSpec(<data.frame>) has changed its behaviour. ",
"Use as.hyperSpec(as.matrix(X)) instead."
)
}
Expand All @@ -60,11 +66,10 @@ setMethod("as.hyperSpec", "matrix", .as.hyperSpec.matrix)
}

#' @rdname as.hyperSpec
#' @note *Note that the behaviour of `as.hyperSpec(X)` was changed: it now
#' assumes `X` to be extra data, and returns a hyperSpec object with 0
#' wavelengths. To get the old behaviour*

# FIXME: it seems that the documentation sentence in incomplete.
#' @note Note that the behaviour of `as.hyperSpec(X)` was changed when `X` is a
#' `data.frame`: it now assumes `X` to be extra data, and returns a `hyperSpec`
#' object with 0 wavelengths. To get the old behaviour, use
#' `as.hyperSpec(as.matrix(X))`.

setMethod("as.hyperSpec", "data.frame", .as.hyperSpec.data.frame)

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