Bind hyperSpec objects — bind • hyperSpec

Functions to bind hyperSpec objects.

cbind2() binds the spectral matrices of two hyperSpec objects by column. All columns besides spc with the same name in x@data and y@data must have the same elements. Rows are ordered before checking.

rbind2() binds two hyperSpec objects by row. They need to have the same columns.

bind(
  direction = stop("direction('c' or 'r') required"),
  ...,
  wl.tolerance = hy_get_option("wl.tolerance")
)

# S3 method for hyperSpec
cbind(...)

# S3 method for hyperSpec
rbind(...)

# S4 method for hyperSpec,hyperSpec
cbind2(x, y)

# S4 method for hyperSpec,missing
cbind2(x, y)

# S4 method for hyperSpec,hyperSpec
rbind2(x, y, wl.tolerance = hy_get_option("wl.tolerance"))

# S4 method for hyperSpec,missing
rbind2(x, y, wl.tolerance)

Arguments

direction: "r" or "c" to bind rows or columns.
...: The hyperSpec objects to be combined.
Alternatively, one list of hyperSpec objects can be given to bind().
wl.tolerance: rbind and rbind2 check for equal wavelengths with this tolerance.
x, y: hyperSpec objects

Value

A hyperSpec object, possibly with different row order (for bind("c", ...) and cbind2()).

Details

The former difficulties with binding S4 objects are resolved since R version 3.2.0 and cbind() and rbind() now work as intended and expected for hyperSpec objects.

Therefore, calling rbind.hyperSpec and cbind.hyperSpec is now deprecated: cbind and rbind should now be called directly.

However, in consequence it is no longer possible to call cbind() or rbind() with a list of hyperSpec objects. In that case, use bind() or base::do.call() (see example).

bind() does the common work for both column- and row-wise binding.

Note

You might have to make sure that the objects either all have or all do not have rownames and/or colnames.

Author

C. Beleites

Examples


faux_cell
#> hyperSpec object
#>    875 spectra
#>    4 data columns
#>    300 data points / spectrum

bind("r", faux_cell, faux_cell)
#> hyperSpec object
#>    1750 spectra
#>    4 data columns
#>    300 data points / spectrum
rbind(faux_cell, faux_cell)
#> hyperSpec object
#>    1750 spectra
#>    4 data columns
#>    300 data points / spectrum
cbind(faux_cell, faux_cell)
#> hyperSpec object
#>    875 spectra
#>    4 data columns
#>    600 data points / spectrum
bind("r", list(faux_cell, faux_cell, faux_cell))
#> hyperSpec object
#>    2625 spectra
#>    4 data columns
#>    300 data points / spectrum

x <- faux_cell[, , 600:605]
x$a <- 1
x@data <- x@data[, sample(ncol(x), ncol(x))] # reorder columns

y <- faux_cell[nrow(faux_cell):1, , 1730:1750] # reorder rows
y$b <- 2

cbind2(x, y) # works
#> hyperSpec object
#>    875 spectra
#>    6 data columns
#>    27 data points / spectrum

y$y[3] <- 5
try(cbind2(x, y)) # error
#> hyperSpec object
#>    875 spectra
#>    6 data columns
#>    27 data points / spectrum

# list of hyperSpec objects

lhy <- list(flu, flu)
do.call("rbind", lhy)
#> hyperSpec object
#>    12 spectra
#>    3 data columns
#>    181 data points / spectrum
bind("r", lhy)
#> hyperSpec object
#>    12 spectra
#>    3 data columns
#>    181 data points / spectrum

Bind `hyperSpec` objects