hyperSpec: asdataframe – R documentation

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asdataframe

Conversion of a hyperSpec object into a data.frame or matrix as.data.frame returns x@data (as data.frame) as.matrix returns the spectra matrix x@data$spc as matrix

Description

The data.frame returned by as.long.df is guaranteed to have columns spc and .wavelength. If nwl (x) == 0 these columns will be NA.

Usage

## S3 method for class 'hyperSpec'
as.data.frame(x, row.names = TRUE, optional = NULL, ...)

## S3 method for class 'hyperSpec'
as.matrix(x, ...)

as.wide.df(x, wl.prefix = "")

as.long.df(x, rownames = FALSE, wl.factor = FALSE, na.rm = TRUE)

as.t.df(x)

Arguments

`x`	a `hyperSpec` object
`row.names`	if `TRUE`, a column `.row` is created containing row names or row indices if no rownames are set. If character vector, the rownames are set accordingly.
`optional`	ignored
`...`	ignored
`wl.prefix`	prefix to prepend wavelength column names
`rownames`	should the rownames be in column `.rownames` of the long-format data.frame?
`wl.factor`	should the wavelengths be returned as a factor (instead of numeric)?
`na.rm`	if `TRUE`, rows where spc is not `NA` are deleted.

Value

x@data and x@data$spc (== x$spc == x [[]]), respectively.

as.wide.df returns a data.frame that consists of the extra data and the spectra matrix converted to a data.frame. The spectra matrix is expanded in place.

as.long.df returns the stacked or molten version of x@data. The wavelengths are in column .wavelength.

as.t.df returns a data.frame similar to as.long.df, but each spectrum in its own column. This is useful for exporting summary spectra, see the example.

Author(s)

C. Beleites

Examples

as.data.frame (chondro [1:3,, 600 ~ 620])
as.matrix (chondro [1:3,, 600 ~ 620])
lm (c ~ spc, data = flu [,,450])

as.wide.df (chondro [1:5,, 600 ~ 610])
summary (as.wide.df (chondro [1:5,, 600 ~ 610]))

as.long.df (flu [,, 405 ~ 410])
summary (as.long.df (flu [,, 405 ~ 410]))
summary (as.long.df (flu [,, 405 ~ 410], rownames = TRUE))
summary (as.long.df (flu [,, 405 ~ 410], wl.factor = TRUE))

df <- as.t.df (apply (chondro, 2, mean_pm_sd))
head (df)

if (require (ggplot2)){
  ggplot (df, aes (x = .wavelength)) +
    geom_ribbon (aes (ymin = mean.minus.sd, ymax = mean.plus.sd),
      fill = "#00000040") +
    geom_line (aes (y = mean))
}

hyperSpec

Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

v0.100.0

GPL (>= 3)

Authors

Claudia Beleites [aut, cre, dtc] (<https://orcid.org/0000-0003-1626-154X>), Valter Sergo [aut], Alois Bonifacio [ctb, dtc], Marcel Dahms [ctb], Björn Egert [ctb], Simon Fuller [ctb], Vilmantas Gegzna [ctb], Rustam Guliev [ctb], Bryan A. Hanson [ctb], Michael Hermes [ctb], Martin Kammer [dtc], Roman Kiselev [ctb], Sebastian Mellor [ctb]

Initial release

2021-09-13