ir_as_ir converts an object to an object of class ir.
Usage
ir_as_ir(x, ...)
# S3 method for class 'ir'
ir_as_ir(x, ...)
# S3 method for class 'data.frame'
ir_as_ir(x, ...)
# S3 method for class 'ir_flat'
ir_as_ir(x, ...)
# S3 method for class 'hyperSpec'
ir_as_ir(x, ...)
# S3 method for class 'Spectra'
ir_as_ir(x, ...)Examples
# conversion from an ir object
ir::ir_sample_data |>
ir_as_ir()
#> # A tibble: 58 × 7
#> id_measurement id_sample sample_type sample_comment klason_lignin
#> <int> <chr> <chr> <chr> <units>
#> 1 1 GN 11-389 needles Abies Firma Momi fir 0.359944
#> 2 2 GN 11-400 needles Cupressocyparis leylandii… 0.339405
#> 3 3 GN 11-407 needles Juniperus chinensis Chine… 0.267552
#> 4 4 GN 11-411 needles Metasequoia glyptostroboi… 0.350016
#> 5 5 GN 11-416 needles Pinus strobus Torulosa 0.331100
#> 6 6 GN 11-419 needles Pseudolarix amabili Golde… 0.279360
#> 7 7 GN 11-422 needles Sequoia sempervirens Cali… 0.329672
#> 8 8 GN 11-423 needles Taxodium distichum Cascad… 0.356950
#> 9 9 GN 11-428 needles Thuja occidentalis Easter… 0.369360
#> 10 10 GN 11-434 needles Tsuga caroliniana Carolin… 0.289050
#> # ℹ 48 more rows
#> # ℹ 2 more variables: holocellulose <units>, spectra <named list>
# conversion from a data frame
x_ir <- ir::ir_sample_data
x_df <-
x_ir |>
ir_drop_spectra() |>
dplyr::mutate(
spectra = x_ir$spectra
) |>
ir_as_ir()
# check that ir_as_ir preserves the input class
ir_sample_data |>
structure(class = setdiff(class(ir_sample_data), "ir")) |>
dplyr::group_by(sample_type) |>
ir_as_ir()
#> # A tibble: 58 × 7
#> # Groups: sample_type [8]
#> id_measurement id_sample sample_type sample_comment klason_lignin
#> * <int> <chr> <chr> <chr> <units>
#> 1 1 GN 11-389 needles Abies Firma Momi fir 0.359944
#> 2 2 GN 11-400 needles Cupressocyparis leylandii… 0.339405
#> 3 3 GN 11-407 needles Juniperus chinensis Chine… 0.267552
#> 4 4 GN 11-411 needles Metasequoia glyptostroboi… 0.350016
#> 5 5 GN 11-416 needles Pinus strobus Torulosa 0.331100
#> 6 6 GN 11-419 needles Pseudolarix amabili Golde… 0.279360
#> 7 7 GN 11-422 needles Sequoia sempervirens Cali… 0.329672
#> 8 8 GN 11-423 needles Taxodium distichum Cascad… 0.356950
#> 9 9 GN 11-428 needles Thuja occidentalis Easter… 0.369360
#> 10 10 GN 11-434 needles Tsuga caroliniana Carolin… 0.289050
#> # ℹ 48 more rows
#> # ℹ 2 more variables: holocellulose <units>, spectra <named list>
# conversion from an ir_flat object
x_ir <-
ir::ir_sample_data |>
ir::ir_flatten() |>
ir::ir_as_ir()
# conversion from a hyperSpec object from package hyperSpec
if(requireNamespace("hyperSpec")) {
x_hyperSpec <- hyperSpec::laser
x_ir <- ir_as_ir(x_hyperSpec)
}
# conversion from a Spectra object from class ChemoSpec
if(requireNamespace("ChemoSpec")) {
## sample data
x <- ir_sample_data
x_flat <- ir_flatten(x)
## creation of the object of class "Spectra" (the ChemoSpec package does
## not contain a sample Spectra object)
n <- nrow(x)
group_vector <- seq(from = 1, to = n, by = 1)
color_vector <- rep("black", times = n)
x_Spectra <- list() # dummy list
x_Spectra$freq <- as.numeric(x_flat[,1, drop = TRUE]) # wavenumber vector
x_Spectra$data <- as.matrix(t(x_flat[,-1])) # absorbance values as matrix
x_Spectra$names <- as.character(seq_len(nrow(x))) # sample names
x_Spectra$groups <- as.factor(group_vector) # grouping vector
x_Spectra$colors <- color_vector # colors used for groups in plots
x_Spectra$sym <- as.numeric(group_vector) # symbols used for groups in plots
x_Spectra$alt.sym <- letters[as.numeric(group_vector)] # letters used for groups in plots
x_Spectra$unit <- c("wavenumbers", "intensity") # unit of x and y axes
x_Spectra$desc <- "NULL" # optional descriptions in plots
attr(x_Spectra, "class") <- "Spectra"
# conversion to ir
x_ir <- ir_as_ir(x_Spectra)
}
#> Loading required namespace: ChemoSpec