Loads spectra from files and adds these to the data frame with the file names.

pm_load_spectra takes a column with file names for files containing mid infrared spectra from a data frame, imports the spectra into a list column spectra and adds them to the data frame which then becomes an ir::ir_new_ir[ir] object.

pm_load_spectra(
  x,
  directory = ".",
  .col_files = "mirs_file",
  .col_sample_id = "id_sample"
)

Arguments

x	A data frame.
directory	A character value specifying the directory where the files accompanying the 'pmird' database are stored.
.col_files	The name of the column of x with file names for the files storing mid infrared spectra.
.col_sample_id	The name of the column of x with names for the samples for which to load spectra. This column is used as column sample_id when constructing the ir object.

Value

x as an object of class ir and with a new column spectra.

Details

Currently, the following file formats are supported for files storing mid infrared spectra:

1. csv files

2. Thermo Galactic's .spc files

Examples

if (FALSE) {
# connect to database
con <-
  RMariaDB::dbConnect( # ---todo: change this
    drv = RMariaDB::MariaDB(),
    dbname = "pmird",
    default.file = "~/my.cnf"
  )

# extract data
x <-
  pm_get_dm(con, learn_keys = TRUE) %>%
  dm::dm_zoom_to(data) %>%
  dplyr::filter(id_measurement < 1000 & ! is.na(mirs_file)) %>%
  dm::pull_tbl() %>%
  as.data.frame()

# close connection
RMariaDB::dbDisconnect(con)

# get spectra
x <-
  pm_load_spectra(x, directory = "..", .col_files = "mirs_file", .col_sample_id = "id_measurement")

class(x)
}