eem_checkdata {staRdom}

Check your EEM, absorption and metadata before processing

Description

The function tries to lead you to possible problems in your data.

Usage

eem_checkdata(
  eem_list,
  absorbance,
  metadata = NULL,
  metacolumns = NULL,
  correction = FALSE,
  error = TRUE
)

Arguments

eem_list

eemlist continaing EEM data.

absorbance

data.frame containing absorbance data.

metadata

optional data.frame containing metadata.

metacolumns

character vector of columns that are checkt for complete data sets

correction

logical, whether EEMs should be checked for applied corrections

error

logical, whether a problem should cause an error or not.

Details

The returned list contains character vectors with sample names where possible problems were found: problem (logical, whether a severe problem was found), nas (sample names with NAs in EEM data), missing_correction (correction of EEM samples was not done or not done successfully),eem_no_abs (EEM samples with no absorbance data), abs_no_eem (samples with present absorbance but no EEM data), duplse (duplicate sample names in EEM data), duplsa (duplicate sample names in absorbance data), invalid_eem (invalid EEM sample name), invalid_abs (invalid absorbance sample name), range_mismatch (wavelength ranges of EEM and absorbance data are mismatching), metadupls (duplicate sample names in metadata), metamissing (EEM samples where metadata is missing), metaadd (samples in metadata without EEM data)

Value

writes out possible porblems to command line, additionally list with sample names where possible problems were found, see details.

Examples

folder <- system.file("extdata/EEMs", package = "staRdom") # load example data
eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv)

abs_folder <- system.file("extdata/absorbance", package = "staRdom") # load example data
absorbance <- absorbance_read(abs_folder, cores = 2)

metatable <- system.file("extdata/metatable_dreem.csv",package = "staRdom")
meta <- read.table(metatable, header = TRUE, sep = ",", dec = ".", row.names = 1)

checked <- eem_checkdata(eem_list, absorbance, metadata = meta,
metacolumns = "dilution", error = FALSE)
# This example returns a message, that absorbance data for the
# blank samples are missing. As absorbance is supposed to be 0 over
# the whole spectrum when you measure blanks, there is no need
# to supply the data and do an inner-filter effect correction.