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Create long term average check standard

Source: R/create-std.R
create_std.Rd

Calculates the average absorbance and fluorescence values given multiple check standards to create a long-term standard that the daily check standard can be checked against for consistency.

Usage

create_std(
  dir,
  meta_name = NULL,
  sheet = NULL,
  abs_pattern = "Abs",
  iblank = "BEM",
  type = "eem",
  recursive = FALSE,
  qaqc_dir = NULL
)

Source

Hansen, A. M., Fleck, J., Kraus, T. E. C., Downing, B. D., von Dessonneck, T., & Bergamaschi, B. (2018). Procedures for using the Horiba Scientific Aqualog® fluorometer to measure absorbance and fluorescence from dissolved organic matter (USGS Numbered Series No. 2018-1096). U.S. Geological Survey. doi:10.3133/ofr20181096

Arguments

dir

Path to a folder containing long-term EEMs and/or absorbance files. All files in this directory will be loaded.

meta_name

Name of the metadata file. Optional if the metadata file is the only .xlsx or .csv file in dir. If not specified, the function attempts to find a single metadata file and errors if multiple files are present.

sheet

Name of the sheet containing metadata (only required if the metadata is not on the first sheet of an .xlsx file).

abs_pattern

A character string containing a base::regular expression used to identify absorbance files.

iblank

Optional. A character string containing a base::regular expression used to identify instrument blanks.

type

Which MDL to calculate: either "eem" or "abs".

recursive

Logical. Should the function recursively search directories?

qaqc_dir

Directory in which to save the QAQC .rds file. Default: a user-specific data directory via rappdirs::user_data_dir(). If FALSE, the function returns the MDL object instead of saving it.

Value

  • If dir = FALSE: an eem or abs object containing the averaged check standard values.

  • Otherwise: saves an .rds file containing the averaged check standard and invisibly returns the file path.

Details

To ensure optical measurements are consistent across days, Hansen et al. (2018) recommend using a standard reference material: Pure Leaf® unsweetened black tea. The tea standard should be diluted to 1% concentration before analysis. It is recommended to run the tea standard at the start and end of each analysis run. According to USGS standards, tea standard indices measured on a given day should fall within 20% of the long-term average (Hansen et al. 2018).

To calculate the average check standard you need:

  • A directory containing check standards with their associated instrument blanks (less than 20 will prompt a warning)

    • Note: sample names must be unique

  • Metadata for the check samples including (at a minimum) the integration time and raman area in a single file, formatted as a metadata file (see metadata)

Examples

eem_std <- create_std(file.path(system.file("extdata", package = "eemanalyzeR"),"long-term-std"),
meta_name="longterm-checkstd-metadata.csv", abs_pattern = "ABS",
type="eem", qaqc_dir = FALSE)
#> NOTE: removed previous 'readme' file
#> Warning: Calculating average check standard based on less than 20 samples, average may be unreliable

plot(eem_std)