Extract TDL valve information from file name

Determines the TDL valve number from a photosynthetic gas exchange system log file name.

Usage

get_sample_valve_from_filename(
    exdf_obj,
    reference_table = NULL
  )

Arguments

exdf_obj

An exdf object representing data from a photosynthetic gas exchange measurement system. The exdf_obj$file_name field must be defined and contain the file name; this will automatically be the case if exdf_obj was created by read_gasex_file.

reference_table

An optional list of named elements, where the name of each element is a Licor sample line valve number (as a character) and the value of each element is the corresponding Licor reference line valve number.

Details

When making combined gas exchange and isotope discrimination measurements using a portable photosynthetic gas exchange system (such as a Licor LI-6800) coupled with a tunable diode laser (TDL) absorption spectroscopy system, the TDL's gas handling system cycles through several gas lines (or sites) by opening and closing valves. When analyzing such data, a key step is to identify which TDL valve numbers correspond to the sample and reference gas lines of the Licor.

At UIUC, there is a convention for designating the sample line valve numbers in the Licor file names, where "siteNN" or "site NN" means that the Licor's sample line is valve NN in the TDL data file. The get_sample_valve_from_filename function extracts the valve number from the file name and stores it in a new column in exdf_obj called valve_number_s.

Optionally, it is also possible to specify the reference line valve number corresponding to each sample line valve number using the reference_table input argument. Reference line valve numbers will be stored in the valve_number_r column.

Value

An exdf object based on exdf_obj that includes the Licor sample line valve number as a new column called valve_number_s and (optionally) the Licor reference line valve number as a new column called valve_number_r.

Examples

## In this example we load a gas exchange data file and determine the TDL valve
## numbers from its file name

# Read the gas exchange data
licor_data <- read_gasex_file(
  PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
)

# Get TDL valve information from Licor file name; for this TDL system, the
# reference valve is 12 when the sample valve is 11
licor_data <- get_sample_valve_from_filename(licor_data, list('11' = 12))

# View the results
licor_data[, c('obs', 'valve_number_s', 'valve_number_r')]
#>    obs valve_number_s valve_number_r
#> 1    1             11             12
#> 2    2             11             12
#> 3    3             11             12
#> 4    4             11             12
#> 5    5             11             12
#> 6    6             11             12
#> 7    7             11             12
#> 8    8             11             12
#> 9    9             11             12
#> 10  10             11             12
#> 11  11             11             12
#> 12  12             11             12