get_oxygen_from_preamble: Extract oxygen information from a Licor file

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Extract oxygen information from a Licor file

Description

Ensures that the oxygen percentage (contained in the preamble of a Licor file) is properly documented (including units).

Usage

  get_oxygen_from_preamble(licor_exdf)

Arguments

licor_exdf

An exdf object representing data from a photosynthetic gas exchange measurement system. It should contain a column called Oxygen; this should automatically be the case if licor_exdf was created by read_gasex_file.

Details

Licor LI-6800 log files include the oxygen concentration as an entry in the preamble, which is automatically converted to a column by read_licor_6800_Excel and read_licor_6800_plaintext. However, the Licor log files do not specify units for this value; they should be percent.

This function adds the correct units to the Oxygen column, or creates one (with values initialized to NA) if the Oxygen column is not present.

Also note that this function is called automatically by read_licor_6800_Excel and read_licor_6800_plaintext whenever get_oxygen is TRUE; this happens by default, so it is rare for a user to call this function directly.

Value

An exdf object based on licor_exdf that includes the Oxygen column units.

Examples

# Example: Read data from a Licor log file and get the oxygen information from
# the preamble

# Read the file without automatically specifying oxygen units
licor_data <- read_gasex_file(
  PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
  get_oxygen = FALSE
)

# Here we can see that the oxygen column is included, but without units
print(licor_data$categories$Oxygen)
print(licor_data$units$Oxygen)
print(licor_data[, 'Oxygen'])

# Include the oxygen units
licor_data <- get_oxygen_from_preamble(licor_data)

# The units have changed, but the category and values have not
print(licor_data$categories$Oxygen)
print(licor_data$units$Oxygen)
print(licor_data[, 'Oxygen'])

PhotoGEA documentation built on Aug. 25, 2025, 5:13 p.m.