Extract oxygen information from a Licor file
get_oxygen_from_preamble.Rd
Ensures that the oxygen percentage (contained in the preamble of a Licor file) is properly documented (including units).
Arguments
- licor_exdf
An
exdf
object representing data from a photosynthetic gas exchange measurement system. It should contain a column calledOxygen
; this should automatically be the case iflicor_exdf
was created byread_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.
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)
#> [1] "SysConst"
print(licor_data$units$Oxygen)
#> [1] "NA"
print(licor_data[, 'Oxygen'])
#> [1] 21 21 21 21 21 21 21 21 21 21 21 21
# 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)
#> [1] "SysConst"
print(licor_data$units$Oxygen)
#> [1] "percent"
print(licor_data[, 'Oxygen'])
#> [1] 21 21 21 21 21 21 21 21 21 21 21 21