Extract oxygen information from a Licor file
get_oxygen_from_preamble.RdExtracts oxygen information from a Licor file's preamble and adds it to the main data as a new column so it is easier to access.
Arguments
- licor_exdf
An
exdfobject representing data from a photosynthetic gas exchange measurement system. Theexdf_obj$preamblefield must be defined and contain the preamble contents; this will automatically be the case iflicor_exdfwas created byread_gasex_file.
Details
Licor LI-6800 log files include the oxygen concentration as an entry in the
preamble, but it is more helpful to include this information as a column in
the main data. The get_oxygen_from_preamble function attempts to move
the oxygen concentration (as a percentage) from the preamble into a column.
Value
An exdf object based on licor_exdf that includes the oxygen
percentage as a new column called oxygen.
Examples
# Example: Read data from a Licor log file and get the oxygen information from
# the preamble
# Read the file
licor_data <- read_gasex_file(
PhotoGEA_example_file_path('licor_for_gm_site11.xlsx'),
)
# Here we can see the oxygen percentage in the preamble
str(licor_data$preamble)
#> 'data.frame': 1 obs. of 67 variables:
#> $ File opened : chr "2023-08-04 07:54:01"
#> $ Console s/n : chr "68C-571076"
#> $ Console ver : chr "Bluestem v.2.1.08"
#> $ Scripts ver : chr "2022.05 2.1.08, Aug 2022"
#> $ Head s/n : chr "68H-581076"
#> $ Head ver : chr "1.4.22"
#> $ Head cal : chr "{\"oxygen\": \"21\", \"co2azero\": \"0.850833\", \"co2aspan1\": \"1.00272\", \"co2aspan2\": \"-0.03976\", \"co2"| __truncated__
#> $ CO2 rangematch: chr "Wed Mar 8 15:59"
#> $ H2O rangematch: chr "Wed Mar 8 16:05"
#> $ Chamber type : chr "6800-13"
#> $ Chamber s/n : chr "CHM-10960"
#> $ Chamber rev : chr "0"
#> $ Chamber cal : chr "8.12"
#> $ HeadLS type : chr "6800-03"
#> $ HeadLS s/n : chr "181040"
#> $ HeadLS f : chr "0.065 0.0828 0.1212 0.0686"
#> $ HeadLS u0 : chr "278 337 932 412"
#> $ SysConst : chr NA
#> $ AvgTime : chr "4"
#> $ Oxygen : chr "21"
#> $ ChambConst : chr NA
#> $ Chamber : chr "6800-13"
#> $ Aperture : chr NA
#> $ blc_a : chr "0.43"
#> $ blc_b : chr "0.26782699999999998"
#> $ blc_c : chr "-1.164018E-4"
#> $ blc_d : chr "2.2482019999999999E-3"
#> $ blc_e : chr "-5.1094620000000004E-3"
#> $ blc_minS : chr "6"
#> $ blc_maxS : chr "36"
#> $ blc_Po : chr "96.8"
#> $ LTConst : chr NA
#> $ deltaTw : chr "0"
#> $ fT1 : chr "1"
#> $ fT2 : chr "0"
#> $ fTeb : chr "0"
#> $ LQConst : chr NA
#> $ Leaf : chr "standard"
#> $ Ambient : chr "Sun+Sky"
#> $ abs_ambient : chr "0.8"
#> $ abs_redLED : chr "0.84"
#> $ abs_greenLED : chr "0.7"
#> $ abs_blueLED : chr "0.87"
#> $ abs_whiteLED : chr "0.75"
#> $ abs_redFlr : chr "0.84"
#> $ abs_blueFlr : chr "0.87"
#> $ k_ambient : chr "0.19109999999999999"
#> $ k_redLED : chr "0.1512"
#> $ k_greenLED : chr "0.161"
#> $ k_blueLED : chr "0.22620000000000001"
#> $ k_whiteLED : chr "0.1575"
#> $ k_redFlr : chr "0.15959999999999999"
#> $ k_blueFlr : chr "0.2175"
#> $ QConst : chr NA
#> $ fQ_Amb_in : chr "0"
#> $ fQ_Amb_out : chr "0"
#> $ fQ_HeadLS : chr "1"
#> $ fQ_ConsoleLS : chr "0"
#> $ fQ_Flr : chr "0"
#> $ LeakConst : chr NA
#> $ fan_a : chr "-6276"
#> $ fan_b : chr "6.6"
#> $ fan_c : chr "1.7090000000000001E-5"
#> $ fan_d : chr "3.11"
#> $ Fs_meas : chr "9.9798 88.7742 373.458 604.839 838.545 1049.16 1238.82 1421.25"
#> $ Fs_true : chr "-0.0182238 101.978 404.227 600.718 801.26 1000.46 1201.87 1400.6"
#> $ leak_wt : chr "0"
# Include the oxygen info as a column in the file
licor_data <- get_oxygen_from_preamble(licor_data)
licor_data[, c('replicate', 'oxygen'), TRUE]
#>
#> Converting an `exdf` object to a `data.frame` before printing
#>
#> replicate [UserDefCon] (NA) oxygen [in] (percent)
#> 1 1 21
#> 2 1 21
#> 3 1 21
#> 4 1 21
#> 5 1 21
#> 6 1 21
#> 7 1 21
#> 8 1 21
#> 9 1 21
#> 10 1 21
#> 11 1 21
#> 12 1 21