In order to perform DM for CHLA you should
- STEP 1 : Estimate the DARK OFFSET of the CHLA
- https://github.com/catsch/dark_offset_chla on one core or
- https://github.com/qjutard/dark_offset_chla on several cores
- STEP 2 : Correct the profile from the DARK and estimate the quenching correction (Xing 2018, Terrats 2020, Sackmann 2008)
You need :
=> A working directory containing Argo B files and C files (Be careful the program will write a new CHLA_ADJUSTED in your B files !!!)
=> WMO.DARK : a file containing the OFFSET of the CHLA (the CHLA will be corrected as CHLA - OFFSET ) of the WMO float of interest
=> coriolis_CHLA.list is the list of all the WMO floats you want to correct (for every entry, you need a WMO.DARK file)
-lance_STEP2 is my launching script :
-It defines the pathway to the working directory
-It reads the coriolis_CHLA.list to know the WMO
-It reads the working directory to build the list of the Bfiles : "liste_all_B"
-MLD_calc.R is calculating the MLD
-IPAR_15_DEPTH.R is estimating the depth at which the PAR is equal to 15 (Limit under which there is no longer quenching)
-RunningFilter.R is used to filter (mean, median) the data
-Quenching_correction.R is the main program (you will need oce, stringR, ncdf4 library)
The outputs are files ready for STEP3 : estimation of the SLOPE