Updating documentation

Author: gremau

README.md

@@ -53,30 +53,38 @@ Common tasks have scripts that can be run with common configurations, and are ea
 
 ### Create new "fluxall" files
 
-Fluxall files ({site}_{year}_fluxall.txt') should contain raw data from all sensors at a site for one year. The [script_make_fluxall.m](/scripts/script_make_fluxall.m) script will make these files, primarily by calling `card_data_processor.m` in various configurations and reading the raw data in 'toa5' and 'ts_data' directories. Though these files should contain all sensor data, in practice there are some sites with dataloggers that have not been configured to be merged into the fluxall file (namely the Valles Caldera sites).
+Fluxall files (`{site}_{year}_fluxall.txt`) should contain raw data from all sensors at a site for one year. The [script_make_fluxall.m](/scripts/script_make_fluxall.m) script will make these files, primarily by calling [card_data_processor.m](card_data_processor.m) in various configurations and reading the raw data in 'toa5' and 'ts_data' directories. Though these files should contain all sensor data, in practice there are some sites with dataloggers that have not been configured to be merged into the fluxall file (namely the Valles Caldera sites).
 
 ### Create new "qc", "for_gapfilling", and "for_gapfilling_filled" files
 
 There are several files created from the NMEG quality control pipeline, all output to the "processed_flux" directory. These are:
 
-1. qc files ({site}_{years}_fluxall_qc.txt): Contain all variables that are quality-controlled and then output by the [UNM_RemoveBadData.m](UNM_RemoveBadData.m) script.
+1. "qc" files (`{site}_{years}_fluxall_qc.txt`): Contain all variables that are quality-controlled and then output by the [UNM_RemoveBadData.m](UNM_RemoveBadData.m) script.
 
-2. for_gapfilling files ({site}_flux_all_{year}_for_gap_filling.txt): Also output by [UNM_RemoveBadData.m](UNM_RemoveBadData.m) script and contain a subset of quality-controlled variables in a format ready to be filled with ancillary met data.
+2. "for_gapfilling" files (`{site}_flux_all_{year}_for_gap_filling.txt`): Also output by [UNM_RemoveBadData.m](UNM_RemoveBadData.m) script and contain a subset of quality-controlled variables in a format ready to be filled with ancillary met data.
 
-3. for_gapfilling_filled files ({site}_flux_all_{year}_for_gap_filling_filled.txt): Same as the file above, but gaps in the met variables have been filled with ancillary met data by the [UNM_fill_met_gaps_from_nearby_site.m](UNM_fill_met_gaps_from_nearby_site.m) script.
+3. "for_gapfilling_filled" files (`{site}_flux_all_{year}_for_gap_filling_filled.txt`): Same as the file above, but gaps in the met variables have been filled with ancillary met data by the [UNM_fill_met_gaps_from_nearby_site.m](UNM_fill_met_gaps_from_nearby_site.m) script.
 
 To make these files, run the [script_make_qc_gf.m](/scripts/script_make_qc_gf.m). This script may also run the REddyProc gapfilling tool by calling on the [R code from the Max Planck institute](https://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWebRPackage), and the output (also in 'processed_flux') can be used to make AmeriFlux files, below, if desired.
 
 ### Create new AmeriFlux files
 
-AmeriFlux files ({af-site}_{year}_gapfilled.txt and {af-site}_{year}_with_gaps.txt) contain quality controlled sensor data, gapfilled met data, gapfilled fluxes, and partitioned C fluxes. There are several steps currently needed to create them.
+AmeriFlux files (`{af-site}_{year}_gapfilled.txt` and `{af-site}_{year}_with_gaps.txt`) contain quality controlled sensor data, gapfilled met data, gapfilled fluxes, and partitioned C fluxes. There are several steps currently needed to create them.
 
-1. Send the 'for_gapfilling_filled' file for each site/year to the [MPI EddyProc web service](http://www.bgc-jena.mpg.de/~MDIwork/eddyproc/upload.php). This service provides gapfilled and partitioned flux data, and is the way we currently have to get Lasslop partitioned fluxes used for the lower elevation NMEG sites.
+1. Send the "for_gapfilling_filled" file for each site/year to the [MPI EddyProc web service](http://www.bgc-jena.mpg.de/~MDIwork/eddyproc/upload.php). This service provides gapfilled and partitioned flux data, and is the way we currently have to get Lasslop partitioned fluxes used for the lower elevation NMEG sites.
 
-2. Once you receive notification that the partitioner has finished (by email), copy the job number and run [download_gapfilled_partitioned_flux.m](/retrieve_card_data/download_gapfilled_partitioned_flux.m) with the job number as an argument. This will download the resulting files to the 'processed_flux' directory.
+2. Once you receive notification that the partitioner has finished (by email), copy the job number and run [download_gapfilled_partitioned_flux.m](/retrieve_card_data/download_gapfilled_partitioned_flux.m) with the job number as an argument. This will download the resulting files to the "processed_flux" directory.
 
 3. Run [script_make_ameriflux.m](/scripts/script_make_ameriflux.m), which will call the `UNM_Ameriflux_File_Maker.m` with the specified configuration options and output the new AmeriFlux files to "FLUXROOT/FluxOut/".
 
+### Create soil "qc" and "qc_rbd" files
+
+Running the [script_make_soilmet_qc.m](/scripts/script_make_soilmet_qc.m) script for a site/year runs [soil_met_correct.m](soil_met_correct.m), which assembles all soil temperature, water content, heat flux, and TCAV sensor outputs, applies temperature corrections to VWC, and then removes bad data. The two output files, which are placed in "processed_soil", are:
+
+1. "qc" files (`{site}_{year}_soilmet_qc.txt`): Contains all sensor outputs, with raw outputs converted to VWC and temperature corrected (if applicable), for a site/year.
+
+2. "qc_rbd" files (`{site}_{year}_soilmet_qc.txt`): Same as above, but with outliers, level shifts, and other bad data removed on a site/year basis (see [soil_met_correct.m](soil_met_correct.m) for details.
+
 
 ## Additional documentation (in doc/)