Automated processing, calibration, and delivery pipeline for measurement data
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Repository structure

The trace gas processing tools are broken into five components

  1. is the shell scripting control layer called by cron that sets environment variables and executes necessary processing code.
  2. run/stid.r called in parallel and executes site-specific processing code.
  3. src/ contains the bulk of processing source code as R functions.
  4. bad/ contains site/instrument specific bad data files for manual correction or removal of data. Changes are reflected at the qaqc and calibrated data levels.
  5. config/ contains json configurations for data structure and site metadata.
  6. .lock/ contains lock files in the form of site.lock to indicate active site processing and prevent duplicate execution.

Revising historic data

Changes in the historic datasets can be made using the bad/ data text files. When a new commit is made, the historic record for the given site is reprocessed on the next run (every 5 minutes).

Site metadata

Site metadata can be found in config/site_config.csv and at

Instrument naming conventions

Additional instrument metadata can be found in config/data_config.json.

Instrument Abbreviation
Licor 6262 IRGA licor_6262
Los Gatos Research UGGA lgr_ugga
MetOne ES642 metone_es642

QAQC flagging conventions

Numeric values are assigned to observations that meet certain automated or human identified criterion. The meaning of these identifiers are as follows.

Flag Description
1 Measurement data filled from backup data recording source
0 Data passes all QAQC metrics
-1 Data manually removed
-2 System flush
-3 Invalid valve identifier
-4 Flow rate or cavity pressure out of range
-5 Drift between adjacent reference tank measurements out of range
-6 Time elapsed between reference tank measurements out of range
-7 Reference tank measurements out of range
-8 Cavity humidity out of range