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README file for bayesian-osse-R source code Author: Lewis Kunik (lewiskunik@gmail.com) University of Utah LAIR group ------------------------- Overview of inverse model code ------------------------- This Bayesian inverse model code is based loosely on NOAA CarbonTracker-Lagrange software (see https://www.esrl.noaa.gov/gmd/ccgg/carbontracker-lagrange/), but written in the R programming language. This particular set-up performs an Observing System Simulation Experiment (OSSE), meaning that a set of "true" emissions are defined so as to generate synthetic enhancements which serve as the model data, in hopes of recovering the "true" emissions in the posterior/optimized result. This framework is equipped with random-normal (Gaussian) perturbations in the synthetic data in order to simulate the presence of model-data mismatch errors in the observations. Code can be downloaded and run as-is, provided that the proper input files are supplied. See the config.r file in inversion/ directory for sample naming conventions of input files. Required input files should be placed in the include/ directory: prior_emiss.nc true_emiss.nc prior_uncert.nc lonlat_domain.rds The following packages must be installed to successfully run the model code: "ncdf4" "lubridate" "geosphere" "data.table" In addition, netCDF library library version 4.1 or later is required, as well as R version 3.1.0 or later After inputs are supplied, the program may be run from the inversion/ directory. If running in the R programming environment (R or Rstudio), run by typing: source("run_all.r") If running directly from the terminal, run by typing: Rscript run_all.r NOTE: input NetCDF files (prior_emiss.nc, prior_uncert.nc, etc) should exist in (lon x lat x time) format, with lon/lat values indicating center-of-grid-cell, and time values expressed as beginning of time-step in either POSIX time or seconds since R epoch (1970-01-01 00:00:00 UTC). In addition, footprint files must be supplied in the footprints/ directory. Files should be in NetCDF format with dimensions (lon x lat x time). Source code is designed to work with files matching output format from STILT-R (https://uataq.github.io/stilt/). This inversion code works with files that abide by the naming convention where the first 10 characters of the filename indicate the start time of the footprint in format: YYYYmmddHH (i.e. year, month, day, hour). There is no required naming convention after 10 characters (the rest of the filename can be whatever you want).
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source code for Bayesian inverse flux estimation, written in R and using an Observing System Simulation Experiment (OSSE) framework driven by synthetic data
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