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AGU 2016 Release
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@robkooper robkooper released this 10 Dec 19:24
· 14176 commits to master since this release
v1.4.9
d7080db

Security Issue

There was a security issue in all of the previous versions of PEcAn. All users are highly encouraged to upgrade to the latest version of PEcAn that fixes this issue. Feel free to contact us for more information about this issue and how to check your instance.

New Models

  • FATES
  • MAAT

Code Clean-up

  • Massive rework of almost the entire code base to better adhere to coding standards and making far more explicit use of R namespaces. A large thanks goes to Ben Bond-Lamberty for initiating this!
  • Code clean up uncovered (and in some places created) a wide range of small bugs in the code
  • A long standing bug in PEcAn's met processing workflow was an inability to change the temporal range of processed data (i.e. subsequent runs at a site needed to be for the same years). This has now been generalizied across the workflow to update the union of current and new years. The workflow also now distinguishes models that can choose dates from a directory of met data versus models that have to be fed a met driver that is the exact years of the run.

Benchmarking

  • Fully-functional workflow now exists that can run benchmarks in the PEcAn database through the workflow based just on settings XML.
  • This required splitting read.settings in two and having reference runs inserted in from database
  • Generation of FACE benchmarks
  • Addition of additional metric functions
  • TODO: make it easier to create benchmarks and leverage these tools for general visualization and validation

Parameter Data Assimilation (PDA)

  • Fixed mismatch in data alignment due to time zone differences
  • Saving covariance matrix for running the MCMC longer
  • handling the priors better
  • PDA with derived variables (as in SA and EA, although I didn't have a case I needed to use it)
  • More likelihoods (Gaussian and multiplicative Laplacian) than Heteroskedastic Laplacian (normal was always there but never really functional I think)
  • Building emulator on sufficient statistics surface allowing us to update variances (but we don't insert posteriors for variances to the DB yet)
  • Ability to handle non-model parameters like bias terms and precision
  • Building one emulator per constraining variable

State Data Assimilation (SDA)

  • Generalized SDA code to work better across models with a more standardized interface design
  • Also generalized SDA's date handling code so that SDA can be run at different temporal frequencies (previously was hard-coded to annual)
  • Added ability to calculate autocorrelation of observation data products and inflate observation covariance
  • Generalized from multivariate normal model to multivariate Tobit model to handle zero- and range-bound data (e.g. AGB, fractional composition) in a way that is zero-inflated while also accounting for covariances.
  • Initial work (incomplete) toward adding ED2 and LPJ-GUESS couplers for read.restart and write.restart.

Misc

  • make: Switched PEcAn build to a make based system. This makes rebuilding quicker and also allows R to more automatically handle downloading required packages.
  • add site: Added ability to add new sites on the PEcAn map by right-clicking on the map
  • RTM PDA: RTM module now has a system in place to do stand-level parameter data assimilation using the ED2 radiative transfer model.

DOI

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