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Camp PEON: Assimilation, multi-site, soil params, Maespa, LPJ-GUESS, improvements to web & tutorials
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@robkooper robkooper released this 12 Aug 12:56
· 15744 commits to master since this release
v1.4.8
ee00732

Virtual machine available for download

State Data Assimilation (SDA)

One of the main goals of this release was to re-generalize the EnKF and generalized ensemble filter that @araiho has been using with LINKAGES back to also working with SIPNET and to bring the design one step closer to working with many models. This is working (yeah!), but not yet fully generalized.

The revised SDA tutorial has been migrated to documentation/tutorials/StateAssimilation and the gitbook updated to explain the use of SDA tags in the settings file and the main functions used.

Multisite runs

The basic PEcAn workflow was substantially re-organized to allow PEcAn to more easily run multiple sites at once (see Site Groups below). The core of the design is to split PEcAn’s settings object (what’s read from the XML) into a list of settings objects, one for each run, and applied to existing functions. Both Settings and SettingsList are now R classes. Within the settings file itself, there is now a <runs> block that can include any number of individual <run>. Where appropriate, PEcAn gathers information across runs — for example, the meta-analysis is performed on the set of PFTs extracted across all runs, rather than being done run-by-run. This change is the first step in a large plan to re-organize the PEcAn workflow to be more modular and also support multi-model runs.

Note: Multisite/multimodel run SettingLists cannot yet be generated through the web interface.

Parameter data assimilation

  • Generalized to multiple PFTs
  • Emulator now supports a range of additional features that can be controlled through the XML settings:
    • multiple chains
    • extending chains (additional samples) starting from their latest state
    • adding additional knots
    • automated burnin detection

The revised PDA tutorial has been migrated to documentation/tutorials/ParameterAssimilation and the PDA vignette contains a more detailed explanation of how to use the new features.

Non-PFT parameter constraint

As an experiment in giving PEcAn control of non-PFT parameters, we've created a 'soil' PFT for SIPNET that contains soil biogeochemical parameters. If successful, we will extend this approach to other models. This change already improves model calibration and validation and has allowed us to assess the relative contribution of plant vs soil parameters to model output uncertainty.

Models

  • Maespa has basic functionality (thanks @mdekauwe for all the help!)
  • LPJ-GUESS running, but without PEcAn controlling parameters

Drivers

  • Fluxnet LaThuile

Web Interface

  • PEcAn landing page updated to be links to tools. Avoids confusion when users forget to add the /pecan, /bety, /rstudio, etc. to the web address.
  • Site groups has been populated with a number of major research networks: Ameriflux, Fluxnet, Fluxnet 2015 Tier 1 (open), LTER, NEON, ForestGEO, PalEON
  • Links to documentation, gitter, and bug reports from all pages
  • Additional mouseover text and links to model and variables tables
  • Legend in default plot, removed spline from Shiny plot

Camp PalEON

  • This is a special release for the PalEON summer course, and comes pre-installed with extra libraries and data for the course

Tutorials

In addition to migrating the PDA and SDA tutorials to RMarkdown, the model-data comparison at the end of Demo 1 has also been migrated to documentation/tutorials/AnalyzeOutput

Benchmarking

While still in alpha development, @bcow contributed a large chunk of code bringing us much closer to automated benchmark execution and a first pass at a Shiny page for benchmark visualization.

Bugfixes

  • C_stack bug in run.sensitivity.analysis: fixed on new VM but older users should upgrade gridExtra R package
  • Units in figures and reading of model output #792 -- downstream applications/code should check for changes.
  • Can skip meta-analysis in pecan settings. May require updating old pecan.xml, particularly for integration tests.
  • Interface: met date checking
  • Misc: #906 #916 #919 #923 #948 #950 #951

Known Issues

  • This version of PEcAn is misconfigured and is using the wrong server for Brown Dog. The server that is used is the development server for Brown Dog and might result in no data being returned. During the Camp PEON the development server will be using the same code as the production server. If you want to use BrownDog after Camp PEON we highly encourage you to sign up with Brown Dog. We will at that point contact you and send you the instructions to modify your VM to use your new account and the production servers.
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