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The BETY database

This is the official documentation for BETY: https://pecan.gitbook.io/betydb-documentation/betydb-tables

There is also a good bit of information about BETY in the PEcAn documentation as well https://pecanproject.github.io/pecan-documentation/develop

There are many instances of the database that are synced periodically. The master version is https://www.betydb.org/

The version you will be using is the copy that is hosted at BU on the psql-pecan server. It can be found at http://psql-pecan.bu.edu/bety You will never need to ssh directly to this server. You can access it from test-pecan.

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On test pecan there are two locations you should know about.

First is your home directory home/ - this is the home directory that was automatically generated for you. You don’t want to store anything there except your R library because it doesn’t actually have a lot of space.

The second is /fs/data3/ which is a shared directory among all the pecan serves. You want to make a directory in /fs/data3/ with your username as the name. For example, you can see my directory ecowdery is in /fs/data3. This is where you will put pecan. If you want to access pecan from your home directory, you can create a symlink.

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PEcAn has the (optional) ability to initiate large ensembles of runs to perform different types of analyses:

• Sensitivity Analysis (Global Sensitivity Analysis)
• Uncertainty Analysis
• State Data Assimilation
• Parameter Data Assimilation

For now we will not focus on data assimilation, but we should keep in mind ways to generalize and expand the app to eventually support visualizations for these analyses as well.

• PEcAn runs ensembles of runs as part of the PEcAn Workflow and then saves all the run outputs to .Rdata files at the get.results step.

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• dv_user_guide_cmd/adv_users_guide_cmd.Rmd
• dv_user_guide_cmd/extra_tools.Rmd
• dv_user_guide_cmd/replicate_ens_sens_cmd.Rmd
• dv_user_guide_cmd/replicate_run_cmd.Rmd
• dv_user_guide_cmd/working_with_vm.Rmd
• dv_user_guide_web/advanced_setup.Rmd
• dv_user_guide_web/Advanced_Users_Guide.Rmd
• dv_user_guide_web/Connecting-pecan-to-a-remote-server.Rmd
• dv_user_guide_web/curl-web-submit.Rmd
• dv_user_guide_web/DART_state_data_assimilation.Rmd

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rhdf5::h5read(file = "/projectnb/dietzelab/pecan.data/input/FACE_a_ED2_site_0-853/2004JUN.h5", "co2")

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Figures

• Add ellipse instead of data points for observations in pft plots
• Try with plotted means
• Read ggplot2 stat_ellipse code