6.3 Selecting Plant Functional Types (PFTs) and other parameter groupings.
6.3.1 Using existing PFTs
PEcAn does not automatically know what vegetation types are present at your study site so you need to select the PFT.
Some models, such as ED2 and LINKAGES, support competition among multiple PFTs and thus you are encouraged to highlight multiple choices. Other models, such as SIPNET and DALEC, only support one PFT at a site.
Many models also have parameters that control non-vegetation processes (e.g. soil biogeochemistry and hydrology). PEcAn allows users to assign these parameters to functional groups as well (e.g. a
6.3.2 Creating new PFTs
To modify or add a new Plant Functional Type (PFT), or to change a PFT’s priors, navigate on the grey menu bar to Data > PFTs
To add a new pft, click “new PFT” at the top and enter a name and description. (hint: we’re trying to name PFTs based on model.biome.pft, ED2 is the default model if one isn’t specified)
To add new species to a PFT click on [+] View Related Species and type the species, genus, or family you are looking for into the Search box. Click on the + to add.
To remove a species from a PFT, click on [+] View Related Species and click on the X of the species you want to remove from the PFT.
To remove a prior, click [-] View Related Prior and click on the X of the variable who’s prior you want to remove. This will cause the parameter to be excluded from all analyses (meta-analysis, sensitivity analysis, etc) and revert to its default value.
To add a prior, choose one from the white box of priors on the right to choose.
To view the specification of a prior, or to add a new prior, click BETY-DB > Priors and enter the information on the variable, distribution name, distribution parameters, etc. N is the sample size underlying the prior specification (0 is ok for uninformative priors).
You can also got to Data > Variables in order to use the search function to find an existing variable (or create a new one). Please try not to create new variables unnecessarily (e.g. changes of variable name or units to what your model uses is handled internally, so you want to find the trait with the correct MEANING).
Additional information on adding PFTs, Species, and Priors can be found in Adding An [Ecosystem Model].
6.3.3 Choosing initial vegetation
On the Input Selection webpage, in addition to selecting PFTs, start & end dates, and meteorology, many models also require some way of specifying the initial conditions for the vegetation, which may range from setting the aboveground biomass and LAI up to detailed inventory-like data on species composition and stand structure.
At the moment, PEcAn has three cases for initial conditions:
If files already exist in the database, they can simply be selected from the menu. For ED2, there are 3 different veg files (site, pss, css) and it is important that you select a complete set, not mix and match.
If files don’t exist they can be uploaded following the instructions in Create a database file record for the input data.
Automated vegetation initial condition workflow
As with meteorology, PEcAn is working to develop a model-agnostic workflow for converting various sources of vegetation data to common standards, developing common processing tools, and then writing out to model-specific formats. This process is in a much early stage than the meteorology workflow, as we are still researching what the options are for standard formats, but ultimately aims to be much more broad in scope, considering not just plot inventory data but also historical documentation, paleoecological proxies, satellite remote sensing (e.g. LANDSAT), airborne hyperspectral imagery, and active remote sensing (Lidar, Radar).
At the moment, what is functional is a prototype workflow that works for inventory-based vegetation data. This data can come from either files that have been registered with the BETY Inputs and Formats tables or can be queried from the USFS Forest Inventory and Analysis (FIA). For more information visit Section 18.104.22.168 Vegetation Data
6.3.4 US FIA
This tool works with an internal copy of the FIA that is uploaded to a postGRES database along side BETY, however for space reasons this database does not ship with the PEcAn VM. To turn this feature on:
- Download and Install the FIA database. Instructions in Installing data for PEcAn
- For web-base runs, specify the database settings in the config.php
- For R-based runs, specify the database settings in the THE PEcAn XML
More detailed information on how PEcAn processes inputs can be found on our [Input Conversion]page.
6.3.5 Spin up
A number of ecosystem models are typically initialized by spinning up to steady state. At the moment PEcAn doesn’t handle spin up automatically (e.g. looping met, checking for stability), but there are various ways to achieve a spin-up within the system.
Option 1: If there are model-specific settings in a model’s settings/config file, then that file can be accessed by clicking on the Edit model config check box. If this box is selected then PEcAn will pause the site run workflow after it has generated your model config file, but before it runs the model, and give you an opportunity to edit the file by hand, allowing you to change any model-specific spin up settings (e.g met recycling, spin up length)
Option 2: Set start_year very early and set the met drivers to be a long time series (e.g. PalEON, something custom uploaded to Inputs)
Option 3: In the MODEL_TYPE table, add your model’s restart format as an optional input, modify the model specific write.config function to use that restart, and then load a previous spin-up to the Inputs table
Beyond these options, we hope to eventually develop more general, model-agnostic tools for spin up. In particular, we have started to explore the accelerated spin-up and semi-analytical techniques being developed by Yiqi Luo’s lab
6.3.6 Selecting a soils product
Many models have requirements for soils information, which may include: site-specific soil texture and depth information; soil biogeochemical initial conditions (e.g. soil carbon and nitrogen pools); soil moisture initial conditions; and soil thermal initial conditions.
As with Choosing initial vegetation, we eventually hope to develop data standards, soils workflows, and spin-up tools, but at the moment this workflow is in the early stages of development. Model requirements need to be met byCreating a new Input record in BETY into the database or using files that have already been uploaded. Similar to met, we recommend that this file be in the PEcAn-standard netCDF described below, but model-specific files can also be registered.
6.3.7 Soil texture, depth, and physical parameters
A PEcAn-standard netCDF file format exists for soil texture, depth, and physical parameters, using PEcAn standard names that are largely a direct extention of the CF standard.
The easiest way to create this file is with the PEcAn R function
soil2netcdf as described in the Soil Data section of the Advanced Users Guide.
A table of standard names and units can be listed using
PEcAn.data.land::soil.units() with no arguments.
More detailed information on how PEcAn processes inputs can be found on our [Input Conversion] page.
6.3.8 Other model inputs
Finally, any other model-specific inputs (e.g. N deposition, land use history, etc), should be met by Creating a new Input record in BETY or using files that have already been uploaded.