State Data Assimilation

This function is housed within: /pecan/modules/assim.sequential/R

sda.enkf.R

This is the main ensemble Kalman filter and generalized filter code. Originally, this was just ensemble Kalman filter code. Mike Dietze and Ann Raiho added a generalized filter to avoid filter divergence.

The main parts of the function are:

Setting up run:

• read settings

• load climate data

• open database connection

• get new workflow ids

• create ensemble ids

• set up model specific functions

Performing the initial set of runs (spinup)

Set up for data assimilation

Loop over time

• read.restart - read netcdfs corresponding to year that you want to assimilate data into

• analysis - if observation is available run either kalman filter or generalized ensemble filter

• write.restart - write model specific write.configs to run model with state variables from analysis

• run model

Save outputs

Create diagnostics

State Data Assimilation Tags

<state.data.assimilation>
    <process.variance>FALSE</process.variance>
  <sample.parameters>FALSE</sample.parameters>
  <state.variable>AGB.pft</state.variable>
  <state.variable>TotSoilCarb</state.variable>
  <spin.up>
      <start.year>2004</start.year>
      <end.year>2006</end.year>
  </spin.up>
  <forecast.time.step>1</forecast.time.step>
    <start.year>2004</start.year>
    <end.year>2006</end.year>
</state.data.assimilation>

• process.variance : [optional] TRUE/FLASE flag for if process variance should be estimated (TRUE) or not (FALSE). If TRUE, a generalized ensemble filter will be used. If FALSE, an ensemble Kalman filter will be used. Default is FALSE.
• sample.parameters : [optional] TRUE/FLASE flag for if parameters should be sampled for each ensemble member or not. This allows for more spread in the intial conditions of the forecast.
• NOTE: If TRUE, you must also assign a vector of trait names to pick.trait.params within the sda.enkf function.
• state.variable : [required] State variable that is to be assimilated (in PEcAn standard format). Default is "AGB" - Above Ground Biomass.
• spin.up : [required] start.date and end.date for model spin up.
• NOTE: start.date and end.date are distinct from values set in the run tag because spin up can be done over a subset of the run.
• forecast.time.step : [optional] start.date and end.date for model spin up.
• start.date : [required?] start date of the state data assimilation (in YYYY/MM/DD format)
• end.date : [required?] end date of the state data assimilation (in YYYY/MM/DD format)
• NOTE: start.date and end.date are distinct from values set in the run tag because this analysis can be done over a subset of the run.

read.restart.MODEL.R

This model specific function reads the netcdfs of a specific year. Takes out the applicable state variable for state data assimilation, and give it to a matrix in sda.enkf.R

write.restart.MODEL.R

This model specific function takes in an analysis matrix from sda.enkf.R and translates the state variables back to the model variables. Then, writes a write.config.MODEL to restart the model.