Model vignettes

Includes vignettes for running several different models in PEcAn

BioCro/DARPA/ folder

This location has all of the vignettes for running BioCro on Setaria data for the Sentinel project.

Do the following tasks before knitting vignettes.

• Access RStudio in a browser by navigating to welsch.cyverse.org:8787/. Log in using your username and password.
• In the home directory, clone both the analysis and data repos:

git clone https://github.com/cct-datascience/model-vignettes.git
git clone https://github.com/cct-datascience/model-vignettes-data.git

Vignettes and inputs/outputs:

1. partitioned_biomass_datagets data prepared for estimating biomass coefficients from BioCro (see 2 & 3)
   • Inputs: biomass data from private data repo
   • Outputs: opt_biomass.csv and opt_weather.csv in opt_inputs
2. biomass_coeffs_0.95 estimates biomass coefficients using BioCro version 0.95
   • Inputs: opt_biomass.csv and opt_weather.csv
   • Outputs: biomass coefficients (these aren't saved anywhere)
3. biomass_coeffs_1.0 estimates biomass coefficients using BioCro version 1.0
   • Inputs: opt_biomass.csv, opt_weather.csv, setaria_initial_state.RData, and setaria_parameters.RData (latter two generated by create_params.R)
   • Outputs: biomass coefficients (these aren't saved anywhere)
4. plot_biomass_meas plots biomass data from all seven experiments
   • Inputs: biomass data from private data repo
5. temp_exps_biomass does three runs of BioCro and creates plots of biomass estimates against measured biomass values
   • Inputs: for each run in temp_exps_inputs* folder, there are temp_exps*.xml, workflow.R, setaria.constants.xml, and generate_*_weather.R
   • Outputs: BioCro results are all in temp_exps_results folder, and outputs in temp_exps_inputs* folder are danforth-*-chamber.2019.csv, biomass_ests*.csv, and *_biomass_measu.csv
6. high_light does biomass partitioning and biomass/transpiration estimates from BioCro for high light condition
   • Inputs: in high_light_inputs are workflow_*.R, config_*.xml, and constants_*.xml
   • Outputs: BioCro results are in high_light_results folder
7. (needs to be updated) pecan_runs shows how to do BioCro runs for two Setaria cultivars
8. (needs to be updated) regional_runs creates gif of BiCro runs across a large regional extent