Codes to run multiple APSIM simulations on Illinois-US
This codes allow to obtain a database simulated with APSIM for 4200 fields over 30 years. The codes start by obtianing the field information , the soils parameters and the weather files Then it run simulations with increasing Nitrogen rates Finally it merges the output and evaluates different N recommendation tools.
Questions about the code and methodology: German Mandrini, Dpt of Crop Sciences, University of Illinois at Urbana-Champaign, [email protected]
Questions about collaborations: Nicolas F Martin, Dpt of Crop Sciences, University of Illinois at Urbana-Champaign, [email protected]
The scripts used to obtain soil data and transform it into APSIM files is adapted from https://github.com/rmartinezferia/APssurgo
</style>| FOLDER WITH ALL DATA FILES | ||
| https://uofi.box.com/s/d6a9rcwv1znpy9ipmsj6r33vet2qxvq5 | Download it and link it to the codes files when needed | |
| INITIAL SET UP OF FILES FOR RUNNING THE SIMULATIONS | ||
| Order | File name | Objective |
| 1 | grid_10_creation.R | Code to create a grid of 10x10 km over Illinois |
| 2 | grid_10_update.R | Update the grid with the area of corn |
| 3 | z_downloader.R | Code to download the weather of the centroid of each cell |
| 4 | z_creator_nov20.R | Randomize the weather |
| 5 | fields_selector_manager.R | Code to spit the the grid file in tiles and call the fields selector in parallel |
| 6 | fields_selector_parallel_focal_v2.R | Code to select fields on each cell in parallel |
| 7 | clean_fields_step1.R | Clean fields. Leave only three soils |
| 8 | soils_manager_Nov29.R | Download horizons for each soil |
| 9 | clean_fields_step2.R | Clean fields again, remove soils polygon whose horizons were not found |
| 10 | planting_dates_soil_temp_jul24.R | Select planting dates for each cell |
| RUNNING THE SIMULATIONS | ||
| Order | File name | Objective |
| 11 | walltime_updater.R | Creates a table with the id_10 and the expected walltime |
| 12 | A_walltime_sender.sh | For cluster: calls B_bash for each cell |
| 13 | B_bash.sh | For cluster: calls R using sigularity container |
| 14 | APSIM_package.R | Loads APSIM package (is deprecated for some R versions) |
| 15 | simA_manager.R | Controls the simulations. Calls the other scripts |
| 16 | simB_create_instructions.R | Creates the weather and soil files and the instructions for all simulations inside a cell |
| 17 | simC_make_z_and_met_files.R | Makes the met files |
| 18 | simD_create_apsim_files.R | Makes the apsim files |
| 19 | simE_update_ic.R | Updates the Initial conditions |
| 20 | simF_run_files.R | Run all the APSIM files |
| 21 | simG_merge_results.R | Merges APSIM output |
| 22 | simH_daily_to_yearly.R | Transforms APSIM output from daily data to yearly |
| PROCESSING AND ANALYZING THE RESULTS | ||
| Order | File name | Objective |
| 23 | parameters.R | Setting parameters used during the work, like prices and fees |
| 24 | 2_post_processing_nov29.R | Clean restuls. Remove outliers |
| 25 | 3a_regional_stations.R | Selects the regional stations, used for training |
| 26 | 3b_fields_splitter.R | Splits APSIM output by field, and aggregates it considering the area of each soil |
| 27 | 3d_train_and_evaluate_loyo_mar10.R | Trains and evaluates models to provide N recommendation tools |