FE Project Template

File Descriptions

folder	subfolder	filename	generated by?	description
-	-	site_setup.py	built-in	actual script that is executed to generate input files ("setup_climate" or "setup_migration"), run simulations ("burnin" or "pickup") and analyze outputs ("calibrate")
-	-	manifest.py	built-in	helper for setting input/output/experiment paths
-	-	utils_slurm.py	built-in	helper for buld_burnin_df used to serialize simulations.
simulation_inputs/	-	demographics.csv	user	Describes location of site(s) to include in simulations. Required to generate climate or migration files before running any simulations. Columns: node_id, pop, lat, lon Be very careful adding new columns, as the to_csv() function of emodpi-api demographics may automatically recognize them as parameters
-	-	generate_climate.py	built-in	Creates weather files for nodes in demographics.csv over a specified date range, with options for - constant temperature - shifted rainfall. Stores files in simulation_inputs/<site_name>/climate/<DateRange>/<RainShift_Temperature>/
simulation_inputs/	climate/	...	site_setup: step = 'setup_climate'	Subfolders containing weather files created by generate_climate.py during the "setup_climate" step. Each will be named according to <site_name>/<DateRange>/<RainShift_Temperature>
-	-	generate_migration_files.py	built-in	For multi-node simulations, builds migration binary files from input .csv files that exist in simulation_inputs/migration/ for the migration types listed in the migration_files dictionary within the "OPTIONS" block of site_setup.py
simulation_inputs/	migration/	..._migration.csv	user	Input spreadsheet describing migration between nodes in spatial simulations. Ex. local_migration.csv, vector_local_migration.csv, etc. Columns are FromNode, ToNode, Rate without headers
simulation_inputs/	migration/	..._migration.bin	site_setup: step = 'setup_migration'	Migration binary files created by generate_migration_files.py during the "setup_migration" step. Each will match the corresponding name and migration type based on the input .csv files (above) and the migration_files dictionary in the "OPTIONS" block of site_setup.py
simulation_inputs/	-	interventions_CM.csv	user	input file to setup Case Management via add_treatment_seeking. Columns: node_id, phase, start_day, duration, trigger, age_min, age_max, coverage, seek, rate, drug, year
simulation_inputs/	-	interventions_SMC.csv	user	input to setup Seasonal Malaria Chemoprevention via add_drug_campaign with drug-code 'SPA'. Columns: node_id, phase, year, round, start_day, coverage
simulation_inputs/	-	interventions_IRS.csv	user	input file to setup Indoor Residual Spraying via scheduled_IRSHousingModification. Columns: node_id, phase,year, start_day, coverage, kill_effect, kill_duration, kill_decay, repel_effect, repel_duration, repel_decay, insecticide_name
simulation_inputs/	-	interventions_ITN.csv	user	input file 1/3 to setup distribution of insecticide-treated bednets via scheduled_usageDependentBednet. Columns: node_id, phase, year start_day, kill_effect, kill_decay, block_effect, block_decay, discard_k, discard_l, coverage
simulation_inputs/	-	interventions_ITN_age.csv	user	input file 2/3 to setup distribution of insecticide-treated bednets via scheduled_usageDependentBednet. Columns: node_id, phase, year, age, age_usage
simulation_inputs/	-	interventions_ITN_season.csv	user	input file 3/3 to setup distribution of insecticide-treated bednets via scheduled_usageDependentBednet. Columns: node_id, season_time, season_usage

Basic instructions:

1. Create a folder within simulation_inputs for a new site (ex. "sapone")
2. Create a new demographics.csv for your site(s)/node(s)
3. Run site_setup.py with step = 'setup_climate' to create a folder with climate files specifying:
   • date range to request from COMPS
   • Constant temperature value (optional)
   • rainfall shift (optional)
4. Populate other input files with information relevant to your site simulations:

   • vectors.csv - for vector species mix and parameters

     Interventions, if applicable:

   • interventions_CM.csv - For treatment-seeking / case management

   • interventions_SMC.csv - For seasonal chemoproprevention

   • interventions_IRS.csv - For indoor residual spraying

   • interventions_ITN.csv - For usage-dependent bednet distributions, also include:

     • interventions_ITN_age.csv - age pattern of net usage
     • interventions_ITN_season.csv - seasonal pattern of net usage

     Migration, if applicable:

   • local_migration.csv - for local human migration between nodes

   • vector_local_migration.csv - for local vector migration between nodes

     4a. Run site_setup.py with step = 'setup_migration' to create migration binary files for spatial simulations

5. Configure the habitat space you would like to sweep over. In the "OPTIONS" block of site_setup.py, select a list of values for:
   • scale_temp_rain
   • scale_water_veg
   • scale_constant (usually left as [1.0])
   • xTLH
6. Run site_setup.py with step = 'burnin'. Copy experiment-id to burnin_id
7. Run site_setup.py with step = 'pickup'. Copy experiment-id to pickup_id
8. Run site_setup.py with step = 'calibrate' or 'analyze_pickup'. Results will be stored in simulation_outputs/site_name/exp_label
9. For now use plot_site_setup.Rmd to visualize outputs