Code to generate synthetic population for Florida to be used for an agent-based model. Current version is 3.1.
The code depends specifically on a library abmgravity that is not available on CRAN. To install that package:
devtools::install_github("kokbent/abmgravity")
To generate statewide or ONE county specific population:
Rscript gen_dataset_for_synth.R config.json
Rscript create_synthpop.R
To generate population for one or multiple PUMA(s):
Rscript gen_dataset_for_synth_puma.R config_puma.json
Rscript create_synthpop.R
config.json is an example on how to setup for statewide/county synthpop generation. The configuration file contains list of paths to retrieve FL dataset required for synthpop generation. Specifically, one can change target_county according to which county they want. Default is Escambia. If the value is Florida or All, the script will generate statewide population.
config_puma.json is an example on how to setup for one or more PUMA(s) synthpop generation. The configuration file contains list of paths like config.json. Specify target_puma in square bracket to generate synthpop for those PUMAs. Default is a list of PUMAs that cover the whole of Miami-Dade and Monroe county.
target_county County name of subpopulation of interest or for statewide synthpop, use Florida or All.
output_name Controls the output SQLITE and TGZ file names (see output section). Required for PUMA synthpop, default to target_county if parameter unspecified in County/statewide synthpop.
extracurricular Toggle for extracurricular activity. 0 = No, 1 = Yes.
use_statewide_census Controls if Households and Persons in the synthpop are sampled from the corresponding area (0; more geographically uneven) or from statewide population (1).
data_folder "Prefix" of the paths.
path_county_shape Path to ESRI shapefile for counties, source: FGDL.
path_cenblock_shape Path to ESRI shapefile for census block group, source: FGDL.
path_centract_puma Path to relationship data frame (CSV) between census tract and PUMA (Public User Microdata Area), source: US Census.
path_ipums_xml Path to XML file for IPUMS data extract, provided by IPUMS.
path_ipums_dat Path to DAT file for IPUMS data extract, provided by IPUMS.
path_hhdens_raster Path to US household density raster (TIFF), source: SEDAC CIESIN.
path_wac_shape Path to ESRI shapefile for Work Area Characteristic (WAC) data by census block, source: FGDL.
path_naics_size Path to data frame (CSV) of US distribution of number of employees per NAICS code, source: BLS.
path_naics_lookup Path to data frame (CSV) of relationship between NAICS 2017 and 2012, source: ???.
path_workplace Path to data frame (CSV) of lat long of workplaces, their NAICS code and their "essential" status, source: NCD.
path_nh Path to data frame (CSV) of nursing homes (including lat long and size), source: FL AHCA.
path_schools_shape Path to ESRI shapefile of schools, source: FGDL.
path_col_uni_size Path to data frame (CSV) of "college/university" in the school file, containing their purported sizes, source: Google search by hand.
path_hf Path to data frame (TSV or CSV) of health facilities (hospital), containing their size and lat long, source: FL AHCA.
path_brfss Path to data frame (CSV) of processed BRFSS data, containing sex, age group, county and probability of having one or more COVID-19 underlying condition, source: BRFSS plus some data wrangling.
path_patterns Path to data frame (CSV) of processed safegraph data, containing prepandemic (Jan and Feb 2020) average raw number of visits to POI (point of interests) that are part of "extracurricular" activity in the ABM with either high (H) or low (L) transmission risk, source: Safegraph plus some data wrangling.
The code automatically create a .tgz file named as sim_pop-<county/output name>-<version>. This .tgz file contains a sqlite database. You can run the extract_sqlite-<version>.R script located inside the synth/ folder to extract four text files that are used as input to the ABM. The .tgz file must be in the same folder as the extract script. Example:
Rscript extract_sqlite-3.0.R sim_pop-escambia-3.0.tgz
You then get a folder called sim_pop-escambia which contains four .txt files.