Bucky Model input graph creation
usage: make_input_graph [-h] [-d DATE] [-o OUTPUT] [--hist_file HIST_FILE] [-v] [--no_update]
Start date of simulation, last date for historical data.
Default: “2020-12-01”
Directory for graph file. Defaults to data/input_graphs/
Default: “config.yml: <data_dir>/input_graphs/”
File to use for historical data
Default: “config.yml: <data_dir>/cases/csse_hist_timeseries.csv”
verbose output (repeat for increased verbosity; defaults to WARN, -v is INFO, -vv is DEBUG)
Default: 0
Skip updating data
Default: True
Bucky Model
usage: model [-h] [--graph GRAPH_FILE] [--n_mc N_MC] [--days DAYS] [--seed SEED] [-v] [-q] [-gpu] [-den] [-opt] [-r] [-o OUTPUT_DIR] [--npi_file [NPI_FILE]] [--disable-npi] [par_file]
File containing paramters
Default: “config.yml: <base_dir>/par/scenario_5.yml”
Pickle file containing the graph to run
Default: “Most recently created graph in <data_dir>/input_graphs”
Number of runs to do for Monte Carlo
Default: 100
Length of the runs in days
Default: 40
Initial seed to generate PRNG seeds from (doesn’t need to be high entropy)
Default: 42
quiet output (only show ERROR and higher)
Use cupy instead of numpy
Default: False
Don’t store the adj matrix as a sparse matrix. This will be faster with a small number of regions or a very dense adj matrix.
Enable cupy kernel optimizations. Do this for large runs using the gpu (n > 100).
Reject Monte Carlo runs with incidence rates that don’t align with historical data
Dir to put the output files
Default: “config.yml: <raw_output_dir>”
File containing NPIs
Disable all active NPI from the npi_file at the start of the run
Bucky Model postprocessing
usage: postprocess [-h] [-g GRAPH_FILE] [-l LEVELS [LEVELS ...]] [-q QUANTILES [QUANTILES ...]] [-o OUTPUT] [--prefix PREFIX] [--end_date END_DATE] [--lookup LOOKUP] [-n NPROCS] [-cpu] [--verify] [--no-sort] [-v] [file]
File to proess
Default: “Most recently created folder in raw_output_dir”
Graph file used for simulation
Levels on which to aggregate
Default: [‘adm0’, ‘adm1’, ‘adm2’]
Quantiles to process
Default: [0.01, 0.025, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 0.975, 0.99]
Directory for output files
Default: “config.yml: <output_dir>”
Prefix for output folder (default is UUID)
Lookup table defining geoid relationships
Number of threads doing aggregations, more is better till you go OOM…
Default: 1
Do not use cupy
Verify the quality of the data
Skip sorting the aggregated files
Print extra information
Bucky model plotting tools
usage: viz.plot [-h] [-i INPUT_DIR] [-o OUTPUT] [-g GRAPH_FILE] [-l LEVELS [LEVELS ...]] [--plot_columns PLOT_COLUMNS [PLOT_COLUMNS ...]] [--lookup LOOKUP] [--min_hist MIN_HIST] [--hist_start HIST_START] [--adm1_name ADM1_NAME] [--end_date END_DATE] [-v] [-hist] [--hist_file HIST_FILE] [-q QUANTILES [QUANTILES ...]] [-w WINDOW_SIZE]
Directory location of aggregated data
Default: “Most recently created folder in output_dir”
Output directory for plots. Defaults to input_dir/plots/
Graph file used during model. Defaults to most recently created graph
Requested plot levels
Default: [‘adm0’, ‘adm1’]
Columns to plot
Default: [‘daily_reported_cases’, ‘daily_deaths’]
Lookup table for geographic mapping info
Minimum number of historical data points to plot.
Start date of historical data. If not passed in, will align with start date of simulation
Admin1 to make admin2-level plots for
Data will not be plotted past this point
Plot historical data in addition to simulation data
Path to historical data file. If None, uses either CSSE or Covid Tracking data depending on columns requested.
Specify the quantiles to plot. Defaults to all quantiles present in data.
Size of window (in days) to apply to historical data
Default: 7
Bucky model mapping tools
usage: viz.map [-h] [-i INPUT_DIR] [-o OUTPUT] [-g GRAPH_FILE] [--columns COLUMNS [COLUMNS ...]] [--linear] [-f {daily,weekly,monthly}] [-d DATES [DATES ...]] [--adm0] [--all_adm1] [--adm1 ADM1 [ADM1 ...]] [--adm1_shape ADM1_SHAPE] [--adm2_shape ADM2_SHAPE] [--adm1_col ADM1_COL] [--adm2_col ADM2_COL] [--lookup LOOKUP] [-c CMAP]
Directory location of processed simulation data
Output directory for maps. Defaults to input_dir/maps/
Graph file used during model
Data columns to plot. Maps are created separately for each requested column
Use linear scaling for values instead of log
Possible choices: daily, weekly, monthly
Frequency at which to create maps
Default: “weekly”
Specific dates to map
Create adm0-level plot
Create adm1-level plot for every available adm1-level area
Create adm1-level plot for the requested adm1 name
Location of admin1 shapefile
Default: “config.yml: <data_dir>/shapefiles/tl_2019_us_state.shp”
Location of admin2 shapefile
Default: “config.yml: <data_dir>/shapefiles/tl_2019_us_county.shp”
Shapefile adm1 column name
Default: “STATEFP”
Shapefile adm2 column name
Default: “GEOID”
Colormap to use. Must be a valid matplotlib colormap.
Default: “Reds”