Quickstart
User Guide
API Reference
Bucky on GitHub
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Z
_
__deepcopy__() (bucky.util.dotdict method)
(bucky.util.util.dotdict method)
__delattr__ (bucky.util.dotdict attribute)
(bucky.util.util.dotdict attribute)
__get__() (bucky.util.cached_prop.cached_property method)
__getattr__ (bucky.util.dotdict attribute)
(bucky.util.util.dotdict attribute)
__getattribute__() (bucky.model.state.buckyState method)
__setattr__ (bucky.util.dotdict attribute)
(bucky.util.util.dotdict attribute)
__setattr__() (bucky.model.state.buckyState method)
_absorb_constraints() (in module bucky.util.spline_smooth)
_banner() (in module bucky.util)
(in module bucky.util.util)
_compute_base_functions() (in module bucky.util.spline_smooth)
_cr() (in module bucky.util.spline_smooth)
_csr_diag() (in module bucky.model.adjmat)
_csr_is_ind_sorted() (in module bucky.model.adjmat)
_find_knots_lower_bounds() (in module bucky.util.spline_smooth)
_generate_param_funcs() (bucky.model.parameters.buckyParams method)
_get_free_crs_dmatrix() (in module bucky.util.spline_smooth)
_get_natural_f() (in module bucky.util.spline_smooth)
_qr (in module bucky.numerical_libs)
_read_edge_mat() (in module bucky.model.adjmat)
_read_node_attr() (in module bucky.model.graph)
_rolling_arithmetic_mean() (in module bucky.util.rolling_mean)
_rolling_geometric_mean() (in module bucky.util.rolling_mean)
_rolling_harmonic_mean() (in module bucky.util.rolling_mean)
A
A() (bucky.model.adjmat.buckyAij property)
ADD_AMERICAN_SAMOA (in module bucky.util.update_data_repos)
add_col_data_to_plot() (in module bucky.viz.plot)
add_daily_history() (in module bucky.util.get_historical_data)
add_hist_data_to_plot() (in module bucky.viz.plot)
add_npi() (bucky.model.mc_instance.buckyMCInstance method)
add_vacc() (bucky.model.mc_instance.buckyMCInstance method)
adm0_cum_case_hist() (bucky.model.graph.buckyGraphData method)
adm0_cum_death_hist() (bucky.model.graph.buckyGraphData method)
adm0_inc_case_hist() (bucky.model.graph.buckyGraphData method)
adm0_inc_death_hist() (bucky.model.graph.buckyGraphData method)
adm0_Ni() (bucky.model.graph.buckyGraphData method)
adm1_cum_case_hist() (bucky.model.graph.buckyGraphData method)
adm1_cum_death_hist() (bucky.model.graph.buckyGraphData method)
adm1_inc_case_hist() (bucky.model.graph.buckyGraphData method)
adm1_inc_death_hist() (bucky.model.graph.buckyGraphData method)
adm1_Nij() (bucky.model.graph.buckyGraphData method)
adm1_Nj() (bucky.model.graph.buckyGraphData method)
age_interp() (bucky.model.parameters.buckyParams static method)
Aij() (bucky.model.mc_instance.buckyMCInstance property)
ALLOW_FUNCTOOLS (in module bucky.util.cached_prop)
approx_betaincinv() (in module bucky.util.distributions)
approx_mPERT() (in module bucky.util.distributions)
args (in module bucky.make_input_graph)
(in module bucky.util.graph2histcsv)
(in module bucky.viz.map)
B
BEST_OPT_FILE (in module bucky.model.optimize)
BETA_eff() (bucky.model.mc_instance.buckyMCInstance method)
bin_age_csv() (in module bucky.util)
(in module bucky.util.util)
bucky
module
bucky.make_input_graph
module
bucky.model
module
bucky.model.__main__
module
bucky.model.adjmat
module
bucky.model.arg_parser_model
module
bucky.model.estimation
module
bucky.model.exceptions
module
bucky.model.graph
module
bucky.model.main
module
bucky.model.mc_instance
module
bucky.model.npi
module
bucky.model.optimize
module
bucky.model.parameters
module
bucky.model.rhs
module
bucky.model.state
module
bucky.model.vacc
module
bucky.numerical_libs
module
bucky.postprocess
module
bucky.util
module
bucky.util.cached_prop
module
bucky.util.distributions
module
bucky.util.extrapolate
module
bucky.util.fractional_slice
module
bucky.util.get_historical_data
module
bucky.util.graph2histcsv
module
bucky.util.ode_constraints
module
bucky.util.read_config
module
bucky.util.readable_col_names
module
bucky.util.rolling_mean
module
bucky.util.scoring
module
bucky.util.spline_smooth
module
bucky.util.update_data_repos
module
bucky.util.util
module
bucky.viz
module
bucky.viz.geoid
module
bucky.viz.map
module
bucky.viz.plot
module
bucky_cfg (in module bucky.util.read_config)
buckyAij (class in bucky.model.adjmat)
buckyGraphData (class in bucky.model.graph)
buckyMCInstance (class in bucky.model.mc_instance)
buckyModelCovid (class in bucky.model.main)
buckyParams (class in bucky.model.parameters)
buckyState (class in bucky.model.state)
buckyVaccAlloc (class in bucky.model.vacc)
C
cached_property (class in bucky.util.cached_prop)
cached_scatter_add() (in module bucky.model.graph)
calc_beta() (in module bucky.model.parameters)
calc_derived_params() (bucky.model.parameters.buckyParams method)
calc_gamma() (in module bucky.model.parameters)
calc_lagged_rate() (bucky.model.main.buckyModelCovid method)
calc_Reff() (in module bucky.model.parameters)
calc_Te() (in module bucky.model.parameters)
calc_Ti() (in module bucky.model.parameters)
case_death_df() (in module bucky.model.optimize)
CI_to_std() (in module bucky.model.parameters)
Cij() (bucky.model.mc_instance.buckyMCInstance method)
clean_historical_data() (bucky.model.graph.buckyGraphData method)
COLUMNS (in module bucky.model.optimize)
compute_population_density() (in module bucky.make_input_graph)
constrain_y_range() (in module bucky.util.ode_constraints)
covid_tracking (in module bucky.util.get_historical_data)
csse (in module bucky.util.get_historical_data)
cupy_found (in module bucky.model.arg_parser_model)
(in module bucky.postprocess)
D
data_locations (in module bucky.util.get_historical_data)
date_to_t_int() (in module bucky.util.util)
DAYS_OF_HIST (in module bucky.make_input_graph)
default_cmap (in module bucky.viz.map)
default_plot_cols (in module bucky.viz.map)
(in module bucky.viz.plot)
default_quantiles (in module bucky.postprocess)
DEFAULT_RET (in module bucky.model.optimize)
diag() (bucky.model.adjmat.buckyAij property)
distribute_data_by_population() (in module bucky.util.update_data_repos)
distribute_mdoc() (in module bucky.util.update_data_repos)
distribute_nyc_data() (in module bucky.util.update_data_repos)
distribute_territory_data() (in module bucky.util.update_data_repos)
distribute_unallocated_csse() (in module bucky.util.update_data_repos)
distribute_utah_data() (in module bucky.util.update_data_repos)
dotdict (class in bucky.util)
(class in bucky.util.util)
dtype (in module bucky.util.spline_smooth)
E
emit() (bucky.util.TqdmLoggingHandler method)
(bucky.util.util.TqdmLoggingHandler method)
empty_like_pinned (in module bucky.numerical_libs)
empty_pinned (in module bucky.numerical_libs)
enable_cupy() (in module bucky.numerical_libs)
epi_params() (bucky.model.mc_instance.buckyMCInstance property)
estimate_cfr() (in module bucky.model.estimation)
estimate_chr() (in module bucky.model.estimation)
estimate_crr() (in module bucky.model.estimation)
estimate_doubling_time() (in module bucky.model.estimation)
estimate_IFR() (in module bucky.util)
(in module bucky.util.util)
estimate_Rt() (in module bucky.model.estimation)
ExperimentalWarning (in module bucky.numerical_libs)
extract_values() (in module bucky.model.optimize)
F
fit() (in module bucky.util.spline_smooth)
force_cpu (in module bucky.model.arg_parser_model)
frac_last_n_vals() (in module bucky.util.fractional_slice)
G
g() (bucky.util.spline_smooth.identity_link method)
(bucky.util.spline_smooth.log_link method)
g_prime() (bucky.util.spline_smooth.identity_link method)
(bucky.util.spline_smooth.log_link method)
generate_params() (bucky.model.parameters.buckyParams method)
generic_distribution() (in module bucky.util.distributions)
get_case_history() (in module bucky.make_input_graph)
get_county_population_data() (in module bucky.util.update_data_repos)
get_dates() (in module bucky.viz.map)
get_historical_data() (in module bucky.util.get_historical_data)
get_lex() (in module bucky.make_input_graph)
get_map_data() (in module bucky.viz.map)
get_mobility_data() (in module bucky.make_input_graph)
get_npi_params() (in module bucky.model.npi)
get_plot_title() (in module bucky.viz.plot)
get_runid() (in module bucky.util.util)
get_safegraph() (in module bucky.make_input_graph)
get_state_outline() (in module bucky.viz.map)
get_timeseries_data() (in module bucky.util.update_data_repos)
git_pull() (in module bucky.util.update_data_repos)
graph_file (in module bucky.util.get_historical_data)
H
hhs_hosp (in module bucky.util.get_historical_data)
hosp_df() (in module bucky.model.optimize)
I
identity_link (class in bucky.util.spline_smooth)
init_S() (bucky.model.state.buckyState method)
integrator_args() (bucky.model.mc_instance.buckyMCInstance property)
interp_extrap() (in module bucky.util.extrapolate)
IS() (in module bucky.util.scoring)
K
kumaraswamy_invcdf() (in module bucky.util.distributions)
L
load_graph() (bucky.model.main.buckyModelCovid method)
log_link (class in bucky.util.spline_smooth)
logistic() (in module bucky.util.scoring)
M
main() (in module bucky.model.main)
(in module bucky.postprocess)
(in module bucky.util.update_data_repos)
(in module bucky.viz.plot)
make_adm1_maps() (in module bucky.viz.map)
make_map() (in module bucky.viz.map)
make_plots() (in module bucky.viz.plot)
map_array() (in module bucky.util.util)
memory (in module bucky.model.graph)
(in module bucky.util.spline_smooth)
MI_PRISON_UIDS (in module bucky.util.update_data_repos)
MockExperimentalWarning
module
bucky
bucky.make_input_graph
bucky.model
bucky.model.__main__
bucky.model.adjmat
bucky.model.arg_parser_model
bucky.model.estimation
bucky.model.exceptions
bucky.model.graph
bucky.model.main
bucky.model.mc_instance
bucky.model.npi
bucky.model.optimize
bucky.model.parameters
bucky.model.rhs
bucky.model.state
bucky.model.vacc
bucky.numerical_libs
bucky.postprocess
bucky.util
bucky.util.cached_prop
bucky.util.distributions
bucky.util.extrapolate
bucky.util.fractional_slice
bucky.util.get_historical_data
bucky.util.graph2histcsv
bucky.util.ode_constraints
bucky.util.read_config
bucky.util.readable_col_names
bucky.util.rolling_mean
bucky.util.scoring
bucky.util.spline_smooth
bucky.util.update_data_repos
bucky.util.util
bucky.viz
bucky.viz.geoid
bucky.viz.map
bucky.viz.plot
most_recent_graph (in module bucky.model.arg_parser_model)
mPERT() (in module bucky.util.distributions)
mu() (bucky.util.spline_smooth.identity_link method)
(bucky.util.spline_smooth.log_link method)
N
N() (bucky.model.graph.buckyGraphData method)
Nj() (bucky.model.graph.buckyGraphData method)
norm_Cij() (in module bucky.model.mc_instance)
normalize() (bucky.model.adjmat.buckyAij method)
nunique() (in module bucky.util.spline_smooth)
O
opt_func() (in module bucky.model.optimize)
opt_lam() (in module bucky.util.spline_smooth)
optimize_kernels (in module bucky.numerical_libs)
P
parser (in module bucky.make_input_graph)
(in module bucky.model.arg_parser_model)
(in module bucky.postprocess)
(in module bucky.util.graph2histcsv)
(in module bucky.viz.map)
(in module bucky.viz.plot)
path (in module bucky.util.read_config)
perturb() (bucky.model.adjmat.buckyAij method)
pinned_array() (in module bucky.postprocess)
PIRLS() (in module bucky.util.spline_smooth)
plot() (in module bucky.viz.plot)
postprocess_run() (bucky.model.main.buckyModelCovid method)
preprocess_historical_dates() (in module bucky.viz.plot)
process_csse_data() (in module bucky.util.update_data_repos)
process_usafacts() (in module bucky.util.update_data_repos)
R
ravel_3d() (in module bucky.model.optimize)
read_descartes_data() (in module bucky.make_input_graph)
read_geoid_from_graph() (in module bucky.viz.geoid)
read_lex_data() (in module bucky.make_input_graph)
read_lookup() (in module bucky.viz.geoid)
read_npi_file() (in module bucky.model.npi)
read_yml() (bucky.model.parameters.buckyParams static method)
readable_col_names (in module bucky.util.readable_col_names)
rebuild_params() (in module bucky.model.optimize)
recursive_dict_update() (in module bucky.model.parameters)
reimport_cache (in module bucky.numerical_libs)
reimport_numerical_libs() (in module bucky.numerical_libs)
remove_chars() (in module bucky.util)
(in module bucky.util.util)
reroll_distribution() (bucky.model.vacc.buckyVaccAlloc method)
reroll_doses() (bucky.model.vacc.buckyVaccAlloc method)
reroll_params() (bucky.model.parameters.buckyParams method)
reset() (bucky.model.main.buckyModelCovid method)
RHS_func() (in module bucky.model.rhs)
ridge() (in module bucky.util.spline_smooth)
rolling_adm1_curr_hosp() (bucky.model.graph.buckyGraphData method)
rolling_adm1_inc_hosp() (bucky.model.graph.buckyGraphData method)
rolling_cum_cases() (bucky.model.graph.buckyGraphData method)
rolling_cum_deaths() (bucky.model.graph.buckyGraphData method)
rolling_inc_cases() (bucky.model.graph.buckyGraphData method)
rolling_inc_deaths() (bucky.model.graph.buckyGraphData method)
rolling_mean() (in module bucky.util.rolling_mean)
rolling_window() (in module bucky.util.rolling_mean)
run_multiple() (bucky.model.main.buckyModelCovid method)
run_once() (bucky.model.main.buckyModelCovid method)
S
S_eff() (bucky.model.mc_instance.buckyMCInstance method)
(bucky.model.vacc.buckyVaccAlloc method)
save_run() (bucky.model.main.buckyModelCovid method)
scatter_add (in module bucky.numerical_libs)
SCENARIO_HUB (in module bucky.model.main)
set_tmax() (bucky.model.mc_instance.buckyMCInstance method)
SimulationException
slice_to_cpu() (in module bucky.model.state)
smooth_IS() (in module bucky.util.scoring)
special (in module bucky.numerical_libs)
state() (bucky.model.mc_instance.buckyMCInstance property)
state_shape() (bucky.model.state.buckyState property)
StateValidationException
sum_adm1() (bucky.model.graph.buckyGraphData method)
sync_numerical_libs() (in module bucky.numerical_libs)
T
TERRITORY_DATA (in module bucky.util.update_data_repos)
test_opt() (in module bucky.model.optimize)
to_cpu (in module bucky.numerical_libs)
to_cpu_noop() (in module bucky.numerical_libs)
TqdmLoggingHandler (class in bucky.util)
(class in bucky.util.util)
truncnorm() (in module bucky.util.distributions)
truncnorm_from_CI() (in module bucky.util.distributions)
U
update_covid_tracking_data() (in module bucky.util.update_data_repos)
update_hhs_hosp_data() (in module bucky.util.update_data_repos)
update_params() (bucky.model.main.buckyModelCovid method)
(bucky.model.parameters.buckyParams method)
update_params_from_file() (bucky.model.parameters.buckyParams method)
update_usafacts_data() (in module bucky.util.update_data_repos)
UT_LHD_UIDS (in module bucky.util.update_data_repos)
V
V_eff() (bucky.model.vacc.buckyVaccAlloc method)
V_tot() (bucky.model.vacc.buckyVaccAlloc method)
vacc (in module bucky.util.get_historical_data)
validate_state() (bucky.model.state.buckyState method)
VALUES_FILE (in module bucky.model.optimize)
W
WIS() (in module bucky.util.scoring)
X
xp (in module bucky.numerical_libs)
xp_ivp (in module bucky.numerical_libs)
xp_sparse (in module bucky.numerical_libs)
Z
zeros_like() (bucky.model.state.buckyState method)
zeros_like_pinned (in module bucky.numerical_libs)
zeros_pinned (in module bucky.numerical_libs)