Covasim
1.6.0
Parameters
What’s new
Contributing to Covasim
Run Covasim in the web UI
Build and test in Docker
Data scrapers
API reference
Covasim
Covasim website
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Documentation
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Index
Index
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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P
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Q
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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
A
add_contacts() (covasim.base.BasePeople method)
age_histogram (class in covasim.analysis)
AlreadyRunError
Analyzer (class in covasim.analysis)
animate() (covasim.analysis.TransTree method)
append() (covasim.base.Layer method)
apply() (covasim.analysis.age_histogram method)
(covasim.analysis.Analyzer method)
(covasim.analysis.snapshot method)
(covasim.interventions.change_beta method)
(covasim.interventions.clip_edges method)
(covasim.interventions.contact_tracing method)
(covasim.interventions.dynamic_pars method)
(covasim.interventions.Intervention method)
(covasim.interventions.sequence method)
(covasim.interventions.test_num method)
(covasim.interventions.test_prob method)
(covasim.interventions.vaccine method)
B
BasePeople (class in covasim.base)
BaseSim (class in covasim.base)
binomial_arr() (in module covasim.utils)
binomial_filter() (in module covasim.utils)
brief() (covasim.sim.Sim method)
C
change_beta (class in covasim.interventions)
check_critical() (covasim.people.People method)
check_death() (covasim.people.People method)
check_diagnosed() (covasim.people.People method)
check_inds() (covasim.people.People method)
check_infectious() (covasim.people.People method)
check_quar() (covasim.people.People method)
check_recovery() (covasim.people.People method)
check_save_version() (in module covasim.misc)
check_sciris() (in module covasim.requirements)
check_scirisweb() (in module covasim.requirements)
check_severe() (covasim.people.People method)
check_symptomatic() (covasim.people.People method)
check_synthpops() (in module covasim.requirements)
check_version() (in module covasim.misc)
choose() (in module covasim.utils)
choose_r() (in module covasim.utils)
choose_w() (in module covasim.utils)
clip_edges (class in covasim.interventions)
combine() (covasim.run.MultiSim method)
compare() (covasim.run.MultiSim method)
compute() (covasim.analysis.Fit method)
compute_diffs() (covasim.analysis.Fit method)
compute_doubling() (covasim.sim.Sim method)
compute_fit() (covasim.sim.Sim method)
compute_gen_time() (covasim.sim.Sim method)
compute_gof() (in module covasim.misc)
compute_gofs() (covasim.analysis.Fit method)
compute_losses() (covasim.analysis.Fit method)
compute_mismatch() (covasim.analysis.Fit method)
compute_prev_inci() (covasim.sim.Sim method)
compute_r_eff() (covasim.sim.Sim method)
compute_results() (covasim.sim.Sim method)
compute_windows() (covasim.analysis.age_histogram method)
compute_yield() (covasim.sim.Sim method)
contact_tracing (class in covasim.interventions)
Contacts (class in covasim.base)
copy() (covasim.base.BaseSim method)
count() (covasim.base.BasePeople method)
count_not() (covasim.base.BasePeople method)
count_targets() (covasim.analysis.TransTree method)
covasim
module
covasim.analysis
module
covasim.base
module
covasim.data
module
covasim.data.country_age_data
module
covasim.data.household_size_data
module
covasim.data.loaders
module
covasim.data.state_age_data
module
covasim.defaults
module
covasim.interventions
module
covasim.misc
module
covasim.parameters
module
covasim.people
module
covasim.plotting
module
covasim.population
module
covasim.requirements
module
covasim.run
module
covasim.sim
module
covasim.utils
module
covasim.version
module
covasim.webapp
module
covasim.webapp.cova_app
module
D
date() (covasim.base.BaseSim method)
(in module covasim.misc)
date_keys() (covasim.base.BasePeople method)
date_range() (in module covasim.misc)
datevec() (covasim.base.BaseSim property)
day() (covasim.analysis.TransTree method)
(covasim.base.BaseSim method)
(in module covasim.misc)
daydiff() (in module covasim.misc)
defined() (covasim.base.BasePeople method)
(in module covasim.utils)
disp() (covasim.interventions.Intervention method)
dur_keys() (covasim.base.BasePeople method)
dynamic_pars (class in covasim.interventions)
E
export_pars() (covasim.base.BaseSim method)
export_results() (covasim.base.BaseSim method)
F
false() (covasim.base.BasePeople method)
(in module covasim.utils)
finalize() (covasim.sim.Sim method)
find_contacts() (covasim.base.Layer method)
Fit (class in covasim.analysis)
FlexDict (class in covasim.base)
from_df() (covasim.base.Layer method)
from_people() (covasim.base.BasePeople method)
from_sim() (covasim.analysis.age_histogram method)
G
get() (covasim.analysis.age_histogram method)
(covasim.analysis.snapshot method)
(covasim.base.BasePeople method)
(in module covasim.data.country_age_data)
(in module covasim.data.household_size_data)
(in module covasim.data.state_age_data)
get_age_distribution() (in module covasim.data.loaders)
get_colors() (in module covasim.defaults)
get_country_aliases() (in module covasim.data.loaders)
get_defaults() (in module covasim.webapp.cova_app)
get_doubling_time() (in module covasim.misc)
get_gantt() (in module covasim.webapp.cova_app)
get_household_size() (in module covasim.data.loaders)
get_licenses() (in module covasim.webapp.cova_app)
get_location_options() (in module covasim.webapp.cova_app)
get_output_files() (in module covasim.webapp.cova_app)
get_pdf() (in module covasim.utils)
get_png_metadata() (in module covasim.misc)
get_prognoses() (in module covasim.parameters)
get_scen_plots() (in module covasim.defaults)
get_sim_plots() (in module covasim.defaults)
get_version() (in module covasim.webapp.cova_app)
git_info() (in module covasim.misc)
H
healthcheck() (in module covasim.webapp.cova_app)
I
idefined() (in module covasim.utils)
idefinedi() (in module covasim.utils)
ifalse() (in module covasim.utils)
ifalsei() (in module covasim.utils)
indices() (covasim.base.BasePeople method)
infect() (covasim.people.People method)
init_analyzers() (covasim.sim.Sim method)
init_contacts() (covasim.base.BasePeople method)
init_interventions() (covasim.sim.Sim method)
init_people() (covasim.sim.Sim method)
init_results() (covasim.sim.Sim method)
init_sims() (covasim.run.MultiSim method)
initialize() (covasim.analysis.age_histogram method)
(covasim.analysis.Analyzer method)
(covasim.analysis.snapshot method)
(covasim.interventions.change_beta method)
(covasim.interventions.clip_edges method)
(covasim.interventions.contact_tracing method)
(covasim.interventions.Intervention method)
(covasim.interventions.sequence method)
(covasim.interventions.test_num method)
(covasim.interventions.test_prob method)
(covasim.interventions.vaccine method)
(covasim.people.People method)
(covasim.sim.Sim method)
Intervention (class in covasim.interventions)
InterventionDict() (in module covasim.interventions)
items() (covasim.base.FlexDict method)
itrue() (in module covasim.utils)
itruei() (in module covasim.utils)
K
keys() (covasim.base.BasePeople method)
(covasim.base.FlexDict method)
L
Layer (class in covasim.base)
layer_keys() (covasim.base.BasePeople method)
(covasim.sim.Sim method)
load() (covasim.base.BaseSim static method)
(covasim.run.MultiSim static method)
(covasim.run.Scenarios static method)
(in module covasim.misc)
load_data() (covasim.sim.Sim method)
(in module covasim.misc)
load_population() (covasim.sim.Sim method)
log_err() (in module covasim.webapp.cova_app)
M
make_age_histogram() (covasim.sim.Sim method)
make_detailed() (covasim.analysis.TransTree method)
make_edgelist() (covasim.base.BasePeople method)
make_hybrid_contacts() (in module covasim.population)
make_metapars() (in module covasim.run)
make_microstructured_contacts() (in module covasim.population)
make_pars() (in module covasim.parameters)
make_people() (in module covasim.population)
make_random_contacts() (in module covasim.population)
make_randpop() (in module covasim.population)
make_susceptible() (covasim.people.People method)
make_synthpop() (in module covasim.population)
make_transtree() (covasim.sim.Sim method)
map_entries() (in module covasim.data.loaders)
merge() (covasim.run.MultiSim static method)
meta_keys() (covasim.base.Layer method)
module
covasim
covasim.analysis
covasim.base
covasim.data
covasim.data.country_age_data
covasim.data.household_size_data
covasim.data.loaders
covasim.data.state_age_data
covasim.defaults
covasim.interventions
covasim.misc
covasim.parameters
covasim.people
covasim.plotting
covasim.population
covasim.requirements
covasim.run
covasim.sim
covasim.utils
covasim.version
covasim.webapp
covasim.webapp.cova_app
multi_run() (in module covasim.run)
MultiSim (class in covasim.run)
N
n() (covasim.base.BaseSim property)
n_binomial() (in module covasim.utils)
n_multinomial() (in module covasim.utils)
n_neg_binomial() (in module covasim.utils)
n_poisson() (in module covasim.utils)
not_defined() (covasim.base.BasePeople method)
npts() (covasim.base.BaseSim property)
(covasim.base.Result property)
P
parse_interventions() (in module covasim.webapp.cova_app)
parse_parameters() (in module covasim.webapp.cova_app)
ParsObj (class in covasim.base)
People (class in covasim.people)
Person (class in covasim.base)
person() (covasim.base.BasePeople method)
person_keys() (covasim.base.BasePeople method)
plot() (covasim.analysis.age_histogram method)
(covasim.analysis.Fit method)
(covasim.analysis.TransTree method)
(covasim.interventions.Intervention method)
(covasim.people.People method)
(covasim.run.MultiSim method)
(covasim.run.Scenarios method)
(covasim.sim.Sim method)
plot_compare() (covasim.run.MultiSim method)
(in module covasim.plotting)
plot_histograms() (covasim.analysis.TransTree method)
plot_people() (in module covasim.plotting)
plot_result() (covasim.run.MultiSim method)
(covasim.sim.Sim method)
(in module covasim.plotting)
plot_scens() (in module covasim.plotting)
plot_sim() (in module covasim.plotting)
plotly_animate() (in module covasim.plotting)
plotly_people() (in module covasim.plotting)
plotly_sim() (in module covasim.plotting)
poisson() (in module covasim.utils)
poisson_test() (in module covasim.misc)
pop_inds() (covasim.base.Layer method)
Q
quarantine() (covasim.people.People method)
R
r0() (covasim.analysis.TransTree method)
reconcile_inputs() (covasim.analysis.Fit method)
reduce() (covasim.run.MultiSim method)
remove_duplicates() (covasim.base.BasePeople static method)
rescale() (covasim.sim.Sim method)
reset() (covasim.run.MultiSim method)
reset_layer_pars() (covasim.sim.Sim method)
(in module covasim.parameters)
Result (class in covasim.base)
result_keys() (covasim.base.BaseSim method)
(covasim.run.MultiSim method)
(covasim.run.Scenarios method)
run() (covasim.run.MultiSim method)
(covasim.run.Scenarios method)
(covasim.sim.Sim method)
run_sim() (in module covasim.webapp.cova_app)
S
sample() (in module covasim.utils)
save() (covasim.base.BaseSim method)
(covasim.run.MultiSim method)
(covasim.run.Scenarios method)
(in module covasim.misc)
savefig() (in module covasim.misc)
scaled_pop_size() (covasim.base.BaseSim property)
Scenarios (class in covasim.run)
sequence (class in covasim.interventions)
set() (covasim.base.BasePeople method)
set_metadata() (covasim.sim.Sim method)
set_pars() (covasim.base.BasePeople method)
set_prognoses() (covasim.people.People method)
set_seed() (covasim.base.BaseSim method)
(in module covasim.utils)
shrink() (covasim.base.BaseSim method)
Sim (class in covasim.sim)
single_run() (in module covasim.run)
snapshot (class in covasim.analysis)
split() (covasim.run.MultiSim method)
state_keys() (covasim.base.BasePeople method)
step() (covasim.sim.Sim method)
summarize() (covasim.run.MultiSim method)
(covasim.sim.Sim method)
T
test() (covasim.people.People method)
test_num (class in covasim.interventions)
test_prob (class in covasim.interventions)
to_arr() (covasim.base.BasePeople method)
to_df() (covasim.base.BasePeople method)
(covasim.base.Layer method)
to_excel() (covasim.base.BaseSim method)
(covasim.run.Scenarios method)
to_json() (covasim.base.BaseSim method)
(covasim.interventions.Intervention method)
(covasim.run.Scenarios method)
to_people() (covasim.base.BasePeople method)
trace() (covasim.people.People method)
transmissions() (covasim.analysis.TransTree property)
TransTree (class in covasim.analysis)
true() (covasim.base.BasePeople method)
(in module covasim.utils)
tvec() (covasim.base.BaseSim property)
U
undefined() (in module covasim.utils)
update_contacts() (covasim.people.People method)
update_pars() (covasim.base.ParsObj method)
(covasim.sim.Sim method)
update_states_post() (covasim.people.People method)
update_states_pre() (covasim.people.People method)
upload_file() (in module covasim.webapp.cova_app)
upload_pars() (in module covasim.webapp.cova_app)
V
vaccine (class in covasim.interventions)
validate() (covasim.base.BasePeople method)
(covasim.base.Layer method)
validate_layer_pars() (covasim.sim.Sim method)
validate_pars() (covasim.sim.Sim method)
values() (covasim.base.FlexDict method)