EpiNow2-package	EpiNow2-package
!=.dist_spec	equals-.dist_spec
$.epinow	cash-.epinow
$.estimate_infections	cash-.estimate_infections
$.estimate_secondary	cash-.estimate_secondary
+.dist_spec	plus-.dist_spec
.extract_to_dist_spec	dot-extract_to_dist_spec
.get_dist_id	dot-get_dist_id
.get_param_names	dot-get_param_names
.prepare_linelist_data	dot-prepare_linelist_data
==.dist_spec	equals-.dist_spec
add_breakpoints	add_breakpoints
add_day_of_week	add_day_of_week
add_horizon	add_horizon
allocate_delays	allocate_delays
allocate_empty	allocate_empty
apply_default_cdf_cutoff	apply_default_cdf_cutoff
apply_zero_threshold	apply_zero_threshold
as_forecast_sample	as_forecast_sample
as_forecast_sample.epinow	as_forecast_sample
as_forecast_sample.estimate_infections	as_forecast_sample
as_forecast_sample.estimate_truncation	as_forecast_sample
as_forecast_sample.forecast_secondary	as_forecast_sample
backcalc_opts	backcalc_opts
bootstrapped_dist_fit	bootstrapped_dist_fit
bound_dist	bound_dist
build_np_est_data	build_np_est_data
c.dist_spec	c.dist_spec
calc_CrI	calc_CrI
calc_CrIs	calc_CrIs
calc_summary_measures	calc_summary_measures
calc_summary_stats	calc_summary_stats
check_generation_time	check_generation_time
check_reports_valid	check_reports_valid
check_simulation_input	check_simulation_input
check_sparse_pmf_tail	check_sparse_pmf_tail
check_stan_delay	check_stan_delay
check_truncation_length	check_truncation_length
check_truncation_obs_opts	check_truncation_obs_opts
clean_nowcasts	clean_nowcasts
clean_regions	clean_regions
collapse	collapse
collapse.dist_spec	collapse
combine_tv_and_static_params	combine_tv_and_static_params
construct_output	construct_output
convert_to_logmean	convert_to_logmean
convert_to_logsd	convert_to_logsd
convert_to_natural	convert_to_natural
convolve_and_scale	convolve_and_scale
copy_results_to_latest	copy_results_to_latest
create_backcalc_data	create_backcalc_data
create_delay_inits	create_delay_inits
create_future_rt	create_future_rt
create_gp_data	create_gp_data
create_infection_summary	create_infection_summary
create_initial_conditions	create_initial_conditions
create_obs_model	create_obs_model
create_rt_data	create_rt_data
create_sampling_log_message	create_sampling_log_message
create_shifted_cases	create_shifted_cases
create_stan_args	create_stan_args
create_stan_data	create_stan_data
create_stan_delays	create_stan_delays
create_stan_params	create_stan_params
delay_opts	delay_opts
Dirichlet	Distributions
discrete_pmf	discrete_pmf
discretise	discretise
discretise.dist_spec	discretise
discretize	discretise
Distributions	Distributions
dist_fit	dist_fit
dist_id_to_name	dist_id_to_name
epinow	epinow
EpiNow2	EpiNow2-package
epinow2_cmdstan_model	epinow2_cmdstan_model
epinow2_rstan_model	epinow2_rstan_model
epinow2_stan_model	epinow2_stan_model
estimates_by_report_date	estimates_by_report_date
estimate_delay	estimate_delay
estimate_dist	estimate_dist
estimate_infections	estimate_infections
estimate_secondary	estimate_secondary
estimate_truncation	estimate_truncation
example_confirmed	example_confirmed
example_generation_time	example_generation_time
example_incubation_period	example_incubation_period
example_reporting_delay	example_reporting_delay
example_truncated	example_truncated
Exp	Distributions
expose_stan_fns	expose_stan_fns
extract_CrIs	extract_CrIs
extract_delays	extract_delays
extract_delay_params	extract_delay_params
extract_inits	extract_inits
extract_latent_state	extract_latent_state
extract_parameters	extract_parameters
extract_params	extract_params
extract_samples	extract_samples
extract_scalar_params	extract_scalar_params
extract_single_dist	extract_single_dist
extract_stan_param	extract_stan_param
fill_missing	fill_missing
filter_leading_zeros	filter_leading_zeros
filter_opts	filter_opts
fit_model	fit_model
fit_model_approximate	fit_model_approximate
fit_model_with_nuts	fit_model_with_nuts
Fixed	Distributions
fix_parameters	fix_parameters
fix_parameters.dist_spec	fix_parameters
forecast_infections	forecast_infections
forecast_opts	forecast_opts
forecast_secondary	forecast_secondary
format_fit	format_fit
format_quantile_predictions	format_quantile_predictions
format_samples_with_dates	format_samples_with_dates
format_sample_predictions	format_sample_predictions
format_simulation_output	format_simulation_output
Gamma	Distributions
generation_time_opts	generation_time_opts
get_accumulate	get_accumulate
get_distribution	get_distribution
get_element	get_element
get_parameters	get_parameters
get_parameters.dist_spec	get_parameters
get_parameters.epinowfit	get_parameters
get_parameters.estimate_dist	get_parameters
get_pmf	get_pmf
get_predictions	get_predictions
get_predictions.estimate_infections	get_predictions
get_predictions.estimate_secondary	get_predictions
get_predictions.estimate_truncation	get_predictions
get_predictions.forecast_infections	get_predictions
get_predictions.forecast_secondary	get_predictions
get_raw_result	get_raw_result
get_regional_results	get_regional_results
get_regions	get_regions
get_regions_with_most_reports	get_regions_with_most_reports
get_samples	get_samples
get_samples.epinow	get_samples
get_samples.estimate_infections	get_samples
get_samples.estimate_secondary	get_samples
get_samples.estimate_truncation	get_samples
get_samples.forecast_infections	get_samples
get_samples.forecast_secondary	get_samples
get_seeding_time	get_seeding_time
gp_opts	gp_opts
growth_to_R	growth_to_R
gt_opts	generation_time_opts
is_constrained	is_constrained
is_constrained.dist_spec	is_constrained
lapply_func	lapply_func
LogNormal	Distributions
lower_bounds	lower_bounds
make_conf	make_conf
make_init_priors	make_init_priors
make_param	make_param
map_prob_change	map_prob_change
match_output_arguments	match_output_arguments
max.dist_spec	max.dist_spec
mean.dist_spec	mean.dist_spec
merge_trunc_pred_obs	merge_trunc_pred_obs
natural_params	natural_params
ndist	ndist
new_dist_spec	new_dist_spec
NonParametric	Distributions
nonparametric_pmf_data	nonparametric_pmf_data
Normal	Distributions
obs_opts	obs_opts
opts_list	opts_list
pack_init_prior	pack_init_prior
pad_reported_cases	pad_reported_cases
plot.dist_spec	plot.dist_spec
plot.estimate_infections	plot.estimate_infections
plot.estimate_secondary	plot.estimate_secondary
plot.estimate_truncation	plot.estimate_truncation
plot.forecast_infections	plot.forecast_infections
plot.forecast_secondary	plot.forecast_secondary
plot_CrIs	plot_CrIs
plot_estimates	plot_estimates
plot_summary	plot_summary
posterior_to_normal	posterior_to_normal
prepare_truncation_obs	prepare_truncation_obs
print.dist_spec	print.dist_spec
print.epinowfit	print.epinowfit
process_region	process_region
process_regions	process_regions
rdirichlet	rdirichlet
reconstruct_delay	reconstruct_delay
reconstruct_nonparametric	reconstruct_nonparametric
reconstruct_parametric	reconstruct_parametric
regional_epinow	regional_epinow
regional_runtimes	regional_runtimes
regional_summary	regional_summary
report_plots	report_plots
report_summary	report_summary
rt_opts	rt_opts
run_region	run_region
R_to_growth	R_to_growth
save_estimate_infections	save_estimate_infections
save_input	save_input
sd	sd
sd.dist_spec	sd
secondary_opts	secondary_opts
select_plots	select_plots
setup_default_logging	setup_default_logging
setup_dt	setup_dt
setup_future	setup_future
setup_logging	setup_logging
setup_target_folder	setup_target_folder
set_dt_single_thread	set_dt_single_thread
simulate_infections	simulate_infections
simulate_secondary	simulate_secondary
stable_convolve	stable_convolve
stan_laplace_opts	stan_laplace_opts
stan_opts	stan_opts
stan_pathfinder_opts	stan_pathfinder_opts
stan_sampling_opts	stan_sampling_opts
stan_vb_opts	stan_vb_opts
summarise_key_measures	summarise_key_measures
summarise_results	summarise_results
summary	summary.epinow
summary.epinow	summary.epinow
summary.estimate_dist	summary.estimate_dist
summary.estimate_infections	summary.estimate_infections
summary.estimate_secondary	summary.estimate_secondary
summary.estimate_truncation	summary.estimate_truncation
summary.forecast_infections	summary.forecast_infections
trunc_opts	trunc_opts
update_horizon	update_horizon
update_secondary_args	update_secondary_args
Weibull	Distributions
[[.epinow	sub-sub-.epinow
[[.estimate_infections	sub-sub-.estimate_infections
[[.estimate_secondary	sub-sub-.estimate_secondary
