diff --git a/analyses/estimate_severity/cfr-stratified-severity.qmd b/analyses/estimate_severity/cfr-stratified-severity.qmd index efbd19e..542ffe1 100644 --- a/analyses/estimate_severity/cfr-stratified-severity.qmd +++ b/analyses/estimate_severity/cfr-stratified-severity.qmd @@ -107,7 +107,7 @@ dat_incidence delay_onset_death <- epiparameter::epiparameter_db( disease = "ebola", - epi_dist = "onset to death", + epi_name = "onset to death", single_epiparameter = TRUE ) diff --git a/analyses/forecast_cases/projections_incidence_epitrix.qmd b/analyses/forecast_cases/projections_incidence_epitrix.qmd index 9405208..7230efc 100644 --- a/analyses/forecast_cases/projections_incidence_epitrix.qmd +++ b/analyses/forecast_cases/projections_incidence_epitrix.qmd @@ -79,9 +79,9 @@ incidence2_fit <- # Extract parameter by disease, distribution, author epidist_ebola_si <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "Ebola", - epi_dist = "serial_interval", + epi_name = "serial_interval", single_epiparameter = TRUE ) diff --git a/analyses/reconstruct_transmission/estimate_infections.qmd b/analyses/reconstruct_transmission/estimate_infections.qmd index b33928f..29fc14d 100644 --- a/analyses/reconstruct_transmission/estimate_infections.qmd +++ b/analyses/reconstruct_transmission/estimate_infections.qmd @@ -74,9 +74,9 @@ incidence_data # Define parameters # Extract infection-to-death distribution (from Aloon et al) incubation_period_in <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "covid", - epi_dist = "incubation", + epi_name = "incubation", single_epiparameter = TRUE ) @@ -97,9 +97,9 @@ incubation_period <- EpiNow2::LogNormal( ## Set onset to death period (from Linton et al) onset_to_death_period_in <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "covid", - epi_dist = "onset to death", + epi_name = "onset to death", single_epiparameter = TRUE ) @@ -126,9 +126,9 @@ infection_to_death <- incubation_period + onset_to_death_period # Extract serial interval distribution distribution (from Yang et al) serial_interval_in <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "covid", - epi_dist = "serial", + epi_name = "serial", single_epiparameter = TRUE ) @@ -220,9 +220,9 @@ incidence_data_ebola # Extract infection-to-death distribution (from WHO Ebola Response Team) incubation_period_ebola_in <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "ebola", - epi_dist = "incubation", + epi_name = "incubation", single_epiparameter = TRUE ) @@ -247,9 +247,9 @@ incubation_period_ebola <- EpiNow2::Gamma( # Extract serial interval distribution distribution # (from WHO Ebola Response Team) serial_interval_ebola_in <- - epiparameter::epidist_db( + epiparameter::epiparameter_db( disease = "ebola", - epi_dist = "serial", + epi_name = "serial", single_epiparameter = TRUE )