update epiparameter interface

epiverse-trace · Nov 1, 2024 · bc41992 · bc41992
1 parent 199b575
commit bc41992
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git 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
@@ -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
@@ -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
   )