fix delays error from epiparameter epinow2 conflict

config.yaml

@@ -63,7 +63,7 @@ episodes:
 - clean-data.Rmd
 - describe-cases.Rmd
 - simple-analysis.Rmd
-- delays-reuse.Rmd
+- delays-access.Rmd
 # - quantify-transmissibility.Rmd
 - delays-functions.Rmd
 

episodes/delays-functions.Rmd

@@ -112,7 +112,7 @@
 
 If you need it, read in detail about the [R probability functions for the normal distribution](https://sakai.unc.edu/access/content/group/3d1eb92e-7848-4f55-90c3-7c72a54e7e43/public/docs/lectures/lecture13.htm#probfunc), each of its definitions and identify in which part of a distribution they are located!
 
 ![The four probability functions for the normal distribution ([Jack Weiss, 2012](https://sakai.unc.edu/access/content/group/3d1eb92e-7848-4f55-90c3-7c72a54e7e43/public/docs/lectures/lecture13.htm#probfunc))](fig/fig5a-normaldistribution.png)
 
 ::::::::::::::::::::
 
@@ -444,9 +444,8 @@
   )
 
 # adapt epidist to epinow2
-covid_serialint_discrete_max <-
-  covid_serialint %>%
-  discretise() %>%
+covid_serialint_discrete_max <- covid_serialint %>%
+  epiparameter::discretise() %>%
   quantile(p = 0.99)
 
 covid_serialint_parameters <-
@@ -470,9 +469,8 @@
 )
 
 # adapt epiparameter to epinow2
-covid_incubation_discrete_max <-
-  covid_incubation %>%
-  discretise() %>%
+covid_incubation_discrete_max <- covid_incubation %>%
+  epiparameter::discretise() %>%
   quantile(p = 0.99)
 
 covid_incubation_parameters <-
@@ -577,7 +575,7 @@
   read_csv(here::here("data", "raw-data", "ebola_cases.csv"))
 
 # list distributions
-epidist_db(disease = "ebola") %>%
+epiparameter::epidist_db(disease = "ebola") %>%
   epiparameter::parameter_tbl()
 ```
 
@@ -586,14 +584,14 @@
 # generation time ---------------------------------------------------------
 
 # subset one distribution for the generation time
-ebola_serial <- epidist_db(
+ebola_serial <- epiparameter::epidist_db(
   disease = "ebola",
   epi_dist = "serial",
   single_epidist = TRUE
 )
 
 # adapt epiparameter to epinow2
-ebola_serial_discrete <- discretise(ebola_serial)
+ebola_serial_discrete <- epiparameter::discretise(ebola_serial)
 
 serial_interval_ebola <-
   EpiNow2::Gamma(
@@ -605,14 +603,14 @@
 # incubation time ---------------------------------------------------------
 
 # subset one distribution for delay of the incubation period
-ebola_incubation <- epidist_db(
+ebola_incubation <- epiparameter::epidist_db(
   disease = "ebola",
   epi_dist = "incubation",
   single_epidist = TRUE
 )
 
 # adapt epiparameter to epinow2
-ebola_incubation_discrete <- discretise(ebola_incubation)
+ebola_incubation_discrete <- epiparameter::discretise(ebola_incubation)
 
 incubation_period_ebola <-
   EpiNow2::Gamma(
@@ -656,15 +654,15 @@
 
 ```{r,message=FALSE,eval=TRUE}
 # What parameters are available for Influenza?
-epidist_db(disease = "influenza") %>%
+epiparameter::epidist_db(disease = "influenza") %>%
   epiparameter::parameter_tbl() %>%
   count(epi_distribution)
 
 # generation time ---------------------------------------------------------
 
 # Read the generation time
 influenza_generation <-
-  epidist_db(
+  epiparameter::epidist_db(
     disease = "influenza",
     epi_dist = "generation"
   )
@@ -698,7 +696,7 @@
 
 # Read the incubation period
 influenza_incubation <-
-  epidist_db(
+  epiparameter::epidist_db(
     disease = "influenza",
     epi_dist = "incubation",
     single_epidist = TRUE