added argument defaults to sim_* functions, WIP #120

epiverse-trace · Jun 25, 2024 · a70ea29 · a70ea29
1 parent ef350f2
commit a70ea29
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Showing 3 changed files with 13 additions and 13 deletions.
diff --git a/R/sim_contacts.R b/R/sim_contacts.R
@@ -32,9 +32,9 @@
 #'   infectious_period = infectious_period,
 #'   prob_infection = 0.5
 #' )
-sim_contacts <- function(contact_distribution,
-                         infectious_period,
-                         prob_infection,
+sim_contacts <- function(contact_distribution = function(x) stats::dpois(x = x, lambda = 2),
+                         infectious_period = function(x) stats::rlnorm(n = x, meanlog = 2, sdlog = 0.5),
+                         prob_infection = 0.5,
                          outbreak_start_date = as.Date("2023-01-01"),
                          anonymise = FALSE,
                          outbreak_size = c(10, 1e4),

diff --git a/R/sim_linelist.R b/R/sim_linelist.R
@@ -152,11 +152,11 @@
 #'   hosp_risk = age_dep_hosp_risk
 #' )
 #' head(linelist)
-sim_linelist <- function(contact_distribution,
-                         infectious_period,
-                         prob_infection,
-                         onset_to_hosp,
-                         onset_to_death,
+sim_linelist <- function(contact_distribution = function(x) stats::dpois(x = x, lambda = 2),
+                         infectious_period = function(x) stats::rlnorm(n = x, meanlog = 2, sdlog = 0.5),
+                         prob_infection = 0.5,
+                         onset_to_hosp = function(x) stats::rlnorm(n = x, meanlog = 1.5, sdlog = 0.5),
+                         onset_to_death = function(x) stats::rlnorm(n = x, meanlog = 2.5, sdlog = 0.5),
                          onset_to_recovery = NULL,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,

diff --git a/R/sim_outbreak.R b/R/sim_outbreak.R
@@ -53,11 +53,11 @@
 #'   onset_to_hosp = onset_to_hosp,
 #'   onset_to_death = onset_to_death
 #' )
-sim_outbreak <- function(contact_distribution,
-                         infectious_period,
-                         prob_infection,
-                         onset_to_hosp,
-                         onset_to_death,
+sim_outbreak <- function(contact_distribution = function(x) stats::dpois(x = x, lambda = 2),
+                         infectious_period = function(x) stats::rlnorm(n = x, meanlog = 2, sdlog = 0.5),
+                         prob_infection = 0.5,
+                         onset_to_hosp = function(x) stats::rlnorm(n = x, meanlog = 1.5, sdlog = 0.5),
+                         onset_to_death = function(x) stats::rlnorm(n = x, meanlog = 2.5, sdlog = 0.5),
                          onset_to_recovery = NULL,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,