sir model update

inst/starter_models/sir/example.R

@@ -1,11 +1,22 @@
 source("inst/starter_models/sir/model.R")
 
+## -------------------------
+## parameterize model
+## -------------------------
+
+tmb_simulator$update$transformations(Log("beta"))
+tmb_simulator$replace$params(log(init_mats$get("beta")), "log_beta")
+tmb_simulator  ## note the new expression before the simulation loop
+
 ## -------------------------
 ## simulate fake data
 ## -------------------------
 
+time_steps = 100L
 true_beta = 0.4
-observed_data = tmb_simulator$report(true_beta)
+
+tmb_simulator$replace$time_steps(100L)
+observed_data = tmb_simulator$report(log(true_beta))
 observed_data$value = rpois(100, observed_data$value)
 
 if (interactive()) {
@@ -28,13 +39,13 @@ tmb_simulator$update$matrices(
 ## -------------------------
 
 if (interactive()) {
-  betas = seq(from = 0.01, to = 1, length = 100)
+  log_betas = seq(from = log(0.1), to = log(1), length = 100)
   ll = vapply(
-      betas
+      log_betas
     , tmb_simulator$objective
     , numeric(1L)
   )
-  plot(betas, ll, type = "l")
+  plot(exp(log_betas), ll, type = "l")
   abline(v = true_beta)
 }
 

inst/starter_models/sir/model.R

@@ -11,23 +11,20 @@ computations = list(
 ## absolute flow rates (per time only)
 flow_rates = list(
     infection ~ S * I * beta / N
-  , recovered ~ gamma * I
+  , recovery ~ gamma * I
 )
 
 ## state updates
 state_updates = list(
     S ~ S - infection
-  , I ~ I + infection - recovered
-  , R ~ R + recovered
+  , I ~ I + infection - recovery
+  , R ~ R + recovery
 )
 
 model_evaluation = list(
   log_likelihood ~ dpois(I_obs, rbind_time(I, I_obs_times))
 )
 
-## data model comparison
-obj_fn = ~ -sum(log_likelihood)
-
 ## simple unstructured scalar expression
 expr_list =  ExprList(
     before = computations
@@ -44,27 +41,21 @@ init_mats = MatsList(
    , gamma = 0.1
    , N = 100
    , infection = empty_matrix
-   , recovered = empty_matrix
+   , recovery = empty_matrix
    , log_likelihood = empty_matrix
    , I_obs = empty_matrix
    , I_obs_times = empty_matrix
    , .mats_to_save = "I"
    , .mats_to_return = "I"
 )
 
+obj_fn = ObjectiveFunction(~ -sum(log_likelihood))
+
 ## simulator
 ###################################################
 
 tmb_simulator = TMBModel(
     init_mats = init_mats
   , expr_list = expr_list
-  , time_steps = Time(100L)
-  , params = OptParamsList(
-       init_mats$get("beta")
-     , par_id = c(0L)
-     , mat = c("beta")
-     , row_id = c(0L)
-     , col_id = c(0L)
-  )
-  , obj_fn = ObjectiveFunction(obj_fn)
+  , obj_fn = obj_fn
 )$simulator()