covid fit code:

Author: stevencarlislewalker

code/initial-fit-covid.R

@@ -0,0 +1,44 @@
+library(macpan2); library(tidyverse)
+sir = mp_tmb_library("starter_models", "sir", package = "macpan2")
+data = read_csv("https://raw.githubusercontent.com/canmod/macpan-workshop/refs/heads/main/data/early_covid_on_reports.csv")
+cleaned_data = (data
+  |> rename(time = date, matrix = var)
+  |> select(-province)
+)
+sir_covid = mp_tmb_insert(sir
+
+    ## Modify the the part of the model that
+    ## is executed once "during" each iteration
+    ## of the simulation loop.
+    , phase = "during"
+
+    ## Insert the new expressions at the 
+    ## end of each iteration.
+    ## (Inf ~ infinity ~ end)
+    , at = Inf
+
+    ## Specify the model for under-reporting as
+    ## a simple fraction of the number of new
+    ## cases every time-step.
+    , expressions = list(report ~ report_prob * infection)
+
+    ## Update defaults to something a little more 
+    ## reasonable for early covid in Ontario.
+    , default = list(
+          gamma = 1/14      ## 2-week recovery
+        , beta = 2.5/14     ## R0 = 2.5
+        , report_prob = 0.1 ## 10% of cases get reported
+        , N = 1.4e7         ## ontario population  
+        , I = 50            ## start with undetected infections
+    )
+)
+cal = mp_tmb_calibrator(sir_covid, cleaned_data
+  , traj = "report"
+  , par = c("beta", "gamma")
+)
+mp_optimize(cal)
+fitted_data = mp_trajectory(cal)
+(ggplot()
+  + geom_line(aes(time, value), data = fitted_data)
+  + geom_point(aes(time, value), data = cleaned_data)
+)