experimenting with vector defaults

misc/experiments/defaults/simulator_defaults.R

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+library(tidyr)
+library(macpan2)
+library(dplyr)
+
+## SIR with state vector ----
+## Taken from here https://canmod.github.io/macpan2/articles/design_concepts.html#vectors-in-the-tmb-engine
+state_labels = c("S", "I", "R")
+
+flow = data.frame(
+  rate = c("infection", "recovery")
+  , from = c("S"        , "I"       )
+  , to   = c("I"        , "R"       )
+)
+
+sir = mp_tmb_model_spec(
+  before = list(
+    state[S] ~ N - 1
+    , state[I] ~ 1
+    , state[R] ~ 0
+  )
+  , during = list(
+    flow_rate[infection] ~ beta * state[S] * state[I] / N
+    , flow_rate[recovery] ~ gamma * state[I]
+    , state ~ state + group_sums(flow_rate, to, state) - group_sums(flow_rate, from, state)
+  )
+  , default = list(
+      state     = mp_zero_vector(state_labels)
+    , flow_rate = mp_zero_vector(flow$rate)
+    , N = 100
+    , beta = 0.25
+    , gamma = 0.1
+  )
+  , integers = list(
+      from = mp_positions(flow$from, state_labels)
+    , to   = mp_positions(flow$to  , state_labels)
+  )
+)
+## --------------------------
+# function to generate simulated data given a state
+# vector of initial conditions to be passed to defaults
+sim_data <- function(state){
+  (mp_tmb_update(sir,default=list(state=state))
+   |> mp_simulator(time_steps = 10, outputs = c("state"))
+   |> mp_trajectory()
+  )
+}
+
+# read in defaults
+# For the use case when state vectors are needed
+# and are read in from a file (ex. NFDS model),
+# or in general when any default is not a single number
+# and is you don't want to initialize the vector to 
+# zeroes.
+sir_defaults = (read.csv(file.path("misc","experiments","defaults","sir","simulator_defaults.csv"))
+                %>% select(matrix,value)
+                %>% pivot_wider(names_from=matrix,values_from=value)
+
+
+)
+
+## state vector objects -----
+
+#1. mp_zero_vector - this works, as expected
+state_mp_zero = mp_zero_vector(state_labels)
+names(state_mp_zero)
+dimnames(state_mp_zero)
+sim_data(state_mp_zero)
+
+#2. tibble/data.frame - this errors
+state_tibble = sir_defaults
+# same names attributes as 1.
+names(state_tibble)
+# diff dimnames attributes from 1.
+dimnames(state_tibble)
+# errors
+sim_data(state_tibble)
+
+#3a. as.matrix - this errors
+state_matrix = as.matrix(sir_defaults,ncol=3)
+# no names, doesn't save names attribute?
+names(state_matrix)
+# has names in dimnames[[2]]
+dimnames(state_matrix)
+# errors
+sim_data(state_matrix) 
+
+#3b. as.matrix, and manually setting names and dimnames - this errors
+state_matrix_2 = as.matrix(sir_defaults,ncol=3)
+names(state_matrix_2)<-names(state_mp_zero)
+names(state_matrix_2)
+dimnames(state_matrix_2)<-dimnames(state_mp_zero)
+dimnames(state_matrix_2)
+sim_data(state_matrix_2) 
+
+#4. convert to vector with c(), and manually setting names and dimnames - this works
+state_vector = c(state_matrix)
+names(state_vector)<-names(state_mp_zero)
+dimnames(state_vector)<-dimnames(state_mp_zero)
+sim_data(state_vector)
+
+#5. 
+# we want to be able to pass matrices without names as well
+# NFDS initial state vector with initial conditions - not named

misc/experiments/defaults/sir/simulator_defaults.csv

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+"matrix","time","row","col","value"
+"I",15,0,0,3.83326260647648
+"R",15,0,0,3.06319055601829
+"S",15,0,0,93.1035468375052