expression lists for remaining unstructured models

inst/starter_models/macpan_base/model.R

@@ -0,0 +1,52 @@
+library(macpan2)
+
+## expression lists
+###################################################
+
+## free form computations for convenience
+computations = list(
+  N ~ sum(S, E, Ia, Ip, Im, Is, R, H, ICUs, ICUd, H2, D)
+)
+
+## absolute flow rates (per time only)
+flow_rates = list(
+    SE ~ S * (beta0 / N) * (Ia * Ca + Ip * Cp + Im * Cm * (1 - iso_m) + Is * Cs *(1 - iso_s))
+  , EIa ~ E * alpha * sigma
+  , EIp ~ E * (1 - alpha)* sigma
+  , IaR ~ Ia * gamma_a
+  , IpIm ~ Ip * mu * gamma_p
+  , ImR ~ Im * gamma_m
+  , IpIs ~ Ip * (1 - mu) * gamma_p
+  , IsICUs ~ Is * (1 - nonhosp_mort) * (1 - phi1) * (1 - phi2) * gamma_s
+  , ICUsH2 ~ ICUs * psi1
+  , H2R ~ H2 * psi3
+  , IsH ~ Is * (1 - nonhosp_mort) * phi1 * gamma_s
+  , IsICUd ~ Is * (1 - nonhosp_mort) * (1 - phi1) * phi2 * gamma_s
+  , ICUdD ~ ICUd * psi2
+  , HR ~ H * rho
+)
+
+## state updates
+state_updates = list(
+    S ~ S - SE
+  , E ~ E + SE - EIa - EIp
+  , Ia ~ Ia + EIa - IaR
+  , Ip ~ Ip + EIp - IpIm - IpIs
+  , Im ~ Im + IpIm
+  , Is ~ Is + IpIs - IsICUs - IsH - IsICUd
+  , R ~ R + IaR + H2R + HR
+  , H ~ H + IsH - HR
+  , ICUs ~ ICUs + IsICUs - ICUsH2
+  , ICUd ~ ICUd + IsICUd - ICUdD
+  , H2 ~ H2 + ICUsH2 - H2R
+  , D ~ D + ICUdD
+)
+
+## simple unstructured scalar expression
+expr_list =  ExprList(
+    before = computations
+  , during = c(
+      flow_rates
+    , state_updates
+  )
+)

inst/starter_models/seir/model.R

@@ -0,0 +1,33 @@
+library(macpan2)
+
+## expression lists
+###################################################
+
+## free form computations for convenience
+computations = list(
+  N ~ sum(S, E, I, R)
+)
+
+## absolute flow rates (per time only)
+flow_rates = list(
+    infection ~ S * I * beta / N
+  , exposure ~ alpha * E
+  , recovery ~ gamma * I
+)
+
+## state updates
+state_updates = list(
+    S ~ S - exposure
+  , E ~ E + exposure - infection
+  , I ~ I + infection - recovery
+  , R ~ R + recovery
+)
+
+## simple unstructured scalar expression
+expr_list =  ExprList(
+    before = computations
+  , during = c(
+      flow_rates
+    , state_updates
+  )
+)

inst/starter_models/sir_demo/model.R

@@ -0,0 +1,36 @@
+library(macpan2)
+
+## expression lists
+###################################################
+
+## free form computations for convenience
+computations = list(
+  N ~ sum(S, I, R)
+)
+
+## absolute flow rates (per time only)
+flow_rates = list(
+    birth ~ birth_rate * N
+  , infection ~ S * I * beta / N
+  , recovery ~ gamma * I
+)
+
+## state updates
+state_updates = list(
+    S ~ S - infection + birth - death_rate * S
+  , I ~ I + infection - recovery - death_rate * I
+  , R ~ R + recovery - death_rate * R
+)
+
+## simple unstructured scalar expression
+## in the general case,
+## birth rate and death rate can differ, N might not be constant
+## nothing can be computed before simulation loop
+expr_list =  ExprList(
+    during = c(
+        computations
+      , flow_rates
+      , state_updates
+  )
+)
+

inst/starter_models/sir_waning/model.R

@@ -0,0 +1,32 @@
+library(macpan2)
+
+## expression lists
+###################################################
+
+## free form computations for convenience
+computations = list(
+  N ~ sum(S, I, R)
+)
+
+## absolute flow rates (per time only)
+flow_rates = list(
+    infection ~ S * I * beta / N
+  , recovery ~ gamma * I
+  , waning_immunity ~ wane * R
+)
+
+## state updates
+state_updates = list(
+    S ~ S - infection + waning_immunity
+  , I ~ I + infection - recovery
+  , R ~ R + recovery - waning_immunity
+)
+
+## simple unstructured scalar expression
+expr_list =  ExprList(
+    before = computations
+  , during = c(
+      flow_rates
+    , state_updates
+  )
+)

inst/starter_models/ww/model.R

@@ -0,0 +1,59 @@
+library(macpan2)
+
+## expression lists
+###################################################
+
+## free form computations for convenience
+computations = list(
+  N ~ sum(S, E, Ia, Ip, Im, Is, R, H, ICUs, ICUd, H2, D, W, A)
+)
+
+## absolute flow rates (per time only)
+flow_rates = list(
+    SE ~ S * (beta0 / N) * (Ia * Ca + Ip * Cp + Im * Cm * (1 - iso_m) + Is * Cs *(1 - iso_s))
+  , EIa ~ E * alpha * sigma
+  , EIp ~ E * (1 - alpha)* sigma
+  , IaR ~ Ia * gamma_a
+  , IpIm ~ Ip * mu * gamma_p
+  , ImR ~ Im * gamma_m
+  , IpIs ~ Ip * (1 - mu) * gamma_p
+  , IsICUs ~ Is * (1 - nonhosp_mort) * (1 - phi1) * (1 - phi2) * gamma_s
+  , ICUsH2 ~ ICUs * psi1
+  , H2R ~ H2 * psi3
+  , IsH ~ Is * (1 - nonhosp_mort) * phi1 * gamma_s
+  , IsICUd ~ Is * (1 - nonhosp_mort) * (1 - phi1) * phi2 * gamma_s
+  , ICUdD ~ ICUd * psi2
+  , HR ~ H * rho
+  , IaW ~ Ia * nu # or * or N?
+  , IpW ~ Ip * nu 
+  , ImW ~ Im * nu
+  , IsW ~ Is * nu
+  , WA ~ W * xi
+)
+
+## state updates
+state_updates = list(
+    S ~ S - SE
+  , E ~ E + SE - EIa - EIp
+  , Ia ~ Ia + EIa - IaR
+  , Ip ~ Ip + EIp - IpIm - IpIs
+  , Im ~ Im + IpIm
+  , Is ~ Is + IpIs - IsICUs - IsH - IsICUd
+  , R ~ R + IaR + H2R + HR
+  , H ~ H + IsH - HR
+  , ICUs ~ ICUs + IsICUs - ICUsH2
+  , ICUd ~ ICUd + IsICUd - ICUdD
+  , H2 ~ H2 + ICUsH2 - H2R
+  , D ~ D + ICUdD
+  , W ~ W + IaW + IpW + ImW + IsW - WA
+  , A ~ A + WA
+)
+
+## simple unstructured scalar expression
+expr_list =  ExprList(
+    before = computations
+  , during = c(
+      flow_rates
+    , state_updates
+  )
+)