starter model updates

canmod · Oct 11, 2024 · c751202 · c751202
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diff --git a/inst/starter_models/awareness/README.R b/inst/starter_models/awareness/README.R
@@ -0,0 +1,116 @@
+## ----include = FALSE----------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  warning = FALSE,
+  message = FALSE,
+  comment = "#>",
+  fig.path = "./figures/"
+)
+
+
+## ----packages, message=FALSE, warning=FALSE-----------------------------------
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+library(macpan2)
+
+
+## ----model_spec---------------------------------------------------------------
+specs = mp_tmb_library(
+    "starter_models"
+  , "awareness"
+  , package = "macpan2"
+  , alternative_specs = TRUE
+)
+print(names(specs))
+
+
+## ----diagram, echo = FALSE, fig.height = 2, fig.width = 5---------------------
+system.file("utils", "box-drawing.R", package = "macpan2") |> source()
+layout = mp_layout_paths(specs$awareness_model)
+plot_flow_diagram(layout)
+
+
+## ----diagram-delayed-death, echo = FALSE, fig.height = 2, fig.width = 5-------
+system.file("utils", "box-drawing.R", package = "macpan2") |> source()
+layout = mp_layout_paths(specs$delayed_death_awareness_model)
+plot_flow_diagram(layout)
+
+
+## ----echo = FALSE-------------------------------------------------------------
+plot_traj = function(traj) {
+  p = (traj
+    |> mutate(matrix = factor(matrix, levels = outputs))
+    |> ggplot()
+    + geom_line(aes(time, value))
+    + facet_wrap(~matrix
+        , scales = "free_y"
+        , ncol = 1
+        , dir = "v"
+      )
+    + scale_y_continuous(limits = c(0, NA), expand = c(0, NA))
+    + scale_x_continuous(
+          minor_breaks = \(x) {
+            y = seq(from = x[1], to = x[2], by = 50L)
+            y[1:(length(y) - 1)]
+          }
+        , expand = c(0, 0)
+      )
+    + ylab("")
+    + xlab("")
+    + theme_bw()
+  )
+  return(p)
+}
+
+
+## ----behavioural_cycles-------------------------------------------------------
+set.seed(8L)
+days = 800
+outputs = c(
+    "infection", "death"
+  , "S", "importation"
+)
+sim = (specs$longer_memory_awareness_model
+  |> mp_euler()
+  |> mp_simulator(days, outputs)
+)
+traj = (sim
+  |> mp_trajectory(include_initial = TRUE)
+)
+plot_traj(traj)
+
+
+## ----importation--------------------------------------------------------------
+set.seed(8L)
+days = 800
+outputs = c(
+    "infection", "death"
+  , "S", "importation"
+)
+sim = (specs$importation_awareness_model
+  |> mp_euler()
+  |> mp_simulator(days, outputs)
+)
+traj = (sim
+  |> mp_trajectory(include_initial = TRUE)
+)
+plot_traj(traj)
+
+
+## ----importation_and_process_error--------------------------------------------
+set.seed(8L)
+days = 800
+outputs = c(
+    "infection", "death"
+  , "S", "importation"
+)
+sim = (specs$importation_awareness_model
+  |> mp_euler_multinomial()
+  |> mp_simulator(days, outputs)
+)
+traj = (sim
+  |> mp_trajectory(include_initial = TRUE)
+)
+plot_traj(traj)
+
diff --git a/inst/starter_models/hiv/README.R b/inst/starter_models/hiv/README.R
@@ -0,0 +1,58 @@
+## ----include = FALSE----------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "./figures/"
+)
+
+
+## ----packages, warning=FALSE, message=FALSE-----------------------------------
+library(macpan2)
+library(ggplot2)
+library(dplyr)
+
+
+## ----model_lib----------------------------------------------------------------
+spec = mp_tmb_library(
+    "starter_models"
+  , "hiv"
+  , package = "macpan2"
+)
+
+
+## ----diagram, echo = FALSE, fig.height = 2.5, fig.width = 8.5-----------------
+system.file("utils", "box-drawing.R", package = "macpan2") |> source()
+layout = mp_layout_grid(spec
+  , east = "^(infection|progression|death)"
+  , south = "^(protection)"
+  , north = "^(unprotection)"
+  , loops = "^(unprotection)"
+  , x_gap = 0.3
+  , y_gap = 0.3
+  , north_south_sep = 0.15
+)
+(layout
+  |> plot_flow_diagram(show_flow_rates = TRUE)
+  |> draw_outflows(layout, show_labels = TRUE, lab = "rate")
+  |> draw_inflows(layout, show_labels = TRUE, lab = "rate")
+)
+
+
+## ----simulations--------------------------------------------------------------
+outputs = c(sprintf("I%s", 1:4), sprintf("A%s", 1:4))
+sim = (spec
+  |> mp_tmb_update(default = list(lambda0 = 0.36, n = 0.2))
+  |> mp_rk4()
+  |> mp_simulator(time_steps = 50L, outputs)
+)
+(sim
+  |> mp_trajectory()
+  |> mutate(matrix = sub("^A([1-4])$", "Infectious and treated, stage \\1", matrix))
+  |> mutate(matrix = sub("^I([1-4])$", "Infectious and untreated, stage \\1", matrix))
+  |> ggplot()
+  + geom_line(aes(time, value))
+  + facet_wrap(~ matrix, ncol = 2, scales = 'free', dir = "v")
+  + scale_y_continuous(limits = c(0, NA), expand = c(0, 0))
+  + theme_bw()
+)
+
diff --git a/inst/starter_models/lotka_volterra_competition/README.R b/inst/starter_models/lotka_volterra_competition/README.R
@@ -0,0 +1,95 @@
+## ----include = FALSE----------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  warning = FALSE,
+  message = FALSE,
+  comment = "#>",
+  fig.path = "./figures/"
+)
+system.file("utils", "round-coef.R", package = "macpan2") |> source()
+
+
+## ----packages, message=FALSE, warning=FALSE-----------------------------------
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+library(macpan2)
+
+
+## ----options------------------------------------------------------------------
+options(macpan2_verbose = FALSE)
+
+
+## ----model_spec---------------------------------------------------------------
+spec = mp_tmb_library(
+    "starter_models"
+  , "lotka_volterra_competition"
+  , package = "macpan2"
+)
+print(spec)
+
+
+## ----fake_data----------------------------------------------------------------
+set.seed(1L)
+# set number of time steps in simulation
+time_steps = 100L
+# ayx value to simulate data with (species X has a carrying capacity of 200)
+true = list(ayx = 0.8/200)
+
+# simulator object
+fake_data = (spec
+  |> mp_tmb_insert(
+      phase = "during"
+    , at = Inf
+    , expressions = list(X_noisy ~ rpois(X), Y_noisy ~ rpois(Y))
+    , default = true
+  )
+  |> mp_simulator(  
+      time_steps = time_steps
+    , outputs = c("X_noisy","Y_noisy")
+  )
+  |> mp_trajectory()
+  |> mutate(matrix = substr(matrix, 1L, 1L))
+)
+
+(fake_data
+  |> ggplot()
+  + geom_line(aes(time, value, colour = matrix))
+  + theme_bw()
+)
+
+
+## -----------------------------------------------------------------------------
+cal = (spec
+  |> mp_tmb_calibrator(
+      data = fake_data
+    , traj = c("X", "Y")
+    , par = c("ayx","rx", "ry")
+  )
+)
+mp_optimize(cal)
+
+
+## ----coef---------------------------------------------------------------------
+mp_tmb_coef(cal, conf.int = TRUE) |> round_coef_tab()
+print(true)
+
+
+## ----traj_fit-----------------------------------------------------------------
+comparison_data = list(
+    obs = fake_data
+  , fit = mp_trajectory_sd(cal, conf.int = TRUE)
+) |> bind_rows(.id = "type")
+(comparison_data
+  |> ggplot()
+  + geom_line(aes(time, value, colour = type))
+  + facet_wrap(~matrix)
+  + geom_ribbon(aes(time, ymin = conf.low, ymax = conf.high)
+    , colour = "red"
+    , fill = "red"
+    , alpha = 0.5
+    , filter(comparison_data, type == "fit")
+  )
+  + theme_bw()
+)
+
diff --git a/inst/starter_models/lotka_volterra_predator_prey/README.R b/inst/starter_models/lotka_volterra_predator_prey/README.R
@@ -0,0 +1,110 @@
+## ----include = FALSE----------------------------------------------------------
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  warning = FALSE,
+  message = FALSE,
+  comment = "#>",
+  fig.path = "./figures/"
+)
+system.file("utils", "round-coef.R", package = "macpan2") |> source()
+
+
+## ----packages, message=FALSE, warning=FALSE-----------------------------------
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+library(macpan2)
+
+
+## ----options------------------------------------------------------------------
+options(macpan2_verbose = FALSE)
+
+
+## ----model_spec---------------------------------------------------------------
+specs = mp_tmb_library(
+    "starter_models"
+  , "lotka_volterra_predator_prey"
+  , package = "macpan2"
+  , alternative_specs = TRUE
+)
+
+
+## ----simple_spec--------------------------------------------------------------
+specs$holling_1
+
+
+## ----logistic_spec------------------------------------------------------------
+specs$holling_2
+
+
+## ----func_resp_spec-----------------------------------------------------------
+specs$holling_3
+
+
+## ----fake_data----------------------------------------------------------------
+spec = specs$holling_1
+set.seed(1L)
+# set number of time steps in simulation
+time_steps = 100L
+# delta value to simulate data with
+true = list(delta = 2.5/10)
+
+# simulator object
+fake_data = (spec
+  |> mp_tmb_insert(
+      phase = "during"
+    , at = Inf
+    , expressions = list(X_noisy ~ rpois(X), Y_noisy ~ rpois(Y))
+    , default = true
+  )
+  |> mp_simulator(  
+      time_steps = time_steps
+    , outputs = c("X_noisy","Y_noisy")
+  )
+  |> mp_trajectory()
+  |> mutate(matrix = substr(matrix, 1L, 1L))
+)
+
+(fake_data
+  |> mutate(species = ifelse(matrix == "X", "prey", "predator"))
+  |> ggplot()
+  + geom_line(aes(time, value, colour = species))
+  + theme_bw()
+)
+
+
+## -----------------------------------------------------------------------------
+cal = (spec
+  |> mp_tmb_calibrator(
+      data = fake_data
+    , traj = c("X", "Y")
+    , par = "delta"
+  )
+)
+mp_optimize(cal)
+
+
+## ----coef---------------------------------------------------------------------
+coef = mp_tmb_coef(cal) |> round_coef_tab()
+coef$true = true[coef$mat]
+print(coef)
+
+
+## ----traj_fit-----------------------------------------------------------------
+comparison_data = list(
+    obs = fake_data
+  , fit = mp_trajectory_sd(cal, conf.int = TRUE)
+) |> bind_rows(.id = "type") |> mutate(species = ifelse(matrix == "X", "prey", "predator"))
+(comparison_data
+  |> ggplot()
+  + geom_line(aes(time, value, colour = type))
+  + facet_wrap(~species)
+  + geom_ribbon(aes(time, ymin = conf.low, ymax = conf.high)
+    , colour = "red"
+    , fill = "red"
+    , alpha = 0.5
+    , filter(comparison_data, type == "fit")
+  )
+  + theme_bw()
+)
+