Record uRBC loss ratios in sensitivity analyses

This is the ratio of uRBC loss (from circulation) to due (a) retention
in the spleen caused by the presence of a malarian infection; to (b)
parasitisation of uRBCs.

NAMESPACE

@@ -5,6 +5,7 @@ export(alpha_r)
 export(baseline_parameters)
 export(beta)
 export(calculate_irbc_ratio)
+export(calculate_urbc_loss_ratio)
 export(credible_intervals)
 export(define_derived_parameters)
 export(delta_i)

R/outputs.R

@@ -135,6 +135,36 @@ infection_flows_and_loss <- function(results) {
 }
 
 
+#' Calculate the ratio of (a) the unparasitised RBC loss due to malaria
+#' (additional uRBC retention in the spleen); to (b) the parasitised RBC loss
+#' due to RBC infection.
+#'
+#' @param results A dataframe of simulation results.
+#'
+#' @return
+#' A dataframe that includes the following column, in addition to those in
+#' `results`:
+#'
+#' \describe{
+#'   \item{uRBC_Loss_Ratio}{The ratio of uRBC loss (from the circulation) due
+#'     to splenic retention and due to parasitisation.}
+#' }
+#'
+#' @export
+calculate_urbc_loss_ratio <- function(results) {
+  results |> dplyr::mutate(
+    flow_uc_to_r_inf = flow_uc_to_r - flow_uc_to_r_no_inf,
+    inf_total = inf_from_ic + inf_from_iq + inf_from_ir,
+    uRBC_Loss_Ratio = dplyr::case_when(
+      inf_total > 0 ~ flow_uc_to_r_inf / inf_total,
+      .default = 0
+    ),
+    flow_uc_to_r_inf,
+    inf_total = NULL
+  )
+}
+
+
 #' Calculate the ratio of (a) the fraction of RBCs in the spleen that are
 #' infected; to (b) the fraction of RBCs in the circulation that are infected.
 #'

run-sensitivity-analysis.R

@@ -46,9 +46,23 @@ run_sensitivity_analysis <- function(species, days = 150, n_samples = 1000) {
   # Save the credible intervals for all simulations.
   cint_all_file <- file.path("outputs", paste0(prefix, "-rbc-cints-all.rds"))
   cint_all <- results |>
-    select(scenario, time, U_t, Ur_t, I_t, Iq_t, Ir_t) |>
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      flow_uc_to_r, flow_uc_to_r_no_inf,
+      inf_from_ic, inf_from_iq, inf_from_ir
+    ) |>
     # Calculate ratio of iRBC % in the spleen to iRBC % in the circulation.
     calculate_irbc_ratio() |>
+    # Calculate ratio of unparasitised uRBC loss to parasitised uRBC loss.
+    calculate_urbc_loss_ratio() |>
+    # Drop intermediate values.
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      iRBC_Ratio,
+      uRBC_Loss_Ratio
+    ) |>
     credible_intervals() |>
     mutate(Species = !!species)
   saveRDS(cint_all, cint_all_file)
@@ -61,9 +75,23 @@ run_sensitivity_analysis <- function(species, days = 150, n_samples = 1000) {
   cint_nonz_file <- file.path("outputs", paste0(prefix, "-rbc-cints-nonz.rds"))
   cint_nonz <- results |>
     filter(! scenario %in% zero_scenarios) |>
-    select(scenario, time, U_t, Ur_t, I_t, Iq_t, Ir_t) |>
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      flow_uc_to_r, flow_uc_to_r_no_inf,
+      inf_from_ic, inf_from_iq, inf_from_ir
+    ) |>
     # Calculate ratio of iRBC % in the spleen to iRBC % in the circulation.
     calculate_irbc_ratio() |>
+    # Calculate ratio of unparasitised uRBC loss to parasitised uRBC loss.
+    calculate_urbc_loss_ratio() |>
+    # Drop intermediate values.
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      iRBC_Ratio,
+      uRBC_Loss_Ratio
+    ) |>
     credible_intervals() |>
     mutate(Species = !!species)
   saveRDS(cint_nonz, cint_nonz_file)
@@ -72,9 +100,23 @@ run_sensitivity_analysis <- function(species, days = 150, n_samples = 1000) {
   cint_zero_file <- file.path("outputs", paste0(prefix, "-rbc-cints-zero.rds"))
   cint_zero <- results |>
     filter(scenario %in% zero_scenarios) |>
-    select(scenario, time, U_t, Ur_t, I_t, Iq_t, Ir_t) |>
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      flow_uc_to_r, flow_uc_to_r_no_inf,
+      inf_from_ic, inf_from_iq, inf_from_ir
+    ) |>
     # Calculate ratio of iRBC % in the spleen to iRBC % in the circulation.
     calculate_irbc_ratio() |>
+    # Calculate ratio of unparasitised uRBC loss to parasitised uRBC loss.
+    calculate_urbc_loss_ratio() |>
+    # Drop intermediate values.
+    select(
+      scenario, time,
+      U_t, Ur_t, I_t, Iq_t, Ir_t,
+      iRBC_Ratio,
+      uRBC_Loss_Ratio
+    ) |>
     credible_intervals() |>
     mutate(Species = !!species)
   saveRDS(cint_zero, cint_zero_file)