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Moved mortality to the end of processes to resolve order of competing… #292

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merged 2 commits into from
May 2, 2024
Merged

Moved mortality to the end of processes to resolve order of competing… #292

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5077d4b
Moved mortality to the end of processes to resolve order of competing…
RJSheppard Apr 15, 2024
a9b495c
Merging dev branch back before merging into main dev branch.
RJSheppard May 1, 2024
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34 changes: 19 additions & 15 deletions R/processes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ create_processes <- function(
create_exponential_decay_process(variables$iva, parameters$rva),
create_exponential_decay_process(variables$id, parameters$rid)
)

if (parameters$individual_mosquitoes) {
processes <- c(
processes,
Expand All @@ -61,7 +61,7 @@ create_processes <- function(
)
)
}

# ==============================
# Biting and mortality processes
# ==============================
Expand All @@ -82,7 +82,6 @@ create_processes <- function(
mixing,
mixing_index
),
create_mortality_process(variables, events, renderer, parameters),
create_asymptomatic_progression_process(
variables$state,
parameters$dd,
Expand Down Expand Up @@ -134,15 +133,15 @@ create_processes <- function(
0
)
)

# ===============
# ODE integration
# ===============
processes <- c(
processes,
create_solver_stepping_process(solvers, parameters)
)

# =========
# RTS,S EPI
# =========
Expand All @@ -159,7 +158,7 @@ create_processes <- function(
)
)
}

# =========
# PMC
# =========
Expand All @@ -178,7 +177,7 @@ create_processes <- function(
)
)
}

# =========
# Rendering
# =========
Expand Down Expand Up @@ -208,7 +207,7 @@ create_processes <- function(
),
create_compartmental_rendering_process(renderer, solvers, parameters)
)

if (parameters$individual_mosquitoes) {
processes <- c(
processes,
Expand All @@ -230,11 +229,11 @@ create_processes <- function(
)
)
}

# ======================
# Intervention processes
# ======================

if (parameters$bednets) {
processes <- c(
processes,
Expand All @@ -247,14 +246,14 @@ create_processes <- function(
net_usage_renderer(variables$net_time, renderer)
)
}

if (parameters$spraying) {
processes <- c(
processes,
indoor_spraying(variables$spray_time, parameters, correlations)
)
}

# ======================
# Progress bar process
# ======================
Expand All @@ -264,7 +263,12 @@ create_processes <- function(
create_progress_process(timesteps)
)
}


# Mortality step
processes <- c(
processes,
create_mortality_process(variables, events, renderer, parameters))

processes
}

Expand All @@ -289,7 +293,7 @@ create_exponential_decay_process <- function(variable, rate) {
#' @title Create and initialise lagged_infectivity object
#'
#' @param variables model variables for initialisation
#' @param parameters model parameters
#' @param parameters model parameters
#' @noRd
create_lagged_infectivity <- function(variables, parameters) {
age <- get_age(variables$birth$get_values(), 0)
Expand All @@ -306,7 +310,7 @@ create_lagged_infectivity <- function(variables, parameters) {
#'
#' @param variables model variables for initialisation
#' @param solvers model differential equation solvers
#' @param parameters model parameters
#' @param parameters model parameters
#' @noRd
create_lagged_eir <- function(variables, solvers, parameters) {
lapply(
Expand Down
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