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Allow p.v subpatent infections #320

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Oct 14, 2024
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Allow p.v subpatent infections #320

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209 changes: 146 additions & 63 deletions R/human_infection.R
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Original file line number Diff line number Diff line change
Expand Up @@ -154,24 +154,27 @@ infection_outcome_process <- function(
parameters,
prob){

incidence_renderer(
variables$birth,
renderer,
infected_humans,
'inc_',
parameters$incidence_rendering_min_ages,
parameters$incidence_rendering_max_ages,
timestep
)

if (infected_humans$size() > 0) {

renderer$render('n_infections', infected_humans$size(), timestep)
incidence_renderer(
variables$birth,
renderer,
infected_humans,
'inc_',
parameters$incidence_rendering_min_ages,
parameters$incidence_rendering_max_ages,
timestep
)

boost_immunity(
variables$ica,
infected_humans,
variables$last_boosted_ica,
timestep,
parameters$uc
)

if(parameters$parasite == "falciparum"){
boost_immunity(
variables$id,
Expand All @@ -180,53 +183,118 @@ infection_outcome_process <- function(
timestep,
parameters$ud
)

clinical <- calculate_clinical_infections(
variables,
infected_humans,
parameters,
renderer,
timestep
)

treated <- calculate_treated(
variables,
clinical,
parameters,
timestep,
renderer
)

update_severe_disease(
timestep,
infected_humans,
variables,
parameters,
renderer
)

## The treated and infected_humans bitsets are re-written so be cautious!
to_D <- treated$not(FALSE)$and(clinical)
to_A <- infected_humans$and(clinical$not(FALSE))
to_U <- NULL

} else if (parameters$parasite == "vivax"){

boost_immunity(
variables$iaa,
infected_humans,
variables$last_boosted_iaa,
timestep,
parameters$ua
)

## Only S and U infections are considered in generating lm-det infections
lm_detectable <- calculate_lm_det_infections(
variables,
variables$state$get_index_of(c("S","U"))$and(infected_humans),
parameters,
renderer,
timestep
)

# Lm-detectable level infected S and U, and all A infections may receive clinical infections
# There is a different calculation to generate clinical infections, based on current infection level
# LM infections must only pass through the clinical calculation, therefore all "A" infections are included
# "S" and "U" infections must pass through the lm-detectable calculation prior to and in addition to the clinical
# calculation. We therefore consider all "A" infections and only the "S" and "U" infections that are now lm-detectable.
clinical <- calculate_clinical_infections(
variables,
variables$state$get_index_of("A")$and(infected_humans)$or(lm_detectable),
parameters,
renderer,
timestep
)

treated <- calculate_treated(
variables,
clinical,
parameters,
timestep,
renderer
)

## The infected_humans,lm_detectable and clinical bitsets are re-written so be cautious!
to_U <- infected_humans$and(lm_detectable$not(F))$and(variables$state$get_index_of(c("S")))
to_A <- lm_detectable$and(clinical$not(F))
to_D <- clinical$and(treated$not(F))
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}
}

clinical_infections <- calculate_clinical_infections(
variables,
infected_humans,
parameters,
renderer,
timestep
)

if(parameters$parasite == "falciparum"){
update_severe_disease(
timestep,
infected_humans,
variables,

schedule_infections(
parameters,
renderer
variables,
timestep,
to_D,
to_A,
to_U
)
}
treated <- calculate_treated(
variables,
clinical_infections,
parameters,
timestep,
renderer
)
renderer$render('n_infections', infected_humans$size(), timestep)
schedule_infections(
}

#' @title Calculate light microscopy detectable infections (p.v only)
#' @description
#' Sample light microscopy detectable infections from all infections
#' @param variables a list of all of the model variables
#' @param infections bitset of infected humans
#' @param parameters model parameters
#' @param renderer model render
#' @param timestep current timestep
#' @noRd
calculate_lm_det_infections <- function(
variables,
clinical_infections,
treated,
infected_humans,
infections,
parameters,
renderer,
timestep
)
) {

iaa <- variables$iaa$get_values(infections)
iam <- variables$iam$get_values(infections)

philm <- anti_parasite_immunity(
min = parameters$philm_min, max = parameters$philm_max, a50 = parameters$alm50,
k = parameters$klm, iaa = iaa, iam = iam)

lm_det_infections <- bitset_at(infections, bernoulli_multi_p(philm))
}

#' @title Calculate clinical infections
Expand Down Expand Up @@ -487,51 +555,46 @@ calculate_successful_treatments <- function(
successfully_treated_list
}


#' @title Schedule infections
#' @description
#' Schedule infections in humans after the incubation period
#' @param events a list of all of the model events
#' @param clinical_infections bitset of clinically infected humans
#' @param treated bitset of treated humans
#' @param infections bitset of infected humans
#' @param parameters model parameters
#' @param variables a list of all of the model variables
#' @param timestep current timestep
#' @param to_D bitset of humans to move to state D
#' @param to_A bitset of humans to move to state A
#' @param to_U bitset of humans to move to state U
#' @noRd
schedule_infections <- function(
variables,
clinical_infections,
treated,
infections,
parameters,
timestep
variables,
timestep,
to_D,
to_A,
to_U
) {

included <- treated$not(TRUE)

to_infect <- clinical_infections$and(included)
to_infect_asym <- clinical_infections$copy()$not(TRUE)$and(infections)$and(
included
)

if(to_infect$size() > 0) {
if(to_D$size() > 0) {
update_infection(
variables$state,
'D',
variables$infectivity,
parameters$cd,
variables$progression_rates,
1/parameters$dd,
to_infect
to_D
)
}

if(to_infect_asym$size() > 0) {
if(to_A$size() > 0) {
if(parameters$parasite == "falciparum"){
# p.f has immunity-determined asymptomatic infectivity
update_to_asymptomatic_infection(
variables,
parameters,
timestep,
to_infect_asym
to_A
)
} else if (parameters$parasite == "vivax"){
# p.v has constant asymptomatic infectivity
Expand All @@ -542,7 +605,27 @@ schedule_infections <- function(
parameters$ca,
variables$progression_rates,
1/parameters$da,
to_infect_asym
to_A
)
}
}

if(parameters$parasite == "vivax"){
# new p.v infections may be pcr-detectable
if(to_U$size() > 0){
# p.v pcr-detectable recovery rate is immunity dependent
update_infection(
variables$state,
'U',
variables$infectivity,
parameters$cu,
variables$progression_rates,
1/anti_parasite_immunity(
parameters$dpcr_min, parameters$dpcr_max, parameters$apcr50, parameters$kpcr,
variables$iaa$get_values(to_U),
variables$iam$get_values(to_U)
),
to_U
)
}
}
Expand Down
12 changes: 6 additions & 6 deletions R/parameters.R
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Original file line number Diff line number Diff line change
Expand Up @@ -37,10 +37,10 @@
#' * da - the delay for humans to move from state A to U; default = 195
#' * du - the delay for humans to move from state U to S (p.f only); default = 110
#'
#' duration of pcr detectable infection: du (p.v only):
#' duration of pcr detectable infections: du (p.v only):
#'
#' * dpcr_max - Maximum duration of subpatent infection: default = 53.69
#' * dpcr_min - Minimum duration of subpatent infection: default = 10
#' * dpcr_max - Maximum duration of PCR-detectable infections: default = 53.69
#' * dpcr_min - Minimum duration of PCR-detectable infections: default = 10
#' * kpcr - Shape parameter: default = 4.021
#' * apcr50 - Scale parameter: default = 9.8
#'
Expand Down Expand Up @@ -112,7 +112,7 @@
#' * id0 - scale parameter; default = 1.577533
#' * kd - shape parameter; default = 0.476614
#'
#' probability of patent infection due to anti-parasite immunity (p.v only):
#' probability of light-microscopy detectable infections due to anti-parasite immunity (p.v only):
#'
#' * philm_max - maximum probability due to no immunity; default = 0.9329
#' * philm_min - maximum reduction due to immunity; default = 0.0131
Expand Down Expand Up @@ -141,7 +141,7 @@
#' * cd - infectivity of clinically diseased humans towards mosquitoes; default = 0.068
#' * ca - infectivity of asymptomatic humans towards mosquitoes (p.v only); default = 0.1
#' * gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425
#' * cu - infectivity of sub-patent infection; default = 0.0062
#' * cu - infectivity of subpatent infection; default = 0.0062
#' * ct - infectivity of treated infection; default = 0.021896
#'
#' mosquito fixed state transitions (including mortality):
Expand Down Expand Up @@ -344,7 +344,7 @@ get_parameters <- function(overrides = list(), parasite = "falciparum") {
# maternal immunity parameters
# probability of pre-erythrocytic infection/blood immunity
# probability of asymptomatic detection (p.f only)
# probability of patent infection (due to anti-parasite immunity, p.v only)
# probability of light-microscopy detectable infection (due to anti-parasite immunity, p.v only)
# probability of clinical infection
# probability of severe infection (p.f only)
# infectivity towards mosquitos
Expand Down
11 changes: 7 additions & 4 deletions R/processes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ create_processes <- function(
immunity_process = create_exponential_decay_process(variables$ica,
parameters$rc)
)

if(parameters$parasite == "falciparum"){
processes <- c(
processes,
Expand All @@ -61,14 +61,17 @@ create_processes <- function(
immunity_process = create_exponential_decay_process(variables$iva,
parameters$rva),
# Immunity to detectability
immunity_process = create_exponential_decay_process(variables$id, parameters$rid)
immunity_process = create_exponential_decay_process(variables$id,
parameters$rid)
)
} else if (parameters$parasite == "vivax"){
processes <- c(
processes,
# Anti-parasite immunity
immunity_process = create_exponential_decay_process(variables$iam, parameters$rm),
immunity_process = create_exponential_decay_process(variables$iaa, parameters$ra)
immunity_process = create_exponential_decay_process(variables$iam,
parameters$rm),
immunity_process = create_exponential_decay_process(variables$iaa,
parameters$ra)
)
}

Expand Down
10 changes: 5 additions & 5 deletions man/get_parameters.Rd
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