Package 'spleenrbc'

Description

Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age a) in the circulation.

Usage

alpha_c(u_rbc, pmf, beta)

Arguments

Description

Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age a) in the spleen.

Usage

alpha_r(u_rbc, pmf, beta)

Arguments

Description

Return the baseline parameter values, including all derived parameters.

Usage

baseline_parameters(species = c("Pf", "Pv"), nospleen = FALSE, derived = TRUE)

Arguments

Description

Age-dependent merozoite preference for uninfected RBCs.

Usage

beta(p, age)

Arguments

Description

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.

Usage

calculate_irbc_ratio(results)

Arguments

Value

A dataframe that includes the following columns, in addition those in results:

iRBC_Ratio

The ratio of infected cell fractions in the spleen and circulation.

Description

Calculate credible intervals for each column, except "time" and "scenario".

Usage

credible_intervals(results, pcnt = c(50, 60, 70, 80, 90, 95))

Arguments

Value

A dataframe with the following columns:

name

The statistic name (character)

time

The time (numeric, hours)

cred_int

The credible interval (ordered factor, widest to narrowest)

ci_min

The credible interval lower bound (numeric)

ci_max

The credible interval upper bound (numeric)

Description

Define parameters whose values are derived from other parameters.

Usage

define_derived_parameters(p)

Arguments

Description

Rate of infected RBC removal from the circulation into the spleen.

Usage

delta_i(p, age)

Arguments

Description

Increase in infected RBC removal into the spleen due to RBC congestion.

Usage

delta_i_fold(p, net_u_rbc, net_i_rbc)

Arguments

Description

Rate of infected RBC reentry into the circulation from the spleen.

Usage

delta_i_prime(p, age)

Arguments

Description

Rate of uninfected RBC removal from the circulation into the spleen.

Usage

delta_u(p, age)

Arguments

Description

Increase in uninfected RBC removal into the spleen due to RBC congestion.

Usage

delta_u_fold(p, net_u_rbc, net_i_rbc)

Arguments

Description

Rate of uninfected RBC reentry into the circulation from the spleen.

Usage

delta_u_prime(p, age)

Arguments

Description

Rate of RBC production.

Usage

erythropoiesis(p, u_rbc)

Arguments

Description

See Pava et al., 2016 for details.

Usage

hhs_asymp

Format

hhs_asymp

A data frame with 803 rows and the following columns:

species

One of "Pf", "Pv", or "neg"

total_rbc

The red blood cell count

Description

Record key outputs for a single scenario.

Usage

individual_results(p, keep)

Arguments

Value

A data frame that includes the following columns:

scenario

The scenario number

time

The simulation time (hours)

U_t

The number of uRBCs in the circulation

Ur_t

The number of uRBCs in the spleen

Retic_c_t

The number of reticulocytes in the circulation

Retic_r_t

The number of reticulocytes in the spleen

I_t

The number of iRBCs in the circulation

Ir_t

The number of iRBCs in the spleen

Iq_t

The number of iRBCs in the microvasculature

M_t

The number of macrophages in the spleen

E_t

The erythropoiesis rate

r_t

The number of reticulocytes in the bone marrow

pmr_c_t_1

The number of merozoites released in the circulation

pmr_r_t_1

The number of merozoites released in the spleen

flow_r_to_c

The number of reticulocytes released from the bone marrow

flow_uc_to_r

The number of uRBCs removed from the circulation into the spleen

flow_uc_to_r_no_inf

The number of uRBCs that would have been removed from the circulation into the spleen, in the absence of a malaria infection

flow_ur_to_c

The number of uRBCs released from the spleen into the circulation

flow_ur_out

The number of uRBCs phagocytised in the spleen

flow_ic_to_r

The number of iRBCs removed from the circulation into the spleen

flow_ic_to_q

The number of iRBCs sequestered into the microvasculature

flow_ir_to_c

The number of iRBCs released from the spleen into the circulation

flow_ir_out

The number of iRBCs phagocytised in the spleen

flow_uc_to_ic

The number of uRBCs in the circulation that became infected

flow_ur_to_ir

The number of uRBCs in the spleen that became infected

inf_from_ic

The number of RBCs infected from iRBCs in the circulation

inf_from_iq

The number of RBCs infected from iRBCs in the microvasculature

inf_from_ir

The number of RBCs infected from iRBCs in the spleen

rho_t

The release rate of the youngest reticulocytes

deltaUfold

The fold increase in uRBC removal from the circulation

deltaIfold

The fold increase in iRBC removal from the circulation

Ur_frac_inf

The fraction of RBCs in the spleen that become infected

Description

Calculate quantities related to uRBC infection and retention in the spleen due to malaria infection.

Usage

infection_flows_and_loss(results)

Arguments

Value

A dataframe that includes the following columns, in addition those in results:

U_and_I_t

The value of $U_c(t) + I_c(t)$

Ur_frac_U

the fraction of uRBCs that are retained in the spleen

flow_uc_to_r_inf

The retention of uRBCs due to malaria infection

flow_uc_to_r_ratio

The rate of uRBC retention that is due to malaria infection, relative to baseline uRBC retention

Uc_loss_ratio_c

The ratio of uRBC retention due to malaria loss, relative to the infection of uRBCs in the circulation

Uc_loss_ratio_cr

The ratio of uRBC retention due to malaria loss, relative to the infection of uRBCs in the circulation and the spleen

inf_total

The number of uRBC infections in the circulation and spleen

inf_from_icq

The number of uRBC infection in the circulation due to merozoites released in the circulation and microvasculature

Description

Construct the initial model state.

Usage

initial_spleenrbc_state(p)

Arguments

Description

Phagocytosis rate of infected RBCs in the spleen.

Usage

lambda_i(p, macrophages)

Arguments

Description

Phagocytosis rate of uninfected RBCs in the spleen.

Usage

lambda_u(p, macrophages, age)

Arguments

Description

Define the distributions from which to sample values for each parameter.

Usage

lhs_distributions(params, lower = 0.8, upper = 1.2)

Arguments

Description

Pf parameter values for each scenario.

Usage

parameters_pf

Format

parameters_pf

A data frame with 34 rows and 3 columns:

name

Parameter name

baseline

Baseline value

dist

Sampling distribution: 'constant' or 'triangle'

Description

Pv parameter values for each scenario.

Usage

parameters_pv

Format

parameters_pv

A data frame with 34 rows and 3 columns:

name

Parameter name

baseline

Baseline value

dist

Sampling distribution: 'constant' or 'triangle'

Description

Construct a list that will record the model state over time.

Usage

prepare_spleenrbc_snapshot(p, time_steps)

Arguments

Description

For this conversion, we assume that 15 g/dL of haemoglobin corresponds to $2.5 \times 10^{13}$ RBCs.

Usage

rbc_counts_to_haemoglobin(rbc_counts)

Arguments

Value

Haemoglobin levels (g/dL).

Examples

rbc_counts_to_haemoglobin(1e15 * c(2.3, 2.4, 2.5, 2.6, 2.7))

Description

Defined as the median red blood cell count for uninfected Papuans in the hhs_asymp data set.

Usage

rbc_steady_state

Format

rbc_steady_state

A scalar value.

Description

Subtract negative U values from other (positive) U values.

Usage

resolve_negative_rbcs(u, t_urbc, pmf, beta_a, alpha_fun)

Arguments

Description

Returns the steady-state values for:

• normoblast population (gamma);

• reticulocyte population in the bone marrow (r_a);

• reticulocyte population in the circulation (R_a);

• normoctye population in the circulation (N_a);

• RBC population in the spleen (Ur_a); and

• circulating RBC imbalance wrt homeostasis (difference).

Usage

retic_steady_state(p)

Arguments

Description

The reticulocyte production rate for the given normoblast population.

Usage

reticulocyte_prod(p, rho_ss, lambdaU, deltaU_a, gamma, z = 0)

Arguments

Description

Age-structured release rate of reticulocytes from the bone marrow into the circulation.

Usage

rho(p, age, u_rbc)

Arguments

Description

The minimum age at which reticulocytes are released from the bone marrow into the circulation.

Usage

rho_release_age(p, u_rbc)

Arguments

Description

Run model scenarios.

Usage

run_spleenrbc(
  scenarios = NULL,
  days = 50,
  time_steps = days * 24,
  verbose = FALSE
)

Arguments

Value

A data frame whose columns capture model state variables at each time-step.

See Also

individual_results() for a description of the returned data frame.

Description

Run a single scenario and return the model state history.

Usage

run_spleenrbc_model(p, time_steps, debug = FALSE)

Arguments

Value

A data frame whose columns capture model state variables at each time-step.

See Also

individual_results() for a description of the returned data frame.

Description

Create parameter samples for each scenario.

Usage

sample_parameters(
  species = c("Pf", "Pv"),
  nospleen = FALSE,
  dists = NULL,
  rbc_ss = NULL,
  n_samples = 1000,
  seed = 1691987
)

Arguments

Description

See Kho et al., 2021 for details.

Usage

splenectomised

Format

splenectomised

A data frame with 17 rows and the following columns:

patient

Patient identifier

infection

One of "Pf", "Pv", or "neg"

irbc_peri

Infected RBC count in the peripheral circulation

irbc_spleen

Infected RBC count in the spleen

urbc_peri

Uninfected RBC count in the peripheral circulation

urbc_spleen

Uninfected RBC count in the spleen

Description

Update the model state by simulating forward one time-step.

Usage

step_spleenrbc_model(p, s, t)

Arguments

Description

Age-structured rate of RBC sequestration into the microvasculature.

Usage

zeta(p, age)

Arguments