Package: spleenrbc 0.0.1

spleenrbc: The role of the spleen in red blood cell loss due to malaria

A mathematical model of red blood cell (RBC) dynamics in a malaria infection, which includes the spleen as a separate model compartment that can retain large amounts of infected and uninfected RBCs.

Authors:Saber Dini [aut], Ali Haghiri [aut], Robert Moss [aut, cre]

spleenrbc_0.0.1.tar.gz
spleenrbc_0.0.1.zip(r-4.7-any)spleenrbc_0.0.1.zip(r-4.6-any)spleenrbc_0.0.1.zip(r-4.5-any)
spleenrbc_0.0.1.tgz(r-4.6-any)spleenrbc_0.0.1.tgz(r-4.5-any)
spleenrbc_0.0.1.tar.gz(r-4.7-any)spleenrbc_0.0.1.tar.gz(r-4.6-any)
spleenrbc_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
spleenrbc/json (API)

# Install 'spleenrbc' in R:
install.packages('spleenrbc', repos = c('https://robmoss.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://gitlab.unimelb.edu.au/rgmoss/malaria-spleen-rbc-loss

Datasets:
  • hhs_asymp - Red blood cell counts collected from asymptomatic Papuans who reported no fever within the preceding 24 hours (708 uninfected, 50 Pf infections, 45 Pv infections) in a cross-sectional household survey conducted in southern Papua, Indonesia.
  • parameters_pf - Pf parameter values for each scenario.
  • parameters_pv - Pv parameter values for each scenario.
  • rbc_steady_state - The red blood cell count at homeostasis.
  • splenectomised - Uninfected and infected RBC counts in the circulation and spleen of 15 asymptomatic adults in Papua, Indonesia (9 Pf infections, 6 Pv infections) who underwent splenectomy, mostly due to trauma.

On CRAN:

Conda:

4.00 score 36 exports 22 dependencies

Last updated from:d743d9e415. Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develWARNING147
source / vignettesOK463
linux-releaseWARNING133
macos-releaseWARNING133
macos-oldrelWARNING167
windows-develWARNING99
windows-releaseWARNING78
windows-oldrelWARNING87
wasm-releaseOK129

Exports:alpha_calpha_rbaseline_parametersbetacalculate_irbc_ratiocalculate_steady_state_outputscalculate_urbc_loss_ratiocalculate_urbc_ratiodefine_derived_parametersdelta_idelta_i_folddelta_i_primedelta_udelta_u_folddelta_u_primeerythropoiesisindividual_resultsinfection_flows_and_lossinitial_spleenrbc_statelambda_ilambda_uprepare_spleenrbc_snapshotqlunifrbc_counts_to_haemoglobinresolve_negative_rbcsretic_steady_statereticulocyte_prodrhorho_release_agerun_spleenrbcrun_spleenrbc_modelsample_parametersstep_spleenrbc_modeluncertainty_distributionsuncertainty_intervalszeta

Dependencies:clicpp11dplyrgenericsgluelhslifecyclemagrittrpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Sensitivity analyses for Pf and Pv
Overview | Sampling distributions | Initial RBC count | Normoblast production | Reticulocyte release | uRBC removal | uRBC release | RBC infection | iRBC removal | iRBC release | iRBC sequestration | Phagocytosis | Quantities of interest | Prior predictive intervals | Rank correlations | Partial rank correlations | Relative errors | Varying all but 2 parameters | References
Rendered fromsensitivity-analyses.Rmdusingknitr::rmarkdown

Last update: 2025-11-18
Started: 2024-03-20

Evidence for parameter values
Macrophage population in the spleen | Maximum fold increase in RBC production | Normoblast population in the bone marrow | Parasite multiplication | Reticulocyte release from bone marrow | Steady-state RBC population | References
Rendered fromevidence-for-parameter-values.Rmdusingknitr::rmarkdown

Last update: 2025-07-28
Started: 2024-03-20

Red blood cell steady-state distribution
Rendered fromrbc-steady-state.Rmdusingknitr::rmarkdown

Last update: 2025-04-08
Started: 2024-03-20

Introduction to spleenrbc
Rendered fromspleenrbc.Rmdusingknitr::rmarkdown

Last update: 2024-03-20
Started: 2024-03-20

Uninfected red blood cell loss due to malaria
Decrease in circulating RBCs | RBC retention in the spleen | RBC infection in the circulation and spleen | RBC infection by source of merozoites | RBC destruction in the spleen | Ratio of RBC retention to infection | Comparison of retention and infection
Rendered fromuninfected-rbc-loss.Rmdusingknitr::rmarkdown

Last update: 2024-03-20
Started: 2024-03-20

Readme and manuals

Help Manual

Help pageTopics
Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age 'a') in the circulation.alpha_c
Age-structured parasite multiplication rates (the number of released merozoites that successfully invade uRBCS of age 'a') in the spleen.alpha_r
Return the baseline parameter values, including all derived parameters.baseline_parameters
Age-dependent merozoite preference for uninfected RBCs.beta
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.calculate_irbc_ratio
Calculate steady-state values for high-level model outputs.calculate_steady_state_outputs
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.calculate_urbc_loss_ratio
Calculate the ratio of (a) the fraction of uRBCs retained in the spleen at time 't'; to (b) the fraction of uRBCs retained in the spleen at homeostasis.calculate_urbc_ratio
Define parameters whose values are derived from other parameters.define_derived_parameters
Rate of infected RBC removal from the circulation into the spleen.delta_i
Increase in infected RBC removal into the spleen due to RBC congestion.delta_i_fold
Rate of infected RBC reentry into the circulation from the spleen.delta_i_prime
Rate of uninfected RBC removal from the circulation into the spleen.delta_u
Increase in uninfected RBC removal into the spleen due to RBC congestion.delta_u_fold
Rate of uninfected RBC reentry into the circulation from the spleen.delta_u_prime
Rate of RBC production.erythropoiesis
Red blood cell counts collected from asymptomatic Papuans who reported no fever within the preceding 24 hours (708 uninfected, 50 Pf infections, 45 Pv infections) in a cross-sectional household survey conducted in southern Papua, Indonesia.hhs_asymp
Record key outputs for a single scenario.individual_results
Calculate quantities related to uRBC infection and retention in the spleen due to malaria infection.infection_flows_and_loss
Construct the initial model state.initial_spleenrbc_state
Phagocytosis rate of infected RBCs in the spleen.lambda_i
Phagocytosis rate of uninfected RBCs in the spleen.lambda_u
Pf parameter values for each scenario.parameters_pf
Pv parameter values for each scenario.parameters_pv
Construct a list that will record the model state over time.prepare_spleenrbc_snapshot
Quantile function for the log-uniform distribution.qlunif
Convert red blood cell counts into haemoglobin (g/dL).rbc_counts_to_haemoglobin
The red blood cell count at homeostasis.rbc_steady_state
Subtract negative U values from other (positive) U values.resolve_negative_rbcs
The reticulocyte production rate at homeostasis.retic_steady_state
The reticulocyte production rate for the given normoblast population.reticulocyte_prod
Age-structured release rate of reticulocytes from the bone marrow into the circulation.rho
The minimum age at which reticulocytes are released from the bone marrow into the circulation.rho_release_age
Run model scenarios.run_spleenrbc
Run a single scenario and return the model state history.run_spleenrbc_model
Create parameter samples for each scenario.sample_parameters
Uninfected and infected RBC counts in the circulation and spleen of 15 asymptomatic adults in Papua, Indonesia (9 Pf infections, 6 Pv infections) who underwent splenectomy, mostly due to trauma.splenectomised
Update the model state by simulating forward one time-step.step_spleenrbc_model
Define uncertainty distributions for each parameter.uncertainty_distributions
Calculate uncertainty intervals for each column, except for "time" and "scenario".uncertainty_intervals
Age-structured rate of RBC sequestration into the microvasculature.zeta