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
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spleenrbc.pdf |spleenrbc.html✨
spleenrbc/json (API)

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

Peer review:

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:

4.18 score 33 exports 24 dependencies

Last updated 1 days agofrom:193dfc5527. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winWARNINGOct 29 2024
R-4.5-linuxWARNINGOct 29 2024
R-4.4-winWARNINGOct 29 2024
R-4.4-macWARNINGOct 29 2024
R-4.3-winWARNINGOct 29 2024
R-4.3-macWARNINGOct 29 2024

Exports:alpha_calpha_rbaseline_parametersbetacalculate_irbc_ratiocalculate_urbc_loss_ratiocredible_intervalsdefine_derived_parametersdelta_idelta_i_folddelta_i_primedelta_udelta_u_folddelta_u_primeerythropoiesisindividual_resultsinfection_flows_and_lossinitial_spleenrbc_statelambda_ilambda_ulhs_distributionsprepare_spleenrbc_snapshotrbc_counts_to_haemoglobinresolve_negative_rbcsretic_steady_statereticulocyte_prodrhorho_release_agerun_spleenrbcrun_spleenrbc_modelsample_parametersstep_spleenrbc_modelzeta

Dependencies:clicpp11dplyrfansigenericsgluelhslifecyclemagrittrpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrsVGAMwithr

Evidence for parameter values

Rendered fromevidence-for-parameter-values.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Introduction to spleenrbc

Rendered fromspleenrbc.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Red blood cell steady-state distribution

Rendered fromrbc-steady-state.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Sensitivity analyses for Pf and Pv

Rendered fromsensitivity-analyses.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Uninfected red blood cell loss due to malaria

Rendered fromuninfected-rbc-loss.Rmdusingknitr::rmarkdownon Oct 29 2024.

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 credible intervals for each column, except "time" and "scenario".credible_intervals
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
Define the distributions from which to sample values for each parameter.lhs_distributions
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
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
Age-structured rate of RBC sequestration into the microvasculature.zeta