Include the documentation files in the repository

Maëlle Salmon (maelle) recommended including the .Rd files in the source
repository, even though they are derived files.

man/.gitignore

-*.Rd

man/alpha_c.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{alpha_c}
+\alias{alpha_c}
+\title{Age-structured parasite multiplication rates (the number of released
+merozoites that successfully invade uRBCS of age \code{a}) in the circulation.}
+\usage{
+alpha_c(u_rbc, pmf, beta)
+}
+\arguments{
+\item{u_rbc}{The RBC count.}
+
+\item{pmf}{The parasite multiplication factor.}
+
+\item{beta}{The (age-dependent) merozoite preference for uninfected RBCs.}
+}
+\description{
+Age-structured parasite multiplication rates (the number of released
+merozoites that successfully invade uRBCS of age \code{a}) in the circulation.
+}

man/alpha_r.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{alpha_r}
+\alias{alpha_r}
+\title{Age-structured parasite multiplication rates (the number of released
+merozoites that successfully invade uRBCS of age \code{a}) in the spleen.}
+\usage{
+alpha_r(u_rbc, pmf, beta)
+}
+\arguments{
+\item{u_rbc}{The RBC count.}
+
+\item{pmf}{The parasite multiplication factor.}
+
+\item{beta}{The (age-dependent) merozoite preference for uninfected RBCs.}
+}
+\description{
+Age-structured parasite multiplication rates (the number of released
+merozoites that successfully invade uRBCS of age \code{a}) in the spleen.
+}

man/baseline_parameters.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parameters.R
+\name{baseline_parameters}
+\alias{baseline_parameters}
+\title{Return the baseline parameter values, including all derived parameters.}
+\usage{
+baseline_parameters(species = c("Pf", "Pv"), nospleen = FALSE, derived = TRUE)
+}
+\arguments{
+\item{species}{The malaria species: \code{'Pf'} or \code{'Pv'}.}
+
+\item{nospleen}{Whether the spleen has been removed.}
+
+\item{derived}{Whether to define parameters whose values are derived from
+other parameters.}
+}
+\description{
+Return the baseline parameter values, including all derived parameters.
+}

man/beta.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{beta}
+\alias{beta}
+\title{Age-dependent merozoite preference for uninfected RBCs.}
+\usage{
+beta(p, age)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{age}{The RBC age.}
+}
+\description{
+Age-dependent merozoite preference for uninfected RBCs.
+}

man/calculate_irbc_ratio.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputs.R
+\name{calculate_irbc_ratio}
+\alias{calculate_irbc_ratio}
+\title{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{
+\item{results}{A dataframe of simulation results.}
+}
+\value{
+A dataframe that includes the following columns, in addition those in
+\code{results}:
+
+\describe{
+\item{iRBC_Ratio}{The ratio of infected cell fractions in the spleen and
+circulation.}
+}
+}
+\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.
+}

man/credible_intervals.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputs.R
+\name{credible_intervals}
+\alias{credible_intervals}
+\title{Calculate credible intervals for each column, except "time" and "scenario".}
+\usage{
+credible_intervals(results, pcnt = c(50, 60, 70, 80, 90, 95))
+}
+\arguments{
+\item{results}{A dataframe of simulation results.}
+
+\item{pcnt}{The credible intervals to calculate, expressed as percentages.}
+}
+\value{
+A dataframe with the following columns:
+
+\describe{
+\item{name}{The statistic name (character)}
+\item{time}{The time (numeric, hours)}
+\item{cred_int}{The credible interval (ordered factor, widest to
+narrowest)}
+\item{ci_min}{The credible interval lower bound (numeric)}
+\item{ci_max}{The credible interval upper bound (numeric)}
+}
+}
+\description{
+Calculate credible intervals for each column, except "time" and "scenario".
+}

man/define_derived_parameters.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parameters.R
+\name{define_derived_parameters}
+\alias{define_derived_parameters}
+\title{Define parameters whose values are derived from other parameters.}
+\usage{
+define_derived_parameters(p)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+}
+\description{
+Define parameters whose values are derived from other parameters.
+}

man/delta_i.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_i}
+\alias{delta_i}
+\title{Rate of infected RBC removal from the circulation into the spleen.}
+\usage{
+delta_i(p, age)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{age}{The RBC age.}
+}
+\description{
+Rate of infected RBC removal from the circulation into the spleen.
+}

man/delta_i_fold.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_i_fold}
+\alias{delta_i_fold}
+\title{Increase in infected RBC removal into the spleen due to RBC congestion.}
+\usage{
+delta_i_fold(p, net_u_rbc, net_i_rbc)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{net_u_rbc}{The total number of uninfected RBCs in the circulation.}
+
+\item{net_i_rbc}{The total number of infected RBCs in the circulation.}
+}
+\description{
+Increase in infected RBC removal into the spleen due to RBC congestion.
+}

man/delta_i_prime.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_i_prime}
+\alias{delta_i_prime}
+\title{Rate of infected RBC reentry into the circulation from the spleen.}
+\usage{
+delta_i_prime(p, age)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{age}{The infected RBC age(s).}
+}
+\description{
+Rate of infected RBC reentry into the circulation from the spleen.
+}

man/delta_u.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_u}
+\alias{delta_u}
+\title{Rate of uninfected RBC removal from the circulation into the spleen.}
+\usage{
+delta_u(p, age)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{age}{The RBC age.}
+}
+\description{
+Rate of uninfected RBC removal from the circulation into the spleen.
+}

man/delta_u_fold.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_u_fold}
+\alias{delta_u_fold}
+\title{Increase in uninfected RBC removal into the spleen due to RBC congestion.}
+\usage{
+delta_u_fold(p, net_u_rbc, net_i_rbc)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{net_u_rbc}{The total number of uninfected RBCs in the circulation.}
+
+\item{net_i_rbc}{The total number of infected RBCs in the circulation.}
+}
+\description{
+Increase in uninfected RBC removal into the spleen due to RBC congestion.
+}

man/delta_u_prime.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{delta_u_prime}
+\alias{delta_u_prime}
+\title{Rate of uninfected RBC reentry into the circulation from the spleen.}
+\usage{
+delta_u_prime(p, age)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{age}{The RBC age.}
+}
+\description{
+Rate of uninfected RBC reentry into the circulation from the spleen.
+}

man/erythropoiesis.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{erythropoiesis}
+\alias{erythropoiesis}
+\title{Rate of RBC production.}
+\usage{
+erythropoiesis(p, u_rbc)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{u_rbc}{The RBC count.}
+}
+\description{
+Rate of RBC production.
+}

man/hhs_asymp.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{hhs_asymp}
+\alias{hhs_asymp}
+\title{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.}
+\format{
+\subsection{\code{hhs_asymp}}{
+
+A data frame with 803 rows and the following columns:
+\describe{
+\item{species}{One of \code{"Pf"}, \code{"Pv"}, or \code{"neg"}}
+\item{total_rbc}{The red blood cell count}
+}
+}
+}
+\usage{
+hhs_asymp
+}
+\description{
+See \href{https://doi.org/10.1371/journal.pone.0165340}{Pava et al., 2016}
+for details.
+}
+\keyword{datasets}

man/individual_results.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputs.R
+\name{individual_results}
+\alias{individual_results}
+\title{Record key outputs for a single scenario.}
+\usage{
+individual_results(p, keep)
+}
+\arguments{
+\item{p}{The scenario parameters.}
+
+\item{keep}{The model state at each of the relevant time-steps.}
+}
+\value{
+A data frame that includes the following columns:
+
+\describe{
+\item{scenario}{The scenario number}
+\item{time}{The simulation time (hours)}
+\item{U_t}{The number of uRBCs in the circulation}
+\item{Ur_t}{The number of uRBCs in the spleen}
+\item{Retic_c_t}{The number of reticulocytes in the circulation}
+\item{Retic_r_t}{The number of reticulocytes in the spleen}
+\item{I_t}{The number of iRBCs in the circulation}
+\item{Ir_t}{The number of iRBCs in the spleen}
+\item{Iq_t}{The number of iRBCs in the microvasculature}
+\item{M_t}{The number of macrophages in the spleen}
+\item{E_t}{The erythropoiesis rate}
+\item{r_t}{The number of reticulocytes in the bone marrow}
+\item{pmr_c_t_1}{The number of merozoites released in the circulation}
+\item{pmr_r_t_1}{The number of merozoites released in the spleen}
+\item{flow_r_to_c}{The number of reticulocytes released from the bone
+marrow}
+\item{flow_uc_to_r}{The number of uRBCs removed from the circulation into
+the spleen}
+\item{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}
+\item{flow_ur_to_c}{The number of uRBCs released from the spleen into the
+circulation}
+\item{flow_ur_out}{The number of uRBCs phagocytised in the spleen}
+\item{flow_ic_to_r}{The number of iRBCs removed from the circulation into
+the spleen}
+\item{flow_ic_to_q}{The number of iRBCs sequestered into the
+microvasculature}
+\item{flow_ir_to_c}{The number of iRBCs released from the spleen into the
+circulation}
+\item{flow_ir_out}{The number of iRBCs phagocytised in the spleen}
+\item{flow_uc_to_ic}{The number of uRBCs in the circulation that became
+infected}
+\item{flow_ur_to_ir}{The number of uRBCs in the spleen that became
+infected}
+\item{inf_from_ic}{The number of RBCs infected from iRBCs in the
+circulation}
+\item{inf_from_iq}{The number of RBCs infected from iRBCs in the
+microvasculature}
+\item{inf_from_ir}{The number of RBCs infected from iRBCs in the spleen}
+\item{rho_t}{The release rate of the youngest reticulocytes}
+\item{deltaUfold}{The fold increase in uRBC removal from the circulation}
+\item{deltaIfold}{The fold increase in iRBC removal from the circulation}
+\item{Ur_frac_inf}{The fraction of RBCs in the spleen that become
+infected}
+}
+}
+\description{
+Record key outputs for a single scenario.
+}

man/infection_flows_and_loss.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outputs.R
+\name{infection_flows_and_loss}
+\alias{infection_flows_and_loss}
+\title{Calculate quantities related to uRBC infection and retention in the spleen
+due to malaria infection.}
+\usage{
+infection_flows_and_loss(results)
+}
+\arguments{
+\item{results}{A dataframe of simulation results.}
+}
+\value{
+A dataframe that includes the following columns, in addition those in
+\code{results}:
+
+\describe{
+\item{U_and_I_t}{The value of \eqn{U_c(t) + I_c(t)}}
+\item{Ur_frac_U}{the fraction of uRBCs that are retained in the spleen}
+\item{flow_uc_to_r_inf}{The retention of uRBCs due to malaria infection}
+\item{flow_uc_to_r_ratio}{The rate of uRBC retention that is due to
+malaria infection, relative to baseline uRBC retention}
+\item{Uc_loss_ratio_c}{The ratio of uRBC retention due to malaria loss,
+relative to the infection of uRBCs in the circulation}
+\item{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}
+\item{inf_total}{The number of uRBC infections in the circulation and
+spleen}
+\item{inf_from_icq}{The number of uRBC infection in the circulation due
+to merozoites released in the circulation and microvasculature}
+}
+}
+\description{
+Calculate quantities related to uRBC infection and retention in the spleen
+due to malaria infection.
+}

man/initial_spleenrbc_state.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/state.R
+\name{initial_spleenrbc_state}
+\alias{initial_spleenrbc_state}
+\title{Construct the initial model state.}
+\usage{
+initial_spleenrbc_state(p)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+}
+\description{
+Construct the initial model state.
+}

man/lambda_i.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rate_functions.R
+\name{lambda_i}
+\alias{lambda_i}
+\title{Phagocytosis rate of infected RBCs in the spleen.}
+\usage{
+lambda_i(p, macrophages)
+}
+\arguments{
+\item{p}{The parameter values for the scenario.}
+
+\item{macrophages}{The macrophage count.}
+}
+\description{
+Phagocytosis rate of infected RBCs in the spleen.
+}