diff --git a/DESCRIPTION b/DESCRIPTION index fe4cea9..81b40d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,7 @@ Description: Fit kinetic curves to biomarker data, using a Bayesian hierarchical License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Imports: cmdstanr, data.table, diff --git a/man/biokinetics.Rd b/man/biokinetics.Rd index feb9501..4e5f3f0 100644 --- a/man/biokinetics.Rd +++ b/man/biokinetics.Rd @@ -156,7 +156,7 @@ A CmdStanMCMC fitted model object: \url{https://mc-stan.org/cmdstanr/reference/C Extract fitted population parameters \subsection{Usage}{ \if{html}{\out{
}}\preformatted{biokinetics$extract_population_parameters( - n_draws = 2500, + n_draws = 2000, human_readable_covariates = TRUE )}\if{html}{\out{
}} } @@ -164,7 +164,7 @@ Extract fitted population parameters \subsection{Arguments}{ \if{html}{\out{
}} \describe{ -\item{\code{n_draws}}{Numeric} +\item{\code{n_draws}}{Integer. Default 2000.} \item{\code{human_readable_covariates}}{Logical. Default TRUE.} } @@ -181,7 +181,7 @@ A data.table Extract fitted individual parameters \subsection{Usage}{ \if{html}{\out{
}}\preformatted{biokinetics$extract_individual_parameters( - n_draws = 2500, + n_draws = 2000, include_variation_params = TRUE, human_readable_covariates = TRUE )}\if{html}{\out{
}} @@ -190,7 +190,7 @@ Extract fitted individual parameters \subsection{Arguments}{ \if{html}{\out{
}} \describe{ -\item{\code{n_draws}}{Numeric} +\item{\code{n_draws}}{Integer. Default 2000.} \item{\code{include_variation_params}}{Logical} @@ -211,7 +211,7 @@ Process the model results into a data table of titre values over time. \if{html}{\out{
}}\preformatted{biokinetics$simulate_population_trajectories( t_max = 150, summarise = TRUE, - n_draws = 2500 + n_draws = 2000 )}\if{html}{\out{
}} } @@ -224,7 +224,7 @@ Process the model results into a data table of titre values over time. return 0.025, 0.5 and 0.975 quantiles, labelled lo, me and hi, respectively. If FALSE returns values for individual draws from posterior parameter distributions.} -\item{\code{n_draws}}{Integer. Maximum number of samples to include. Default 2500.} +\item{\code{n_draws}}{Integer. Maximum number of samples to include. Default 2000.} } \if{html}{\out{
}} } @@ -242,13 +242,13 @@ titre_type and a column for each covariate in the hierarchical model. See the da \subsection{Method \code{population_stationary_points()}}{ Process the stan model results into a data.table. \subsection{Usage}{ -\if{html}{\out{
}}\preformatted{biokinetics$population_stationary_points(n_draws = 2500)}\if{html}{\out{
}} +\if{html}{\out{
}}\preformatted{biokinetics$population_stationary_points(n_draws = 2000)}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ -\item{\code{n_draws}}{Integer. Maximum number of samples to include. Default 2500.} +\item{\code{n_draws}}{Integer. Maximum number of samples to include. Default 2000.} } \if{html}{\out{
}} } @@ -267,7 +267,7 @@ computationally expensive and may take a while to run if n_draws is large. \subsection{Usage}{ \if{html}{\out{
}}\preformatted{biokinetics$simulate_individual_trajectories( summarise = TRUE, - n_draws = 2500, + n_draws = 2000, time_shift = 0 )}\if{html}{\out{
}} } @@ -279,7 +279,7 @@ computationally expensive and may take a while to run if n_draws is large. hi values for the population, disaggregated by titre type. If FALSE return the indidivudal trajectories. Default TRUE.} -\item{\code{n_draws}}{Integer. Maximum number of samples to draw. Default 2500.} +\item{\code{n_draws}}{Integer. Maximum number of samples to draw. Default 2000.} \item{\code{time_shift}}{Integer. Number of days to adjust the exposure day by. Default 0.} } diff --git a/man/plot.biokinetics_population_trajectories.Rd b/man/plot.biokinetics_population_trajectories.Rd index 6b57d13..333ae60 100644 --- a/man/plot.biokinetics_population_trajectories.Rd +++ b/man/plot.biokinetics_population_trajectories.Rd @@ -8,7 +8,7 @@ } \arguments{ \item{x}{An object of class "biokinetics_population_trajectories". These are -generated by running biokinetics$simulate_populate_trajectories(). See +generated by running biokinetics$simulate_population_trajectories(). See \href{../../epikinetics/html/biokinetics.html#method-biokinetics-simulate_population_trajectories}{\code{biokinetics$simulate_population_trajectories()}}} \item{\dots}{Further arguments passed to the method.}