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.}