% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/spine.R
\name{biomkrAccrual}
\alias{biomkrAccrual}
\title{Command line}
\usage{
biomkrAccrual(
  target_arm_size = 60,
  target_interim = target_arm_size/2,
  target_control = 180,
  shared_control = TRUE,
  accrual_period = 50/4,
  interim_period = accrual_period/2,
  precision = 10,
  ctrl_ratio = c(1, 1),
  centres_file = "centres.csv",
  prop_file = "proportions.csv",
  arms_file = "arms.json",
  data_path = "extdata/",
  output_path = "../biomkrAccrual_output_data/",
  figs_path = paste0(output_path, "figures/"),
  fixed_centre_starts = TRUE,
  fixed_site_rates = FALSE,
  fixed_region_prevalences = FALSE,
  quietly = FALSE,
  keep_files = TRUE
)
}
\arguments{
\item{target_arm_size}{Number of patients required per
treatment arm}

\item{target_interim}{Number of patients required per
arm for interim analysis; defaults to \verb{target_arm_size \\ 2}}

\item{target_control}{Number of patients required for the
control arm(s)}

\item{shared_control}{TRUE if all treatment arms share the
same control arm; FALSE if each treatment arm has its own
control. Defaults to TRUE.}

\item{accrual_period}{Recruitment period (months).}

\item{interim_period}{Recruitment period to interim (months).}

\item{precision}{For the Dirichlet model of biomarker prevalences,
variability decreases as precision increases. Defaults to 10.}

\item{ctrl_ratio}{Ratio of patient allocation to treatment arm
versus control for all active arms; defaults to c(1, 1).}

\item{centres_file}{Name of CSV file with information about
each recruitment centre; this should have columns "site",
"start_month", "mean_rate", "region" and optionally "site_cap"
if recruitment is capped per site. Defaults to \code{centres.csv}.}

\item{prop_file}{Name of CSV file with expected biomarker prevalences
for each region; this should have one column "category", naming
the biomarkers or biomarker combinations, and one column per
region. Defaults to \code{proportions.csv}.}

\item{arms_file}{Name of JSON file describing which recruitment
arms (defined by biomarkers) recruit to which treatment arms.
Defaults to \code{arms_json}.}

\item{data_path}{Folder where \code{centres_file}, \code{prop_file} and
\code{arms_file} are located. Defaults to the location of the package
example data in the package installation; this should be changed.}

\item{output_path}{Folder where data generated during execution
will be stored; defaults to \verb{../biomkrAccrual_output_data/}.}

\item{figs_path}{Folder where figures generated during execution
will be stored; defaults to the \code{figures} subdirectory in
\code{output_path}.}

\item{fixed_centre_starts}{TRUE if centres are assumed to start
exactly when planned; FALSE if some randomisation should be added.}

\item{fixed_site_rates}{TRUE if centre recruitment rates should
be treated as exact; FALSE if they should be drawn from a gamma
distribution with a mean of the specified rate.}

\item{fixed_region_prevalences}{TRUE if biomarker prevalences
should be considered to be identical for all sites within a
region; FALSE if they should be drawn from a Dirichlet distribution
with a mean of the specified prevalence.}

\item{quietly}{Defaults to FALSE, which displays the output from
each run. Set to TRUE to generate data and figures without displaying
them.}

\item{keep_files}{Save data files and plots generated during the run.
Defaults to TRUE.}
}
\description{
Command line
}
\examples{
biomkrAccrual()

}