% 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()

}