% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prevalence.R
\name{trial_structure}
\alias{trial_structure}
\title{A class for an object to contain the proportions of arriving patients to be
allocated to each arm of the trial.}
\usage{
trial_structure(
  props_df = S7::class_missing,
  arms_ls = S7::class_missing,
  centres_df = S7::class_missing,
  precision = S7::class_missing,
  shared_control = S7::class_missing,
  ctrl_ratio = S7::class_missing,
  fixed_region_prevalences = S7::class_missing
)
}
\arguments{
\item{props_df}{Dataframe of expected biomarker prevalences for the
regions, with one column \code{category} containing names for the
biomarkers, and one column per region.}

\item{arms_ls}{List of lists of recruitment arms which recruit to
each treatment arm.}

\item{centres_df}{Dataframe containing columns \code{site}, the index
number of each site; \code{start_month}, the month in which that site
is expected to start recruiting; \code{mean_rate}, the expected number
of patients from that site per month; \code{region}, the index of the
region the site is in (should be in the same order as the columns
in \code{props_df}); and an optional column \code{site_cap}, if there is a
recruitment cap on any of the sites.}

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

\item{shared_control}{TRUE if all experimental arms share one
control arm; FALSE if they each have separate control arms.}

\item{ctrl_ratio}{Proportion of patients assigned to control}

\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.}
}
\description{
A class for an object to contain the proportions of arriving patients to be
allocated to each arm of the trial.
}
\section{Slots}{

\describe{
\item{\code{recruit_arm_prevalence}}{Numeric vector of the expected proportion
of patients eligible for each recruitment arm.}

\item{\code{recruit_arm_prevalence_start}}{Numeric vector of the initial proportions
of patients eligible for each recruitment arm.}

\item{\code{recruit_arm_names}}{Character vector of the names of the recruitment
arms.}

\item{\code{shared_control}}{TRUE if using a shared control arm for all
experimental arms.}

\item{\code{ctrl_ratio}}{Proportion of patients assigned to control}

\item{\code{treatment_arm_ids}}{Named list of lists of recruitment arms by
treatment arm.}

\item{\code{treatment_arm_ids_start}}{Named list of lists of the initial
configuration of recruitment arms by treatment arm.}

\item{\code{recruit_arm_id}}{Automatically generated integer vector of the ID
numbers of the recruitment arms.}

\item{\code{treatment_counts}}{Automatically generated named integer vector of
number of recruitment arms recruiting to each treatment arm.}

\item{\code{treatment_arm_struct}}{Automatically generated logical matrix of
treatment arms by recruitment arms.}

\item{\code{treatment_arm_struct_start}}{Automatically generated logical matrix of
the initial configuration of treatment arms by recruitment arms.}

\item{\code{experimental_arm_prevalence}}{Automatically generated matrix of
prevalences of treatment arms by recruitment arms}
}}