--- a
+++ b/man/trial_structure.Rd
@@ -0,0 +1,89 @@
+% 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}
+}}
+