inst/ADPopSelApp/ui.r
In medianasoft/MedianaDesigner: Power and Sample Size Calculations for Clinical Trials
library(shiny)
suppressPackageStartupMessages(library(shinydashboard))
library(MedianaDesigner)
library(shinyMatrix)
shinyUI(
dashboardPage(
dashboardHeader(title = "MedianaDesigner"),
dashboardSidebar(
sidebarMenu(id = "sidebar",
menuItem("Design parameters", tabName = "design_parameters", icon = icon("sliders-h")),
menuItem("Endpoint parameters", tabName = "endpoint_parameters", icon = icon("sliders-h")),
menuItem("Interim parameters", tabName = "interim_parameters", icon = icon("sliders-h")),
menuItem("General parameters", tabName = "general_parameters", icon = icon("sliders-h")),
menuItem("Simulation results", tabName = "simulation", icon = icon("table")),
menuItem("Simulation report", tabName = "report", icon = icon("file"))
)
),
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "main.css?2")
),
tabItems(
tabItem(tabName = "design_parameters",
fluidRow(
box(
title = "Adaptive designs with data-driven population selection",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics of an adaptive design for a two-arm Phase III clinical trial with two interim analyses and two pre-defined patient populations (overall population and subpopulation of biomarker-positive patients). The first interim analysis supports early stopping for futility in the overall population and the second interim analysis identifies the most promising patient population or populations."
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Sample size",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("SampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial arm.")
)
),
column(6, class = "col-md-6",
box(
title = "Prevalence",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "prevalence", label = "Prevalence of biomarker-positive patients in the overall population (%)", value = 40)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Endpoint parameters."),
actionButton("jump_to_panel2", "Next tab")
)
)
),
tabItem(tabName = "endpoint_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Endpoint type",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
selectInput("endpoint_index", label = "Primary endpoint's type",
c("Normal" = 1, "Binary" = 2, "Time-to-event" = 3)),
selectInput("direction_index", label = "Direction of favorable outcome",
c("Higher" = 1, "Lower" = 2))
)
),
conditionalPanel(
condition = "input.endpoint_index == 3",
column(6, class = "col-md-6",
box(
title = "Number of events",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "event_count1", label = "Target number of events in the overall population", value = 200),
tags$p(class = "help-block",
"Target number of events in the overall population at the final analysis."),
numericInput(inputId = "event_count2", label = "Target number of events in the biomarker-positive population", value = 100),
tags$p(class = "help-block",
"Target number of events in the biomarker-positive population at the final analysis.")
)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Treatment effect assumptions",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("TreatmentEffectAssumptions"),
tags$p(class = "help-block",
"Treatment effect assumptions within each patient population in each trial arm for the selected primary endpoint under the alternative hypothesis of beneficial effect.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Interim parameters."),
actionButton("jump_to_panel3", "Next tab")
)
)
),
tabItem(tabName = "interim_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Interim analysis 1",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "info_frac1", label = "Interim fraction (%)", value = 40, min = 10, max = 90),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Fraction of the total number of patients in the overall population at Interim analysis 1.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events in the overall population at Interim analysis 1.")
),
numericInput(inputId = "futility_threshold", label = "Futility threshold (%)", value = 10),
tags$p(class = "help-block",
"The trial will be stopped for futility at Interim analysis 1 if the predicted probability of success in the overall population is less than the futility threshold.")
)
),
column(6, class = "col-md-6",
box(
title = "Interim analysis 2",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "info_frac2", label = "Interim fraction (%)", value = 60, min = 10, max = 90),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Fraction of the total number of patients in the overall population at Interim analysis 2.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events in the overall population at Interim analysis 2.")
),
numericInput(inputId = "influence", label = "Influence threshold for population selection", value = 0.1, min = 0, max = 1),
numericInput(inputId = "interaction", label = "Interaction threshold for population selection", value = 1.3, min = 1, max = 2),
tags$p(class = "help-block",
"Influence and interaction thresholds are used in the decision rule for selecting the most promising population or populations at Interim analysis 2.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to General parameters."),
actionButton("jump_to_panel4", "Next tab")
)
)
),
tabItem(tabName = "general_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Patient dropout rate",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "dropout_rate", label = "Patient dropout rate (%)", value = 5, min = 0, max = 50),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Dropout rate at the end of the treatment period.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Annual dropout rate.")
)
)
)
),
conditionalPanel(
condition = "input.endpoint_index == 3",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Patient enrollment period",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "enrollment_period", label = "Length of the patient enrollment period", value = 12)
)
),
column(6, class = "col-md-6",
box(
title = "Patient enrollment pattern",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "enrollment_parameter", label = "Median enrollment time", value = 9),
tags$p(class = "help-block",
"Median enrollment time is defined as the time point by which 50% of the patients will be enrolled.")
)
)
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Alpha",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "alpha", label = "Type I error rate", value = 0.025),
tags$p(class = "help-block",
"One-sided Type I error rate.")
)
),
column(6, class = "col-md-6",
box(
title = "Number of simulations",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "nsims", label = "Number of simulation runs", value = 10000)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation results."),
actionButton("jump_to_panel5", "Next tab")
)
)
),
tabItem(tabName = "simulation",
fluidRow(
box(
title = "Summary of simulation results",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
width = 12
),
column(12, class="col-lg-12",
box(
title = "Futility stopping and population selection",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("FutilityStopping"),
tags$p(class = "help-block",
"OP: Overall population. BPP: Biomarker-positive population.")
)
),
column(12, class="col-lg-12",
box(
title = "Traditional design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TraditionalDesign"),
tags$p(class = "help-block",
"Power for a traditional design conducted in the overall population.")
)
),
column(12, class="col-lg-12",
box(
title = "Adaptive design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("AdaptiveDesign"),
tags$p(class = "help-block",
"Probability of establishing a significant treatment effect in the overall population, biomarker-positive population or at least one of the two patient populations at the final analysis.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation report."),
actionButton("jump_to_panel6", "Next tab")
)
)
),
tabItem(tabName = "report",
fluidRow(
box(
title = "Create a simulation report",
background = "red",
width = 12,
tags$p("Click the Download button to create and save a detailed simulation report in a Microsoft Word format."),
downloadButton("DownloadResults", "Download")
)
)
)
)
)
)
)
medianasoft/MedianaDesigner documentation built on Aug. 28, 2023, 6:33 p.m.
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library(shiny)
suppressPackageStartupMessages(library(shinydashboard))
library(MedianaDesigner)
library(shinyMatrix)
shinyUI(
dashboardPage(
dashboardHeader(title = "MedianaDesigner"),
dashboardSidebar(
sidebarMenu(id = "sidebar",
menuItem("Design parameters", tabName = "design_parameters", icon = icon("sliders-h")),
menuItem("Endpoint parameters", tabName = "endpoint_parameters", icon = icon("sliders-h")),
menuItem("Interim parameters", tabName = "interim_parameters", icon = icon("sliders-h")),
menuItem("General parameters", tabName = "general_parameters", icon = icon("sliders-h")),
menuItem("Simulation results", tabName = "simulation", icon = icon("table")),
menuItem("Simulation report", tabName = "report", icon = icon("file"))
)
),
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "main.css?2")
),
tabItems(
tabItem(tabName = "design_parameters",
fluidRow(
box(
title = "Adaptive designs with data-driven population selection",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics of an adaptive design for a two-arm Phase III clinical trial with two interim analyses and two pre-defined patient populations (overall population and subpopulation of biomarker-positive patients). The first interim analysis supports early stopping for futility in the overall population and the second interim analysis identifies the most promising patient population or populations."
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Sample size",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("SampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial arm.")
)
),
column(6, class = "col-md-6",
box(
title = "Prevalence",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "prevalence", label = "Prevalence of biomarker-positive patients in the overall population (%)", value = 40)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Endpoint parameters."),
actionButton("jump_to_panel2", "Next tab")
)
)
),
tabItem(tabName = "endpoint_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Endpoint type",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
selectInput("endpoint_index", label = "Primary endpoint's type",
c("Normal" = 1, "Binary" = 2, "Time-to-event" = 3)),
selectInput("direction_index", label = "Direction of favorable outcome",
c("Higher" = 1, "Lower" = 2))
)
),
conditionalPanel(
condition = "input.endpoint_index == 3",
column(6, class = "col-md-6",
box(
title = "Number of events",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "event_count1", label = "Target number of events in the overall population", value = 200),
tags$p(class = "help-block",
"Target number of events in the overall population at the final analysis."),
numericInput(inputId = "event_count2", label = "Target number of events in the biomarker-positive population", value = 100),
tags$p(class = "help-block",
"Target number of events in the biomarker-positive population at the final analysis.")
)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Treatment effect assumptions",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("TreatmentEffectAssumptions"),
tags$p(class = "help-block",
"Treatment effect assumptions within each patient population in each trial arm for the selected primary endpoint under the alternative hypothesis of beneficial effect.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Interim parameters."),
actionButton("jump_to_panel3", "Next tab")
)
)
),
tabItem(tabName = "interim_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Interim analysis 1",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "info_frac1", label = "Interim fraction (%)", value = 40, min = 10, max = 90),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Fraction of the total number of patients in the overall population at Interim analysis 1.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events in the overall population at Interim analysis 1.")
),
numericInput(inputId = "futility_threshold", label = "Futility threshold (%)", value = 10),
tags$p(class = "help-block",
"The trial will be stopped for futility at Interim analysis 1 if the predicted probability of success in the overall population is less than the futility threshold.")
)
),
column(6, class = "col-md-6",
box(
title = "Interim analysis 2",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "info_frac2", label = "Interim fraction (%)", value = 60, min = 10, max = 90),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Fraction of the total number of patients in the overall population at Interim analysis 2.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events in the overall population at Interim analysis 2.")
),
numericInput(inputId = "influence", label = "Influence threshold for population selection", value = 0.1, min = 0, max = 1),
numericInput(inputId = "interaction", label = "Interaction threshold for population selection", value = 1.3, min = 1, max = 2),
tags$p(class = "help-block",
"Influence and interaction thresholds are used in the decision rule for selecting the most promising population or populations at Interim analysis 2.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to General parameters."),
actionButton("jump_to_panel4", "Next tab")
)
)
),
tabItem(tabName = "general_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Patient dropout rate",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "dropout_rate", label = "Patient dropout rate (%)", value = 5, min = 0, max = 50),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Dropout rate at the end of the treatment period.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Annual dropout rate.")
)
)
)
),
conditionalPanel(
condition = "input.endpoint_index == 3",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Patient enrollment period",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "enrollment_period", label = "Length of the patient enrollment period", value = 12)
)
),
column(6, class = "col-md-6",
box(
title = "Patient enrollment pattern",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "enrollment_parameter", label = "Median enrollment time", value = 9),
tags$p(class = "help-block",
"Median enrollment time is defined as the time point by which 50% of the patients will be enrolled.")
)
)
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Alpha",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "alpha", label = "Type I error rate", value = 0.025),
tags$p(class = "help-block",
"One-sided Type I error rate.")
)
),
column(6, class = "col-md-6",
box(
title = "Number of simulations",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "nsims", label = "Number of simulation runs", value = 10000)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation results."),
actionButton("jump_to_panel5", "Next tab")
)
)
),
tabItem(tabName = "simulation",
fluidRow(
box(
title = "Summary of simulation results",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
width = 12
),
column(12, class="col-lg-12",
box(
title = "Futility stopping and population selection",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("FutilityStopping"),
tags$p(class = "help-block",
"OP: Overall population. BPP: Biomarker-positive population.")
)
),
column(12, class="col-lg-12",
box(
title = "Traditional design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TraditionalDesign"),
tags$p(class = "help-block",
"Power for a traditional design conducted in the overall population.")
)
),
column(12, class="col-lg-12",
box(
title = "Adaptive design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("AdaptiveDesign"),
tags$p(class = "help-block",
"Probability of establishing a significant treatment effect in the overall population, biomarker-positive population or at least one of the two patient populations at the final analysis.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation report."),
actionButton("jump_to_panel6", "Next tab")
)
)
),
tabItem(tabName = "report",
fluidRow(
box(
title = "Create a simulation report",
background = "red",
width = 12,
tags$p("Click the Download button to create and save a detailed simulation report in a Microsoft Word format."),
downloadButton("DownloadResults", "Download")
)
)
)
)
)
)
)
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