Nothing
inst/ADTreatSelApp/ui.r
In 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 design with data-driven treatment selection",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics of an adaptive design for a multi-arm Phase III clinical trial with two interim analyses. The first interim analysis supports early stopping for futility and the second interim analysis enables adaptive treatment selection to identify the best performing treatments."
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Number of trial arms",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "narms", label = "Number of trial arms", value = 3, min = 2, max = 5),
tags$p(class = "help-block",
"Total number of trial arms, including the control arm.")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Sample size",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("SampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial arm.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Endpoint parameters."),
actionButton("jump_to_panel2", "Next tab")
)
)
),
tabItem(tabName = "endpoint_parameters",
fluidRow(
column(6, class = "col-md-6",
box(
title = "Endpoint type",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
selectInput("endpoint_index", label = "Primary endpoint's type",
c("Normal" = 1, "Binary" = 2, "Time-to-event" = 3)),
selectInput("direction_index", label = "Direction of favorable outcome",
c("Higher" = 1, "Lower" = 2))
)
),
conditionalPanel(
condition = "input.endpoint_index == 3",
column(6, class = "col-md-6",
box(
title = "Number of events",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "event_count", label = "Target number of events", value = 200),
tags$p(class = "help-block",
"Target number of events 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$p(class = "help-block",
"Treatment effect assumptions for the selected primary endpoint under the alternative hypothesis of beneficial effect, i.e., all treatments are effective.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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$p(class = "help-block",
"Fraction of the total number of patients at Interim analysis 1.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events at Interim analysis 1.")
),
numericInput(inputId = "futility_threshold", label = "Futility threshold (%)", value = 10),
tags$p(class = "help-block",
"The trial will be stopped for futility at Interim analysis 1 if the predicted probability of success is less than the futility threshold.")
)
),
column(6, class = "col-md-6",
box(
title = "Interim analysis 2",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "info_frac2", label = "Interim fraction (%)", value = 60, min = 10, max = 90),
conditionalPanel(
condition = "input.endpoint_index == 1 || input.endpoint_index == 2",
tags$p(class = "help-block",
"Fraction of the total number of patients at Interim analysis 2.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events at Interim analysis 2.")
),
numericInput(inputId = "treatment_count", label = "Number of selected treatments", value = 1, min = 1, max = 5),
tags$p(class = "help-block",
"Number of best performing treatments to be selected at Interim analysis 2."),
selectInput("mult_test", label = "Multiple testing procedure", c("Bonferroni" = 1, "Holm" = 2, "Hochberg" = 3))
)
)
),
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 at Interim analysis 1",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("FutilityStopping"),
tags$p(class = "help-block",
"Probability of dropping each treatment due to futility. The trial is terminated at Interim analysis 1 if all treatments are dropped.")
)
),
column(12, class="col-lg-12",
box(
title = "Treatment selection at Interim analysis 2",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TreatmentSelection"),
tags$p(class = "help-block",
"Probability that each treatment is selected for the final analysis. No treatment is selected if the trial is terminated at Interim analysis 1.")
)
),
column(12, class="col-lg-12",
box(
title = "Traditional designs",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TraditionalDesign"),
tags$p(class = "help-block",
"Power for two-arm traditional designs that compare each treatment to control.")
)
),
column(12, class="col-lg-12",
box(
title = "Adaptive design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("AdaptiveDesign")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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$p("Click the Download button to create and save a detailed simulation report in a Microsoft Word format."),
downloadButton("DownloadResults", "Download")
)
)
)
)
)
)
)
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MedianaDesigner documentation built on Aug. 28, 2023, 9:06 a.m.
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library(shiny)
suppressPackageStartupMessages(library(shinydashboard))
library(MedianaDesigner)
library(shinyMatrix)
shinyUI(
dashboardPage(
dashboardHeader(title = "MedianaDesigner"),
dashboardSidebar(
sidebarMenu(id = "sidebar",
menuItem("Design parameters", tabName = "design_parameters", icon = icon("sliders-h")),
menuItem("Endpoint parameters", tabName = "endpoint_parameters", icon = icon("sliders-h")),
menuItem("Interim parameters", tabName = "interim_parameters", icon = icon("sliders-h")),
menuItem("General parameters", tabName = "general_parameters", icon = icon("sliders-h")),
menuItem("Simulation results", tabName = "simulation", icon = icon("table")),
menuItem("Simulation report", tabName = "report", icon = icon("file"))
)
),
dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "main.css?2")
),
tabItems(
tabItem(tabName = "design_parameters",
fluidRow(
box(
title = "Adaptive design with data-driven treatment selection",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics of an adaptive design for a multi-arm Phase III clinical trial with two interim analyses. The first interim analysis supports early stopping for futility and the second interim analysis enables adaptive treatment selection to identify the best performing treatments."
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Number of trial arms",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "narms", label = "Number of trial arms", value = 3, min = 2, max = 5),
tags$p(class = "help-block",
"Total number of trial arms, including the control arm.")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Sample size",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("SampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial arm.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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_count", label = "Target number of events", value = 200),
tags$p(class = "help-block",
"Target number of events at the final analysis.")
)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Treatment effect assumptions",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("TreatmentEffectAssumptions"),
tags$p(class = "help-block",
"Treatment effect assumptions for the selected primary endpoint under the alternative hypothesis of beneficial effect, i.e., all treatments are effective.")
)
)
),
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 at Interim analysis 1.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events at Interim analysis 1.")
),
numericInput(inputId = "futility_threshold", label = "Futility threshold (%)", value = 10),
tags$p(class = "help-block",
"The trial will be stopped for futility at Interim analysis 1 if the predicted probability of success 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$p(class = "help-block",
"Fraction of the total number of patients at Interim analysis 2.")
),
conditionalPanel(
condition = "input.endpoint_index == 3",
tags$p(class = "help-block",
"Fraction of the total number of events at Interim analysis 2.")
),
numericInput(inputId = "treatment_count", label = "Number of selected treatments", value = 1, min = 1, max = 5),
tags$p(class = "help-block",
"Number of best performing treatments to be selected at Interim analysis 2."),
selectInput("mult_test", label = "Multiple testing procedure", c("Bonferroni" = 1, "Holm" = 2, "Hochberg" = 3))
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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$p("Proceed to Simulation results."),
actionButton("jump_to_panel5", "Next tab")
)
)
),
tabItem(tabName = "simulation",
fluidRow(
box(
title = "Summary of simulation results",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
width = 12
),
column(12, class="col-lg-12",
box(
title = "Futility stopping at Interim analysis 1",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("FutilityStopping"),
tags$p(class = "help-block",
"Probability of dropping each treatment due to futility. The trial is terminated at Interim analysis 1 if all treatments are dropped.")
)
),
column(12, class="col-lg-12",
box(
title = "Treatment selection at Interim analysis 2",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TreatmentSelection"),
tags$p(class = "help-block",
"Probability that each treatment is selected for the final analysis. No treatment is selected if the trial is terminated at Interim analysis 1.")
)
),
column(12, class="col-lg-12",
box(
title = "Traditional designs",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("TraditionalDesign"),
tags$p(class = "help-block",
"Power for two-arm traditional designs that compare each treatment to control.")
)
),
column(12, class="col-lg-12",
box(
title = "Adaptive design",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("AdaptiveDesign")
)
)
),
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")
)
)
)
)
)
)
)
Try the MedianaDesigner package in your browser
Any scripts or data that you put into this service are public.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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