Nothing
inst/ADRandApp/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 trials with response-adaptive randomization",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics
of an adaptive design for a dose-finding Phase II clinical trial
with multiple interim analyses aimed at updating the randomization
scheme based on the accumulating efficacy data."
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Number of trial arms",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "n_arms", label = "Number of trial arms", value = 3, min = 2, max = 6),
tags$p(class = "help-block",
"Total number of trial arms, including the placebo arm.")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Dose levels",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("DoseLevels")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Number of trial stages",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "n_stages", label = "Number of trial stages", value = 3, min = 2, max = 5)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Sample size in each stage",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("StageSampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial stage.")
)
)
),
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 = 36)
)
),
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 = 24),
tags$p(class = "help-block",
"Median enrollment time is defined as the time point by which 50% of the patients will be enrolled.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Endpoint parameters."),
actionButton("jump_to_panel2", "Next tab")
)
)
),
tabItem(tabName = "endpoint_parameters",
fluidRow(
column(width = 6,
box(
title = "Endpoint type",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
selectInput("endpoint_index", label = "Primary endpoint's type", c("Normal" = 1)),
selectInput("direction_index", label = "Direction of favorable outcome", c("Higher" = 1, "Lower" = 2))
)
),
column(width = 6,
box(
title = "Treatment period",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "treatment_period", label = "Length of the treatment period", value = 6)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Treatment effect assumptions",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("TreatmentEffectAssumptions")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Interim parameters."),
actionButton("jump_to_panel3", "Next tab")
)
)
),
tabItem(tabName = "interim_parameters",
fluidRow(
column(width = 6,
box(
title = "Randomization ratio",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "ratio_placebo_percent", label = "Fixed randomization ratio in the placebo arm (%)", value = 25, min = 1, max = 99)
)
),
column(width = 6,
box(
title = "Clinically meaningful improvement",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "delta", label = "Threshold for clinically meaningful improvement over placebo", value = 10)
)
)
),
fluidRow(
column(width = 6,
box(
title = "Balance parameter",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "balance", label = "Balance parameter for adaptive randomization", value = 1, min = 0, max = 3)
)
)
),
fluidRow(
column(width = 12,
box(
title = "Parameters of candidate dose-response models",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(
inputId = "exponential_model_parameter",
label = "Exponential model: Delta",
value = 200, min = 0
),
numericInput(
inputId = "emax_model_parameter",
label = "Emax model: ED50",
value = 200, min = 0, max = 0
),
numericInput(
inputId = "logistic_model_ed50",
label = "Logistic model: ED50",
value = 200, min = 0, max = 0
),
numericInput(
inputId = "logistic_model_delta",
label = "Logistic model: Delta",
value = 50, min = 0, max = 0
),
tags$p(class = "help-block",
"Non-linear parameters of the candidate dose-response models used in the MCPMod method. No parameters need to be specified for the linear model."
)
)
)
),
fluidRow(
column(width = 12,
box(
title = "Candidate dose-response models used in the MCPMod method",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
imageOutput("DoseResponseModels", height = "auto"),
tags$p(class = "help-block",
"Black curve: Linear model, Blue curve: Exponential model, Red curve: Emax model, Green curve: Logistic model.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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),
tags$p(class = "help-block",
"Dropout rate at the end of the treatment period.")
)
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Alpha",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "alpha", label = "Type I error rate", value = 0.025),
tags$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 = 100)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation results."),
actionButton("jump_to_panel5", "Next tab")
)
)
),
tabItem(tabName = "simulation",
fluidRow(
box(
title = "Summary of simulation results",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
width = 12
),
column(12, class="col-lg-12",
box(
title = "Sample size by stage",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("SampleSizeByStage")
)
),
column(12, class="col-lg-12",
box(
title = "Sample size by trial arm",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("SampleSizeByTrialArm")
)
),
column(12, class="col-lg-12",
box(
title = "Comparison of traditional and adaptive designs",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("ComparisonOfTraditionalAndAdaptiveDesigns"),
tags$p(class = "help-block",
"Probability of a statistically significant dose-response relationship based on the MCPMod method.")
)
)
),
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 trials with response-adaptive randomization",
solidHeader = FALSE,
collapsible = FALSE,
width = 12,
"The web application computes key operating characteristics
of an adaptive design for a dose-finding Phase II clinical trial
with multiple interim analyses aimed at updating the randomization
scheme based on the accumulating efficacy data."
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Number of trial arms",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "n_arms", label = "Number of trial arms", value = 3, min = 2, max = 6),
tags$p(class = "help-block",
"Total number of trial arms, including the placebo arm.")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Dose levels",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("DoseLevels")
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Number of trial stages",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "n_stages", label = "Number of trial stages", value = 3, min = 2, max = 5)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Sample size in each stage",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("StageSampleSize"),
tags$p(class = "help-block",
"Number of enrolled patients in each trial stage.")
)
)
),
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 = 36)
)
),
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 = 24),
tags$p(class = "help-block",
"Median enrollment time is defined as the time point by which 50% of the patients will be enrolled.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Endpoint parameters."),
actionButton("jump_to_panel2", "Next tab")
)
)
),
tabItem(tabName = "endpoint_parameters",
fluidRow(
column(width = 6,
box(
title = "Endpoint type",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
selectInput("endpoint_index", label = "Primary endpoint's type", c("Normal" = 1)),
selectInput("direction_index", label = "Direction of favorable outcome", c("Higher" = 1, "Lower" = 2))
)
),
column(width = 6,
box(
title = "Treatment period",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "treatment_period", label = "Length of the treatment period", value = 6)
)
)
),
fluidRow(
column(12, class = "col-md-12",
box(
title = "Treatment effect assumptions",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
uiOutput("TreatmentEffectAssumptions")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Interim parameters."),
actionButton("jump_to_panel3", "Next tab")
)
)
),
tabItem(tabName = "interim_parameters",
fluidRow(
column(width = 6,
box(
title = "Randomization ratio",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "ratio_placebo_percent", label = "Fixed randomization ratio in the placebo arm (%)", value = 25, min = 1, max = 99)
)
),
column(width = 6,
box(
title = "Clinically meaningful improvement",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "delta", label = "Threshold for clinically meaningful improvement over placebo", value = 10)
)
)
),
fluidRow(
column(width = 6,
box(
title = "Balance parameter",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "balance", label = "Balance parameter for adaptive randomization", value = 1, min = 0, max = 3)
)
)
),
fluidRow(
column(width = 12,
box(
title = "Parameters of candidate dose-response models",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(
inputId = "exponential_model_parameter",
label = "Exponential model: Delta",
value = 200, min = 0
),
numericInput(
inputId = "emax_model_parameter",
label = "Emax model: ED50",
value = 200, min = 0, max = 0
),
numericInput(
inputId = "logistic_model_ed50",
label = "Logistic model: ED50",
value = 200, min = 0, max = 0
),
numericInput(
inputId = "logistic_model_delta",
label = "Logistic model: Delta",
value = 50, min = 0, max = 0
),
tags$p(class = "help-block",
"Non-linear parameters of the candidate dose-response models used in the MCPMod method. No parameters need to be specified for the linear model."
)
)
)
),
fluidRow(
column(width = 12,
box(
title = "Candidate dose-response models used in the MCPMod method",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
imageOutput("DoseResponseModels", height = "auto"),
tags$p(class = "help-block",
"Black curve: Linear model, Blue curve: Exponential model, Red curve: Emax model, Green curve: Logistic model.")
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$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),
tags$p(class = "help-block",
"Dropout rate at the end of the treatment period.")
)
)
),
fluidRow(
column(6, class = "col-md-6",
box(
title = "Alpha",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
numericInput(inputId = "alpha", label = "Type I error rate", value = 0.025),
tags$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 = 100)
)
)
),
fluidRow(
box(
title = "Next step",
background = "red",
width = 12,
tags$p("Proceed to Simulation results."),
actionButton("jump_to_panel5", "Next tab")
)
)
),
tabItem(tabName = "simulation",
fluidRow(
box(
title = "Summary of simulation results",
status = "primary",
solidHeader = FALSE,
collapsible = FALSE,
width = 12
),
column(12, class="col-lg-12",
box(
title = "Sample size by stage",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("SampleSizeByStage")
)
),
column(12, class="col-lg-12",
box(
title = "Sample size by trial arm",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("SampleSizeByTrialArm")
)
),
column(12, class="col-lg-12",
box(
title = "Comparison of traditional and adaptive designs",
status = "primary",
solidHeader = TRUE,
collapsible = TRUE,
width = NULL,
tableOutput("ComparisonOfTraditionalAndAdaptiveDesigns"),
tags$p(class = "help-block",
"Probability of a statistically significant dose-response relationship based on the MCPMod method.")
)
)
),
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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