knitr::opts_chunk$set(echo = TRUE)
ui.R
codelibrary(shiny) library(shinydashboard) library(shinyjs) source("globals.R") header <- dashboardHeader( title = tags$a(tags$p(strong(style ="font-size: 24px;color: white","Semiparametric Area Under the Curve (sAUC) Regression Model with Discrete Covariates")), href = "https://github.com/sbohora/sAUC", target ="_blank"), disable = FALSE, titleWidth = "1500px", dropdownMenu( type = "messages", # messageItem( # from = "Som", # message = "Stay tuned."), # messageItem( # from = "New User", # message = "How do I register?", # icon = icon("question"), # time = "13:45"), messageItem( from = "Support", message = "The new server is ready.", icon = icon("life-ring"), time = "2017-08-01")), dropdownMenu( type = "notifications", notificationItem( text = "5 new uers today", icon = icon("users")), # notificationItem( # text = "12 items delivered", # icon("truck"), # status = "success"), notificationItem( text = "Server load at 86%", icon = icon("exclamation-triangle"), status = "warning")), dropdownMenu( type = "task", badgeStatus = "success", taskItem(value = 90, color = "aqua","Documention"), taskItem(value = 75, color = "yellow","Server deployment") )) # Define the overall UI dashboardPage( # skin = "green", header = header, title = "sAUC", dashboardSidebar( disable = FALSE, sidebarMenu( id = "sidebar_menu", # menuItem( # text = "Introduction", # tabName = "intro", # icon = icon("book")), menuItem( text = "AUC Regression in R", tabName = "auc_reg", badgeLabel = "Perform", icon = icon("bar-chart")), menuItem( text = "sAUC in R", tabName = "example", badgeLabel = "Example", icon = icon("book")), menuItem( text = "AUC Simulation in R", tabName = "auc_simulate", icon = icon("line-chart"), badgeLabel = "Perform", badgeColor = "green"), menuItem( text = "Source Code (Shiny R)", tabName = "get_code", # href = "https://github.com/sbohora/sAUC/tree/master/inst/shiny", icon = icon("code"), menuSubItem( text = "server.R", tabName = "server_code"), menuSubItem( text = "ui.R", tabName = "ui_code"), menuSubItem( text = "globals.R", tabName = "global_code") ), menuItem( text = "sAUC in Python", tabName = "sauc_python", badgeLabel = "Example", icon = icon("file-code-o")), menuItem( text = "sAUC in Julia", tabName = "sauc_julia", badgeLabel = "Example", icon = icon("code")), menuItem( text = "About Me", tabName = "about_me", icon = icon("picture-o")), menuItem( text = "Feedback", tabName = "feedback", icon = icon("comment-o")), menuItem( text = "Discussion Board", tabName = "disqus_here", icon = icon("info")), sidebarMenuOutput("menu"), tags$hr(), menuItem( text = "", href = "https://github.com/sbohora/sAUC", badgeLabel = "Github Repo for sAUC package", icon = icon("github") ), menuItem( text = "", href = "https://sbohora.github.io/sAUC", badgeLabel = "Web site for sAUC package", icon = icon("tv") ), tags$hr(), menuItem( text = "Contact Me", tabName = "contact", icon = icon("volume-control-phone")), tags$body( a( class = "addtwitter", href = "https://twitter.com/SomBohora", target = "_blank", img(src = "twitter-logo.png", height="30", width="30") ), a( class = "addemail", href = "mailto:energeticsom@gmail.com", img(src = "email-logo.png", height="30", width="30") ), a( class = "addgithub", href = "https://github.com/sbohora", target = "_blank", img(src = "github-logo.png", height="30", width="30") ) ), sidebarSearchForm( textId = "searchText", buttonId = "searchButton", label = "Search..." ) ) ), dashboardBody( shinyjs::useShinyjs(), tags$head( tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")), tags$style(type="text/css", ".shiny-output-error { visibility: hidden; }", ".shiny-output-error:before { visibility: hidden; }" ), tabItems( tabItem( tabName = "auc_simulate", fluidRow( column( width = 3, box( collapsible = TRUE, solidHeader = TRUE, status = "info", title = tags$p(strong(style ="font-size: 18px;", "Enter parameters for simulating a model with one covariate with 3 levels")), width = 12L, height = 8L, background = NULL, numericInput( inputId = "realization", label = "Number of Realizations", value = 100), sliderInput( inputId = "number_treatment", label = "Number of Observations in Treatment Group: ", 1, 1000, 20), sliderInput( inputId = "number_control", label = "Number of Observations in Control Group: ", 1, 1000, 30) ) ), column( width = 3, box( title = tags$p(strong(style ="font-size: 18px;","True regression parameters")), width = NULL, background = NULL, collapsible = TRUE, solidHeader = TRUE, status = "info", p("Below are the true parameter values for the current simulation. You can change 'em if you want."), numericInput( inputId = "b0", label = HTML("True value of β<sub>0</sub>:"), value = 0.15), numericInput( inputId = "b1", label = HTML("True value of β<sub>1</sub>:"), value = 0.50), numericInput( inputId = "b2", label = HTML("True value of β<sub>2</sub>:"), value = 1.00) ) ), column( width = 6, box( title = tags$p(strong(style ="font-size: 18px;","Result of Simulation")), width = 15, div(style = 'overflow-x: scroll', DT::dataTableOutput('result1')), collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL) # p(class = 'text-center', downloadButton('download_simu_result', 'Download Simulation Results')) ) ), fluidRow( column( width = 12, box( title = "Distribution of beta estimates from the above simulation", width = 15, div(style = 'overflow-x: scroll', plotOutput('result_plot_beta')), background = "red", collapsible = TRUE, solidHeader = TRUE, status = "info"), div(style= 'display:inline-block', downloadButton('download_simu_plot', 'Download Simulation Plot'), style="float:right", style= 'display:inline-block', downloadButton('download_simu_result', 'Download Simulation Results'), style="float:right") # p(class = 'text-center', downloadButton('download_simu_plot', 'Download Simulation Plot')) ) ) ), tabItem( tabName = "auc_reg", fluidRow( column( width = 3, box( title="File upload", width = 12, # height = "500px", collapsible = TRUE, solidHeader = TRUE, status = "info", fileInput("file", "Upload a data file (for e.g. CSV) to be analyzed"), shinyjs::hidden(actionButton("reset_file", HTML("Warning <br> You should reset analysis before uploading a file."), style = "color: red;font-size:105%;background-color: white;")), shinyjs::hidden(actionButton("reset", "Reset Analysis", style = "color: white; background-color: red;")), helpText("Default maximum file size is 5MB."), helpText("Input data formats can be comma, semicolon, tab or space delimited."), h5(helpText("Select the read.table parameters below")), checkboxInput( inputId = 'header', label = "Header TRUE?", value = TRUE), checkboxInput( inputId = 'string_factors', label = "String as Factors?", value = FALSE), radioButtons( inputId = 'sep', label = 'Separator', choices = c(Comma = ",", Semicolon = ';', Tab = '\t', Space=''), selected = ',', inline = TRUE) ), div(id = "box_inbuilt_data", box( title="Use a dataset within sAUC package", width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", checkboxInput( inputId = 'use_inbuilt_data', label = 'Would you like to use FASD dataset from sAUC package for trial?', value = FALSE) # radioButtons( # inputId = 'use_inbuilt_data', # label = 'Would you like to use a FASD dataset from sAUC package for trial?', # choices = list("Yes", "No"), selected = "No") )) ), column( width = 9, status = "info", uiOutput("describe_file"), htmlOutput("add_about_sauc") # tabBox( # tabPanel("Histogram", # fluidRow( # column(4, plotOutput("hist_plot")), # column(8, plotOutput("bar_plot")))), )), br(), shinyjs::hidden( fluidRow( id = "show_model", column( width = 3, box(footer = tags$p(strong(style = "font-size: 12px;color:red", "* = required arguments.")), title = tags$p(strong(style ="font-size: 18px;color:green","Data analysis")), width = 12, solidHeader = TRUE, collapsible = TRUE, status = "warning", uiOutput("choose_response"), uiOutput("choose_group"), uiOutput("independent") ) ), column( width = 5, box( title = tags$p(strong(style ="font-size: 18px;color: green","Model Results")), width = 14, collapsible = TRUE, solidHeader = TRUE, status = "warning", DT::dataTableOutput("model_result") ), div(style= 'display:inline-block', downloadButton('download_data', 'Download Data'), style="float:right", style= 'display:inline-block', downloadButton('download_model_result', 'Download Model Results'), style="float:right", style= 'display:inline-block', downloadButton('download_roc_plot', 'Download ROC curve plot'), style="float:right", style= 'display:inline-block', downloadButton('download_hist_plot', 'Download Histogram'), style="float:right", style= 'display:inline-block', downloadButton('download_bar_plot', 'Download Bar Plot'), style="float:right") ), column( width = 4, # box( # # title = tags$p(strong(style ="font-size: 18px;color: green","ROC curve")), # width = 14, # height = 5, # collapsible = TRUE, # solidHeader = TRUE, # status = "warning", plotOutput("roc_plot", height = 350, width = 500) # ) ) ) )), tabItem( tabName = "example", fluidRow( column( width = 9, box( width = 20, collapsible = TRUE, solidHeader = TRUE, status = "info", title = "Example using Semiparametric AUC regression method", background = NULL, # includeMarkdown("example.md") # includeHTML("server.html") # HTML(markdown::markdownToHTML(knitr::knit('server.Rmd', quiet = FALSE))) # includeHTML("example.html") tags$iframe(src = 'example.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') ) ) ) ), tabItem( tabName = "server_code", fluidRow( column( width = 8, box( width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL, # includeMarkdown("server.md") tags$iframe(src = 'server.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') # includeHTML("example.html") # HTML(markdown::markdownToHTML(knitr::knit('server.Rmd', quiet = FALSE))) # tags$iframe( # seamless = "seamless", # style="height:400px; width:100%; scrolling=yes", # src = "https://websitesetup.org/css3-cheat-sheet/") ) ) ) ), tabItem( tabName = "ui_code", fluidRow( column( width = 8, box( width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL, # includeMarkdown("ui.md") tags$iframe(src = 'ui.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') # includeHTML("example.html") ) ) ) ), tabItem( tabName = "global_code", fluidRow( column( width = 8, box( width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL, # includeMarkdown("ui.md") tags$iframe(src = 'globals.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') # includeHTML("example.html") ) ) ) ), tabItem( tabName = "sauc_python", fluidRow( column( width = 9, box( width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL, # includeMarkdown("server.md") tags$iframe(src = 'example-python.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') ) ) ) ), tabItem( tabName = "sauc_julia", fluidRow( column( width = 9, box( width = 12, collapsible = TRUE, solidHeader = TRUE, status = "info", background = NULL, # includeMarkdown("server.md") tags$iframe(src = 'example-julia.html', # put .html to /www width = '100%', height = '1000px', frameborder = 0, scrolling = 'auto') ) ) ) ), tabItem( tabName = "about_me", fluidRow( column( width = 4, box( title = "This is about me", width = 12, status = "primary", background = "navy", collapsible = TRUE, solidHeader = TRUE, # p("This is about me.", style = "font-size:120%"), # tags$a(href = "http://ouhsc.edu/bbmc/team/", img(src = "som.jpg", height = 200, width = 200), target ="_blank") br(), br(), span("I am Som and am a Biostatistician at ", span(tags$a(href = "http://ouhsc.edu/bbmc/team/", "The Department of Pediatrics, The University of Oklahoma Health Sciences Center. ", target ="_blank"), style = "color:blue"), "I received my MApStat and MS in Biostatistics from LSU and OUHSC, respectively. In addition to BBMC, I work as a statistician and data programmer in a number of pediatric research projects. I was trained in biostatistics and epidemiology, and has research experience in Fetal Alcohol Spectrum Disorders (FASD), HIV/AIDS clinical trials and child maltreatment prevention. I am interested in the applications of statistical computing and simulation, data analytics, dynamic reporting, and real-time data decision making. I use mainly R, Python, and Julia programming languages.", style = "font-size:130%"), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br(), br() # downloadLink("download_cv", p("Download my CV", style = "font-size:130%")) ) ), column( width = 8, fluidRow( # box( # title = "I like mornings", # width = 12, # height = 15, # status = "primary", # background = "navy", # collapsible = TRUE, # solidHeader = TRUE, tabBox(width = 12, tabPanel( title = "I like mornings", # p("This is about me.", style = "font-size:100%"), tags$a(href = "http://ouhsc.edu/bbmc/team/", img(src = "nature.jpg", height = 700, width = 1050), target ="_blank") ) )) ) ) ), tabItem( tabName = "feedback", fluidRow( column( width = 4, box( width = 20, height = 20, title = "Feedback Form", status = "info", background = NULL, collapsible = TRUE, solidHeader = TRUE, htmlOutput("googleForm") ) ), column( width = 4, box( width = 20, height = 20, title = "Selected Comments", status = "info", background = NULL, collapsible = TRUE, solidHeader = TRUE, div(style = 'overflow-x: scroll', DT::dataTableOutput('googleFormData')), actionButton("refresh", "Refresh Sheet") ) ), column( width = 4, box( width = 12, title = "Contact me", status = "info", background = NULL, # Valid colors are: red, yellow, aqua, blue, light-blue, green, navy, teal, olive, lime, orange, fuchsia, purple, maroon, black. collapsible = TRUE, solidHeader = TRUE, span("I can be contacted at", a("energeticsom@gmail.com", href = "mailto:energeticsom@gmail.com"), br(), br(), p("Please report any bugs about the sAUC (R package)", span(tags$a(href = "https://github.com/sbohora/sAUC", "here", target = "_blank"))), br(), br(), br(), br(), br(), p("Please report any bugs about the saucpy (python package)", span(tags$a(href = "https://github.com/sbohora/saucpy/", "here", target = "_blank"))), br(), br(), br(), br(), br(), p("Please report any bugs about the SemiparametricAUC.jl (Julia package)", span(tags$a(href = "https://github.com/sbohora/SemiparametricAUC.jl/", "here", target = "_blank"))), br(), br(), br(), br(), br(), em( span("Created by "), a("Som B. Bohora", href = "mailto:energeticsom@gmail.com"), span(", July 2017"), br(), br() ), style = "font-size:140%; color:green") ) ) ) ), tabItem( tabName = "disqus_here", strong(h3("This is a discussion board about sAUC", style = "color:blue", align="center")), div( id = "disqus_thread", HTML( "<script> (function() { var d = document, s = d.createElement('script'); s.src = '//sauc.disqus.com/embed.js'; s.setAttribute('data-timestamp', +new Date()); (d.head || d.body).appendChild(s); })(); </script> <noscript>Please enable JavaScript to view the <a href='https://disqus.com/?ref_noscript' rel='nofollow'>comments powered by Disqus.</a></noscript>" ) ) ) ), div(HTML('<script id="dsq-count-scr" src="//sauc.disqus.com/count.js" async></script>')) ) #End the dashboardBody ) #End the dashboardPage
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