/
ui.R
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ui.R
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#Load packages
source("load_packages.R")
##Load code
source("TB_model.R")
source("graph_tb_model.R")
source("TB_model_diag.R")
source("graph_tb_model_diag.R")
sidebar <- dashboardSidebar(
hr(),
sidebarMenu(id = "menu",
menuItem("TB model", tabName = "tb-model", icon = icon("line-chart")),
menuItem("TB model with diagnostics", tabName = "tb-model-diag", icon = icon("line-chart")),
menuItem("About", tabName = "readme", icon = icon("mortar-board"), selected = TRUE),
menuItem("Code", icon = icon("code"),
menuSubItem("Github", href = "https://github.com/seabbs/intro_to_tb_models", icon = icon("github")),
menuSubItem("ui.R", tabName = "ui", icon = icon("angle-right")),
menuSubItem("server.R", tabName = "server", icon = icon("angle-right")),
menuSubItem("TB_model.R", tabName = "tb_model", icon = icon("angle-right")),
menuSubItem("TB_model_diag.R", tabName = "tb_model_diag", icon = icon("angle-right")),
menuSubItem("graph_tb_model.R", tabName = "graph_tb_model", icon = icon("angle-right"))
)
),
conditionalPanel(condition = 'input.menu == "tb-model"',
sliderInput("ecr",
"Effective Contacts (per year)",
min = 0,
max = 20,
value = 15,
step = 0.5),
sliderInput("wks_inf_p",
"Avg. No. of Weeks Infectious (Positive Sputum Smear)",
min = 0,
max = 102,
value = 51 ),
sliderInput("wks_inf_n",
"Avg. No. of Weeks Infectious (Negative Sputum Smear)",
min = 0,
max = 190,
value = 95),
sliderInput("prot_init_reint",
"Protection from reinfection relative to infection",
min = 0,
max = 1,
value = 0.65),
selectInput("timestep",
"Set timestep",
choices = list(
Week = 52,
Month = 12,
Year = 1),
selected = 1
),
checkboxInput("burn_in",
"Show burn in",
value = FALSE)
),
conditionalPanel(condition = 'input.menu == "tb-model-diag"',
sliderInput("ecr_diag",
"Effective Contacts (per year)",
min = 0,
max = 20,
value = 15,
step = 0.5),
checkboxInput("intervention",
"Intervention",
value = TRUE),
selectInput("timestep_diag",
"Set timestep",
choices = list(
Week = 52,
Month = 12,
Year = 1),
selected = 1
),
checkboxInput("burn_in_diag",
"Show burn in",
value = FALSE)
),
hr(),
helpText("Developed by ", a("Sam Abbott", href = "http://samabbott.co.uk"),
style = "padding-left:1em; padding-right:1em;position:absolute; bottom:1em; ")
)
body <- dashboardBody(
tabItems(
tabItem(tabName = "tb-model",
fluidRow(
tabBox(width = 12,
title = "Model Plots",
side = "right",
tabPanel(title = "Rates",
plotlyOutput("plot_rates")
),
tabPanel(title = "Annual Risk",
plotlyOutput("plot_annual_risk")
),
tabPanel(title = "Proportions",
plotlyOutput("plot_props")
)
),
tabBox(width = 12,
title = "Model Statistics",
side = "right",
tabPanel(title = "Rates and Annual Risk",
DT::dataTableOutput("rates_table")
),
tabPanel(title = "Proportions",
DT::dataTableOutput("props_table")
),
tabPanel(title = "Trajectory",
DT::dataTableOutput("traj_table")
)
)
)
),
tabItem(tabName = "tb-model-diag",
fluidRow(
tabBox(width = 12,
title = "Model Plots",
side = "right",
tabPanel(title = "Rates",
plotlyOutput("plot_rates_diag")
),
tabPanel(title = "Annual Risk",
plotlyOutput("plot_annual_risk_diag")
),
tabPanel(title = "Cumulative Counts",
plotlyOutput("plot_cum")
),
tabPanel(title = "Diagnoses",
plotlyOutput("plot_diag")
),
tabPanel(title = "Proportions",
plotlyOutput("plot_props_diag")
)
),
tabBox(width = 12,
title = "Model Statistics",
side = "right",
tabPanel(title = "Rates and Annual Risk",
DT::dataTableOutput("rates_table_diag")
),
tabPanel(title = "Cumulative Counts",
DT::dataTableOutput("cum_table")
),
tabPanel(title = "Diagnoses",
DT::dataTableOutput("diag_table")
),
tabPanel(title = "Proportions",
DT::dataTableOutput("props_table_diag")
),
tabPanel(title = "Trajectory",
DT::dataTableOutput("traj_table_diag")
)
)
)
),
tabItem(tabName = "readme",
withMathJax(),
includeMarkdown("README.md")
),
tabItem(tabName = "ui",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "UI",
downloadButton('downloadData2', 'Download'),
br(),br(),
pre(includeText("ui.R"))
)
),
tabItem(tabName = "server",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "Server",
downloadButton('downloadData3', 'Download'),
br(),br(),
pre(includeText("server.R"))
)
),
tabItem(tabName = "tb_model",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "TB Model",
downloadButton('downloadData4', 'Download'),
br(),br(),
pre(includeText("TB_model.R"))
)
),
tabItem(tabName = "graph_tb_model",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "TB Model Graphs",
downloadButton('downloadData5', 'Download'),
br(),br(),
pre(includeText("graph_tb_model.R"))
)
),
tabItem(tabName = "tb_model_diag",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "TB Model with Diagnostics",
downloadButton('downloadData6', 'Download'),
br(),br(),
pre(includeText("TB_model_diag.R"))
)
),
tabItem(tabName = "graph_tb_model_diag",
box( width = NULL, status = "primary", solidHeader = FALSE, title = "TB Model with Diagnostics Graphs",
downloadButton('downloadData7', 'Download'),
br(),br(),
pre(includeText("graph_tb_model_diag.R"))
)
)
)
)
dashboardPage(
dashboardHeader(title = "Intro to TB Models"),
sidebar,
body,
skin = "black"
)