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ui.R
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ui.R
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################################################################################
#
#
# This is a Shiny web application to support the implementation of health and
# nutrition coverage surveys in Liberia.
#
# This is the code for the user interface (UI) of the Shiny web application.
#
#
################################################################################
################################################################################
#
# UI for web application
#
################################################################################
#
# Define UI for application
#
ui <- dashboardPage(
skin = "red",
#
# Header
#
dashboardHeader(
title = "Liberia Coverage Surveys",
titleWidth = 300),
#
# Sidebar
#
dashboardSidebar(
width = 300,
sidebarSearchForm(
textId = "searchText",
buttonId = "searchButton"
),
#
# Sidebar menu
#
sidebarMenu(
id = "tabs",
menuItem(text = "Design",
tabName = "design",
icon = icon(name = "pencil",
lib = "font-awesome",
class = "fa-lg")),
menuItem(text = "Collect",
tabName = "collect",
icon = icon(name = "tablet",
lib = "font-awesome",
class = "fa-lg")),
menuItem(text = "Process",
tabName = "process",
icon = icon(name = "database",
lib = "font-awesome",
class = "fa-lg")),
menuItem(text = "Analyse",
tabName = "analyse",
icon = icon(name = "line-chart",
lib = "font-awesome",
class = "fa-lg")),
menuItem(text = "Report",
tabName = "report",
icon = icon(name = "file-text",
lib = "font-awesome",
class = "fa-lg"))
)
),
#
# Body
#
dashboardBody(
#
# Specify a custom.css
#
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
#
# Body outputs for every menu item on sidebar
#
tabItems(
#
# Body output when 'design' menu is selected
#
tabItem(tabName = "design",
fluidRow(
conditionalPanel(condition = "input.design == 'indicators'",
box(title = "Select Indicators",
solidHeader = TRUE,
status = "danger",
width = 4,
checkboxGroupInput(inputId = "designIndicators",
label = "Which indicators are to be assessed?",
choices = c("SAM treatment coverage" = "sam",
"Vitamin A supplementation coverage" = "vita",
"FeFol supplementation coverage" = "fefol",
"Micronutrient powder supplementation coverage" = "mnp",
"Infant and young child feeding counselling coverage" = "iycf"),
selected = NULL)
)
),
conditionalPanel(condition = "input.design == 'sampsize'",
box(title = "Sample size parameters",
solidHeader = TRUE,
status = "danger",
width = 4,
selectInput(inputId = "zValue",
label = "Confidence interval",
choices = list("96% CI ( z-value: 2.05 )" = "2.05",
"95% CI ( z-value: 1.96 )" = "1.96",
"92% CI ( z-value: 1.75 )" = "1.75",
"90% CI ( z-value: 1.645 )" = "1.645"),
selected = "1.96"),
sliderInput(inputId = "sampSizeProp",
label = "Proportion/prevalence (p)",
min = 0, max = 1, value = 0.50, step = 0.01),
sliderInput(inputId = "sampSizePrec",
label = "Level of precision (c)",
min = 0.03, max = 0.15, value = 0.10, step = 0.01),
hr(),
checkboxInput(inputId = "sampSizeFpc",
label = "Apply finite population correction",
value = FALSE),
conditionalPanel(condition = "input.sampSizeFpc",
numericInput(inputId = "sampSizeFpcPop",
label = "Population size",
value = 10000,
min = 1, max = 100000, step = 1)
),
hr(),
radioButtons(inputId = "inputDeffType",
label = "Specify/calculate design effect (DEFF)",
choices = c("Specify" = "specify",
"Calculate" = "calculate"),
selected = "specify",
inline = TRUE),
conditionalPanel(condition = "input.inputDeffType == 'specify'",
sliderInput(inputId = "inputDeffValue",
label = "Specify design effectd (DEFF)",
value = 2.0,
min = 1.0, max = 10.0, step = 0.1)
),
conditionalPanel(condition = "input.inputDeffType == 'calculate'",
fileInput(inputId = "inputDeffFile",
label = "Upload CSV dataset file for DEFF calculation",
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
selectInput(inputId = "inputDeffVar",
label = "Select variable name of indicator to test",
choices = c("Select variable name" = "")),
selectInput(inputId = "inputDeffCluster",
label = "Select variable name of survey cluster",
choices = c("Select variable name" = "")),
sliderInput(inputId = "inputDeffClusterSize",
label = "No. of samples per cluster planned for survey",
min = 0, max = 30, step = 1, value = 10)
),
br(),
actionButton(inputId = "calcSampSize",
label = "Calculate",
icon = icon(name = "calculator",
lib = "font-awesome",
class = "fa-lg")
),
actionButton(inputId = "calcSampSizeReset",
label = "Reset",
icon = icon(name = "refresh",
lib = "font-awesome",
class = "fa-lg")
)
)
),
conditionalPanel(condition = "input.design == 'stage1'",
box(title = "Stage 1 sampling parameters",
solidHeader = TRUE,
status = "danger",
width = 4,
shinyjs::useShinyjs(),
selectInput(inputId = "mapSamplingAreaType",
label = "Select area type to sample",
choices = list("Choose one" = "",
"Country" = "country",
"County" = "county",
"District" = "district"),
selected = NULL),
conditionalPanel(condition = "input.mapSamplingAreaType == 'county'",
selectInput(inputId = "mapSamplingCounty",
label = "Select counties to sample",
choices = list("Select county" = "",
"Counties" = counties$admin1name),
selected = NULL)
),
conditionalPanel(condition = "input.mapSamplingAreaType == 'district'",
selectInput(inputId = "mapSamplingDistrict",
label = "Select districts to sample",
choices = list("Select district" = "",
"Districts" = districts$admin2Name),
selected = NULL)
),
conditionalPanel(condition = "input.mapSamplingAreaType == 'country' | input.mapSamplingCounty != '' | input.mapSamplingDistrict != ''",
hr(),
h5("Spatial sample settings"),
selectInput(inputId = "mapSamplingSpec",
label = "Specify spatial grid parameter to use",
choices = c("Grid area" = "area",
"Number of grids" = "n",
"Max distance to sampling point" = "d"),
selected = "area"),
conditionalPanel(condition = "input.mapSamplingSpec == 'area'",
numericInput(inputId = "mapSamplingGridArea",
label = "Set grid area size (in sq kms)",
value = 100, min = 5, max = 500, step = 5)
),
conditionalPanel(condition = "input.mapSamplingSpec == 'n'",
numericInput(inputId = "mapSamplingGridNumber",
label = "Set grid number",
value = 20, min = 16, max = 30, step = 1)
),
conditionalPanel(condition = "input.mapSamplingSpec == 'd'",
numericInput(inputId = "mapSamplingGridDist",
label = "Set max distance to sampling point (in kms)",
value = 10, min = 5, max = 30, step = 1)
),
numericInput(inputId = "mapSamplingSettlementsNumber",
label = "No. of settlements per sampling point",
value = 1, min = 1, max = 10, step = 1),
br(),
conditionalPanel(condition = "input.mapSamplingAreaType == 'country'",
actionButton(inputId = "mapSamplingPlotCountry",
label = "",
icon = icon(name = "th",
lib = "font-awesome",
class = "fa-lg")
),
actionButton(inputId = "mapSamplingPlotCountryReset",
label = "",
icon = icon(name = "refresh",
lib = "font-awesome",
class = "fa-lg")
),
downloadButton(outputId = "samplingListDownloadCountry",
label = "",
icon = icon(name = "download",
lib = "font-awesome",
class = "fa-lg")
)
),
conditionalPanel(condition = "input.mapSamplingAreaType == 'county'",
actionButton(inputId = "mapSamplingPlotCounty",
label = "",
icon = icon(name = "th",
lib = "font-awesome",
class = "fa-lg")
),
actionButton(inputId = "mapSamplingPlotCountyReset",
label = "",
icon = icon(name = "refresh",
lib = "font-awesome",
class = "fa-lg")
),
downloadButton(outputId = "samplingListDownloadCounty",
label = "",
icon = icon(name = "download",
lib = "font-awesome",
class = "fa-lg")
)
),
conditionalPanel(condition = "input.mapSamplingAreaType == 'district'",
actionButton(inputId = "mapSamplingPlotDistrict",
label = "",
icon = icon(name = "globe",
lib = "font-awesome",
class = "fa-lg")
),
actionButton(inputId = "mapSamplingPlotDistrictReset",
label = "",
icon = icon(name = "refresh",
lib = "font-awesome",
class = "fa-lg")
),
downloadButton(outputId = "samplingListDownloadDistrict",
label = "",
icon = icon(name = "download",
lib = "font-awesome",
class = "fa-lg")
)
)
)
)
),
tabBox(selected = "indicators",
id = "design",
title = "Design",
width = 8,
side = "right",
tabPanel(title = "Stage 1",
value = "stage1",
fluidRow(
box(title = "Stage 1 Sampling",
solidHeader = FALSE,
status = "danger",
width = 12,
leafletOutput("mapSampling", height = 500)
)
),
fluidRow(
conditionalPanel(condition = "input.mapSamplingPlotCountry > 0 | input.mapSamplingPlotCounty > 0 | input.mapSamplingPlotDistrict > 0",
box(title = "Stage 1 sample list",
solidHeader = TRUE,
status = "danger",
width = 12,
DT::dataTableOutput("mapSamplingTable")
)
)
)
),
tabPanel(title = "Sample Size",
value = "sampsize",
#withMathJax(),
#fluidRow(
# box(title = "Sample size calculations",
# solidHeader = FALSE,
# status = "danger",
# width = 12,
# uiOutput("sampSizeCalculations")
# )
#),
shinyjs::useShinyjs(),
conditionalPanel(condition = "input.calcSampSize != 0",
fluidRow(
box(title = textOutput("sampSizeHeader"),
solidHeader = FALSE,
status = "danger",
width = 12,
valueBoxOutput("confIntBox"),
valueBoxOutput("precisionBox"),
valueBoxOutput("clusterSizeBox"),
valueBoxOutput("iccBox"),
valueBoxOutput("deffBox"),
valueBoxOutput("sampSizeBox")
)
)
)
),
tabPanel(title = "Indicators",
value = "indicators",
conditionalPanel(condition = "input.designIndicators.length > 0",
fluidRow(
box(title = "Indicator Sets",
solidHeader = FALSE,
status = "danger",
width = 12,
withMathJax(),
uiOutput("descriptionImam"),
uiOutput("descriptionVita"),
uiOutput("descriptionFefol"),
uiOutput("descriptionMnp"),
uiOutput("descriptionIycf")
)
)
)
)
)
)
),
#
# Body output when 'collect' menu is selected
#
tabItem(tabName = "collect",
tabBox(selected = "papi",
title = "Collect",
width = 12,
side = "right",
tabPanel(title = "Open Data Kit",
value = "odk",
h4("Digital data collection using Open Data Kit"),
uiOutput("collectOdk")),
tabPanel(title = "Pen and paper",
value = "papi",
h4("Pen and Paper Interviews"),
uiOutput("collectPapi")
)
)
),
#
# Body output when 'process' menu is selected
#
tabItem(tabName = "process",
fluidRow(
conditionalPanel(condition = "input.process == 'processData'",
box(title = "Indicators",
solidHeader = TRUE,
status = "danger",
width = 4,
checkboxGroupInput(inputId = "inputIndicators",
label = "Which indicators are to process?",
choices = c("IMAM coverage",
"Vitamin A supplementation coverage",
"FeFol supplementation coverage",
"Micronutrient powder supplementation coverage",
"Infant and young child feeding counselling coverage"),
selected = c("IMAM coverage",
"Vitamin A supplementation coverage",
"FeFol supplementation coverage",
"Micronutrient powder supplementation coverage",
"Infant and young child feeding counselling coverage")
),
br(),
actionButton(inputId = "inputProcessAction",
label = "Process",
icon = icon(name = "database",
lib = "font-awesome",
class = "fa-lg"))
)
),
conditionalPanel(condition = "input.process == 'checkData'",
box(title = "Check data parameters",
solidHeader = TRUE,
status = "danger",
width = 4)
),
conditionalPanel(condition = "input.process == 'coverageData'",
box(title = "Input Coverage Data",
solidHeader = TRUE,
status = "danger",
width = 4,
radioButtons(inputId = "inputDataType2",
label = "How will coverage data be inputted?",
choices = c("Upload data file" = "upload",
"Get data from ODK server" = "odk")),
br(),
conditionalPanel(condition = "input.inputDataType2 == 'upload'",
fileInput(inputId = "inputDataRaw2",
label = "Upload raw coverage data to process",
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv"))
),
conditionalPanel(condition = "input.inputDataType2 == 'odk'",
radioButtons(inputId = "inputOdkData2",
label = "Pull data from ODK remote or local?",
choices = c(Remote = "remote", Local = "local")),
br(),
conditionalPanel(condition = "input.inputOdkData2 == 'remote'",
textInput(inputId = "inputOdkUrl2",
label = "Remote URL",
placeholder = "https://odk.ona.io"),
textInput(inputId = "inputOdkUsername2",
label = "Username",
value = "cadnihead"),
textInput(inputId = "inputOdkPassword2",
label = "Password",
value = "kEv-hAB-Arb-6Cn"),
textInput(inputId = "inputOdkFormId2a",
label = "Form ID",
value = "liberiaCoverage")
),
conditionalPanel(condition = "input.inputOdkData2 == 'local'",
textInput(inputId = "inputOdkDirectory2",
label = "Where is the local ODK directory located?",
value = getwd()),
textInput(inputId = "inputOdkFormId2b",
label = "Form ID",
value = "liberiaCoverage")
),
conditionalPanel(condition = "input.inputOdkFormId2a != ' ' | input.inputOdkFormId2a != ' '",
actionButton(inputId = "inputDataAction2",
label = "Pull data",
icon = icon(name = "arrow-down",
lib = "font-awesome",
class = "fa-lg"))
)
)
)
),
conditionalPanel(condition = "input.process == 'villageData'",
box(title = "Input Village Data",
solidHeader = TRUE,
status = "danger",
width = 4,
radioButtons(inputId = "inputDataType1",
label = "How will village data be inputted?",
choices = c("Upload data file" = "upload",
"Get data from ODK server" = "odk")),
br(),
conditionalPanel(condition = "input.inputDataType1 == 'upload'",
fileInput(inputId = "inputDataRaw1",
label = "Upload raw village data to process",
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv"))
),
conditionalPanel(condition = "input.inputDataType1 == 'odk'",
radioButtons(inputId = "inputOdkData1",
label = "Pull data from ODK remote or local?",
choices = c(Remote = "remote", Local = "local")),
br(),
conditionalPanel(condition = "input.inputOdkData1 == 'remote'",
textInput(inputId = "inputOdkUrl1",
label = "Remote URL",
placeholder = "https://ona.io/cadnihead"),
textInput(inputId = "inputOdkUsername1",
label = "Username",
value = "cadnihead"),
textInput(inputId = "inputOdkPassword1",
label = "Password",
value = "kEv-hAB-Arb-6Cn"),
textInput(inputId = "inputOdkFormId1a",
label = "Form ID",
value = "liberiaVillageForm")
),
conditionalPanel(condition = "input.inputOdkData1 == 'local'",
textInput(inputId = "inputOdkDirectory1",
label = "Where is the local ODK directory located?",
value = getwd()),
textInput(inputId = "inputOdkFormId1b",
label = "Form ID",
value = "liberiaVillageForm")
),
conditionalPanel(condition = "input.inputOdkFormId1a != ' ' | input.inputOdkFormId1b != ' '",
actionButton(inputId = "inputDataAction1",
label = "Pull data",
icon = icon(name = "arrow-down",
lib = "font-awesome",
class = "fa-lg"))
)
)
)
),
tabBox(title = "Process",
id = "process",
selected = "villageData",
side = "right",
width = 8,
tabPanel(title = "Process Indicators",
value = "processData",
fluidRow()
),
tabPanel(title = "Check Data",
value = "checkData",
fluidRow()
),
tabPanel(title = "Coverage Data",
value = "coverageData",
fluidRow(
conditionalPanel(condition = "input.inputDataRaw2.length > 0",
box(title = NULL,
width = 12,
status = "danger",
DT::dataTableOutput("surveyDataTable")
)
)
)
),
tabPanel(title = "Village Data",
value = "villageData",
fluidRow(
conditionalPanel(condition = "input.inputDataRaw1.length > 0",
box(title = NULL,
width = 12,
status = "danger",
DT::dataTableOutput("villageDataTable")
)
)
)
)
)
)
),
#
# Body output when 'analyse' menu is selected
#
tabItem(tabName = "analyse",
box(title = "Analyse",
solidHeader = FALSE,
status = "danger",
width = 12,
fluidRow(
box(title = "Analysis Parameters",
solidHeader = TRUE,
status = "danger",
width = 4,
checkboxGroupInput(inputId = "analysisIndicators",
label = "Select indicators to analyse",
choices = c("IMAM coverage",
"Vitamin A supplementation coverage",
"FeFol supplementation coverage",
"Micronutrient powder supplementation coverage",
"Infant and young child feeding counselling coverage"),
selected = c("IMAM coverage",
"Vitamin A supplementation coverage",
"FeFol supplementation coverage",
"Micronutrient powder supplementation coverage",
"Infant and young child feeding counselling coverage")
),
br(),
numericInput(inputId = "replicates",
label = "No. of bootstrap replicates",
value = 399,
min = 399,
step = 100),
br(),
actionButton(inputId = "analysisAction",
label = "Analyse",
icon = icon(name = "line-chart",
lib = "font-awesome",
class = "fa-lg"))
)
)
)
),
#
# Body output when 'report' menu is selected
#
tabItem(tabName = "report",
fluidRow(
tabBox(id = "gm",
title = "Report",
width = 12,
tabPanel(title = "Urban Montserrado",
value = "gm",
fluidRow(
tabBox(id = "ifaGM",
title = "",
width = 12,
tabPanel(title = "IFA",
value = "ifaGM"
),
tabPanel(title = "IYCF",
value = "iycfGM"
),
tabPanel(title = "MNP",
value = "mnpGM"
),
tabPanel(title = "Vitamin A",
value = "vitGM"
),
tabPanel(title = "Nutrition Screening",
value = "screenGM"
),
tabPanel(title = "CMAM",
value = "cmamGM"
)
)
)
),
tabPanel(title = "Grand Bassa",
value = "gb"
)
)
)
)
)
)
)