rhr: Reproducible Home Ranges with R

library(shinyBS)
library(shiny)

shinyUI(
  navbarPage("Reproducible Home Range Analysis with R", id = "nav_rhr",  
             ## ============================================================================== ##  
             ## Read Files
             tabPanel("Load Data",
                      sidebarLayout(
                        sidebarPanel(  
                          h2("Relocations"), 
                          selectInput("readFileFieldSep", "Field separator",
                                      choices = c("Comma (,)" = ",", "Semicolon (;)" = ";", "Tab (\t)" = "\t")), 
                          selectInput("readFileSepDec", "Decimal Separator",
                                      choices = c("Point (.)" = ".", "Comma (,)" = ",")), 
                          checkboxInput("readFileHasHeader", "First line is a header", value=TRUE), 
                          fileInput("readFileFile", "Relocations", multiple = FALSE,
                                    accept = NULL), 
                          hr(),  
                          numericInput("configInEpsg", "Input EPSG", NA) 
                        ),
                        mainPanel(
                          bsAlert("alertLoadData"),
                          uiOutput("readFileTable")
                        ))),

# Remap fields ------------------------------------------------------------
tabPanel("Map and Project Data", 
         sidebarLayout(
           sidebarPanel(
             h2("Select Fields"), 
             selectInput("mfId", "Id", choices=NA), 
             selectInput("mfX", "Longitude (X)", choices=NA), 
             selectInput("mfY", "Latitude (Y)", choices=NA), 
             selectInput("mfDate", "Date", choices=NULL), 
                          selectInput("mfTime", "Time", choices=NULL), 
                          hr(), 
                          selectInput("mfDateFormat", "Date format", choices=NULL), 
                          selectInput("mfTimeFormat", "Time format", choices=NULL)
                          
                        ),
                        mainPanel(
                          h2("Reproject Data"),
                          uiOutput("reproject"), 
                          bsAlert("alert_data_in_setcrs"),
                          bsAlert("alert_data_in_transformcrs"),
                          hr(),
                          bsAlert("alertMapFields"),
                          verbatimTextOutput("mapDataMSG"), 
                          plotOutput("mapDataPlot")) 
                          #uiOutput("mapTable"))
                      )),
             

# Subset Data -------------------------------------------------------------
             tabPanel("Subset Data",
                      sidebarLayout(
                        sidebarPanel(
                          uiOutput("subsetUI")),
                        mainPanel(
                          plotOutput("subsetPlot"),
                          dataTableOutput("subsetTable")
                        ))), 
             

# Configure data ----------------------------------------------------------
navbarMenu(
  "Configure",
  tabPanel(
    "General", 
    fluidPage(
      navlistPanel(
        "General",
        tabPanel("Output",
                              h2("Set output options"), 
                              hr(), 
                              checkboxInput("configOutputCpWd", "Copy all results to the current working directory",
                                            value=FALSE),
                              helpText("All files will be copied into a new directory in current working directory")
                     ), 
                     tabPanel("Units",
                              selectInput("configOutputInUnits", "Input units are:",
                                          choices=c("I don't know" = "ido", "meters" = "m", "kilometers" = "km"), selectize=FALSE),
                              selectInput("configOutputOutUnits", "Desired output units are:",
                                          choices=c("square meters" = "sqm", "hectars" = "ha", "square km" = "sqkm"), selectize=FALSE)
                     ), 
                     ## Output Grid
                     tabPanel("Output Grid",
                              h2("Specify a grid"), 
                              helpText("Some estimators (e.g. Kernel Density Estimation) require a grid for the results. Here you can specify this grid. The same grid will be used for all animals in the analysis."), 
                              h2("Buffer"),
                              h3("Specify a buffer"),
                              uiOutput("bufferUI"), 
                              helpText("The buffer is in output units"), 
                              h3("Currently used buffer"), 
                              plotOutput("configOuputGridBufferPlot"), 
                              h2("Specify resolution and number of rows/columns"),
                              helpText("A grid can be created based on either number of rows and number of columns, or based on a provided resolution. Note, at the moment only quadratic pixels are supported, this means that the actual number of rows/columns, maybe slightly different to the one provided."),
                              selectInput("configOutputGridGrid", "Create output grid based on:", choices=c("number of rows and columns" = "pixel", "resolution" = "res"), 
                                          selectize=FALSE),
                              conditionalPanel(
                                condition="input.configOutputGridGrid == 'pixel'",
                                sliderInput("gridNColSlider", "Number of columns", 10, 500, 100), 
                                sliderInput("gridNRowSlider", "Number of rows", 10, 500, 100)
                              ), 
                              conditionalPanel(
                                condition="input.configOutputGridGrid == 'res'",
                                uiOutput("gridResUi")
                              ), 
                              h3("Currently used grid"),
                              verbatimTextOutput("printGrid")
                     ), 
                     tabPanel("Levels",
                              h2("Specify levels"), 
                              helpText("Some estimators (e.g. Kernel Density Estimation) require a grid for the results. Here you can specify this grid. The same grid will be used for all animals in the analysis."), 
                              helpText("Levels can be specified either as single number or comma seperated lists (e.g., '10,50,95'). Range from 1 to 100 is permitted, all other values will default back to 95"),
                              textInput("configGlobalLevel", "Levels:", "50,95")
                     ), 
                     well=FALSE)
                 )), 
               tabPanel("Exploratory analysis", 
                        fluidPage(
                          navlistPanel("Configure exploratory analysis",
                                       tabPanel("Site Fidelity",
                                                h2("Site Fidelity"), 
                                                numericInput("configSiteFidelityN", "Number of bootstrap replicates", value=config$pointLevel$sf$n, min=1), 
                                                sliderInput("configSiteFidelityAlpha", "Alpha", min=0, max=1, step=0.01, value=config$pointLevel$sf$alpha)), 
                                       tabPanel("Time to statistical independence",
                                                h2("Time to statistical independence"),
                                                bsAlert("generalNoTimeTTSI"), 
                                                numericInput("configTTSIInterval", "Initial time difference", value=config$pointLevel$ttsi$interval),
                                                helpText("Initial time difference in seconds"), 
                                                selectInput("configTTSISampling", "Sampling regime", choices=config$pointLevel$ttsi$sampling), 
                                                numericInput("configTTSINTimes", "Number of time above critical value", value=config$pointLevel$ttsi$ntimes), 
                                                a("More help", href = "http://jmsigner.github.io/rhrman/methodsTTSI.html", target = "_blank")
                                       ), 
                                       well=FALSE)
                        )), 
               tabPanel("Home Ranges", 
                        fluidPage(
                          navlistPanel("Configure Home Ranges",
                                       tabPanel("Unimodal Bivariate Normal",
                                                h2("Estimate unimodal bivariate normal home ranges")
                                       ), 
                                       tabPanel("Bimodal Bivariate Normal",
                                                h2("Estimate bimodal bivariate normal home ranges")
                                       ), 
                                       tabPanel("Minimum Convex Polygon",
                                                h2("Configure Minimum Convex Polygon")
                                       ),
                                       tabPanel("Kernel Density Estimation",
                                                h2("Kernel Density Estimation"),
                                                selectInput("configKDEbandwidth", "Bandwidth", choices=config$homeRange$kde$bandwidthOptions,
                                                            multiple=FALSE, selectize=FALSE),
                                                uiOutput("configKDEbandwidthUserInput")
                                       ),
                                       tabPanel("Local Convex Polygon",
                                                h2("Local Convex Polygon"),
                                                hr(),
                                                helpText("'n' is determined automatically, see documentation for more information"), 
                                                
                                                selectInput("configLOCOHtypeK", "Type k",
                                                            choices=c("Include (automatic)" = "incla",
                                                                      "Include (manual)" = "inclm", 
                                                                      "Do not include" = "not"),
                                                            selected="incla", selectize=FALSE),
                                                uiOutput("configLOCOHtypeKField"),
                                                selectInput("configLOCOHtypeA", "Type a",
                                                            choices=c(
                                                              "Include (automatic)" = "incla",
                                                              "Include (manual)" = "inclm", 
                                                              "Do not include" = "not"),
                                                                     selected="not", selectize=FALSE), 
                                                         uiOutput("configLOCOHtypeAField"),
                                                         
                                                         selectInput("configLOCOHtypeR", "Type r",
                                                                     choices=c("Include (automatic)" = "incla",
                                                                               "Include (manual)" = "inclm", 
                                                                               "Do not include" = "not"),
                                                                     selectize=FALSE, selected="not"), 
                                                         uiOutput("configLOCOHtypeRField"),
                                                         hr()
                                                ), 
                                                
                                                tabPanel("Brownian Bridges",
                                                         h2("Estimate home ranges with Brownian Bridges"),
                                                         bsAlert("generalNoTimeBBMM"), 
                                                         numericInput("configBBMMSigma2", "Location Error (Sigma 2)", value=10),
                                                         sliderInput("configBBMMRangeSigma1", "Search range for sigma 1", value=c(0, 100),
                                                                     min=0, max=1e4)
                                                ), 
                                                well=FALSE)
                                 )), 
                        tabPanel("Home-range properties", 
                                 fluidPage(
                                   navlistPanel("Home-range Properties",
                                                tabPanel("Home range asymptote",
                                                         h2("Home range asymptote"),
                                                         selectInput("configAsymptoteInclude", "Estimators",
                                                                     choices=config$homeRange$asymptote$include, 
                                                                     multiple=TRUE, selectize=TRUE), 
                                                         numericInput("configAsymptoteMinNP", "Minimum number of points",
                                                                      value=config$homeRange$asymptote$minNP), 
                                                         numericInput("configAsymptoteSI", "Sampling interval",
                                                                      value=config$homeRange$asymptote$SI), 
                                                         numericInput("configAsymptoteNRep", "Number of replications",
                                                                      value=config$homeRange$asymptote$NRep), 
                                                         sliderInput("configAsymptoteTotA", "Tolerance to total area",
                                                                     min=0, max=1, step=0.01,
                                                                     value=config$homeRange$asymptote$TotA), 
                                                         numericInput("configAsymptoteNTimes", "Number of time breakup met",
                                                                      value=config$homeRange$asymptote$NTimes), 
                                                         selectInput("configAsymptoteSampling", "Sampling regime",
                                                                     choices=config$homeRange$asymptote$sampling, 
                                                                     multiple=FALSE, selectize=FALSE)
                                                ), 
                                                tabPanel("Core Area",
                                                         h2("Core Area"),
                                                         selectInput("configCAInclude", "Estimators",
                                                                     choices=config$homeRange$ca$include, 
                                                                     multiple=TRUE, selectize=TRUE)), 
                                                well=FALSE) 
                                   )) 
             ),
             tabPanel("Run Analysis",
                      fluidRow(
                        column(width=5, 
                               ### FLuid 2 sides, one with steps, one with warnings, etc
                               h2("Select analytical steps"),
                               helpText("Select the analyses you want to perform here. Depending to the amount of data you provided, the number of animals and which analyses you chose, this may take some time."), 
                               h3("Home range analysis"), 
                               checkboxGroupInput("runSteps", "Select Steps",
                                                  choices=c(
                                                    "Site Fidelity" = "rhrSiteFidelity", 
                                                    "Time to statistical independence" = "rhrTTSI", 
                                                    "Minimum Convex Polygon" = "rhrMCP",
                                                    "Kernel Density Estimation" = "rhrKDE", 
                                                    "Local Convex Hull" = "rhrLoCoH",
                                                    "Brownian Bridges" = "rhrBBMM",
                                                    "Unimodal Bivariate Normal" = "rhrUniNorm",
                                                    "Unimodal Circular" = "rhrUniCirc",
                                                    "Bimodal Bivariate Normal" = "rhrBiNorm",
                                                    "Bimodal Circular" = "rhrBiCirc")),
                               bsButton("rhrAnalyze", label="Analyze", disabled=TRUE, size="large", style="primary")
                        ),
                        column(width=5,
                               bsAlert("rhrAnalyzeInfo"), 
                               bsAlert("rhrRunNoTimeTTSI"), 
                               bsAlert("rhrRunNoTimeBBMM"),
                               bsAlert("rhrAnalyzeProgress"), 
                               hr(),
                               htmlOutput("result")
                        )
                      )
             ),
             
             inverse=TRUE,
             footer=column(12, list(hr(), HTML("2015 - Department Wildlife Sciences - University of Goettingen, Germany; Visit the package website for <a href = 'http://jmsigner.github.io/rhrman/' target = '_blank'> more information</a> and <a href = 'http://jmsigner.github.io/rhrman/abtCitation.html' target = '_blank'>citation</a>.")))))