inst/shinyApp/ui_layers/ui_gbif_search.R

datasetGBIF <- list('Search for a species'=c(1))
source("load_install_pkgs.R")
# GUI for searching GBIF data
gbif_data <- sidebarLayout(position = "left",
                           sidebarPanel(
                             tags$head(
                               tags$script(src = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML', type = 'text/javascript')
                             ),
                             titlePanel("NicheToolBox"),
                             h3("GBIF data"),
                             #p("Here you can request data to the", a(href="http://www.gbif.org/",target='_blank',"GBIF"),
                             #   "API using the",  a(href="http://cran.r-project.org/web/packages/spocc/vignettes/spocc_vignette.html",
                             #                       target='_blank',"spocc"),"package"),
                             HTML("<p align ='justify'>Here you can request data to the</p>"),
                             a(href="http://www.gbif.org/",target='_blank',"GBIF"),
                             HTML("API using the"),
                             a(href="http://cran.r-project.org/web/packages/spocc/vignettes/spocc_vignette.html",
                               target='_blank',"spocc"),
                             HTML("package</p>"),
                             br(),
                             textInput(inputId= "genus",
                                       label="Enter the species genus:",
                                       value="",placeholder = HTML("i.e. Anolis")),
                             textInput(inputId= "species",
                                       label="Enter the name of species:",
                                       value="",placeholder = "i.e. trinitatis"),
                             numericInput("occlim","Enter a occ search limit",value = 500,min = 1,max = 10000000),
                             br(),
                             actionButton(input="search_gbif_data",label="Search GBIF",styleclass="primary"),
                             busyIndicator("Loading...",wait = 0),
                             br(),
                             br(),
                             h3("Cleaning duplicates"),
                             helpText("In this section you can clean your longitude and latitude data using a threshold distance between points to be considered as duplicates."),
                             tags$div(title="Coordinate data must be in decimal degrees",
                                      selectInput('xLongitudeGBIF', 'Select longitude', names(datasetGBIF)[1])
                             ),
                             tags$div(title="Coordinate data must be in decimal degrees",
                                      selectInput('yLatitudeGBIF', 'Selct latitude', names(datasetGBIF)[1])
                             ),
                             tags$div(tile="Here you can see the dimensions of your data set",
                                      p('The data set has'),
                                      verbatimTextOutput('nRcordsGBIF')
                             ),
                             br(),
                             tags$div(title="distance between points to be considered duplicates (in grades)",
                                      numericInput(inputId = "threshold_gbif",
                                                   label = "Threshold distance for duplicates (\\(\\delta\\))",
                                                   value = 0.0,min = 0,
                                                   max = 100000,step = 0.05)
                             ),

                             tags$div(title="Cleans the duplicates on your dataset according to the threshold distance",
                                      actionButton(input="clean_dup_gbif",label="Clean duplicates",styleclass="primary")
                             ),
                             br(),

                             # Clean duplicates by group

                             h4("Clean duplicates by group"),
                             helpText("Sometimes you may want to clean your data on a specific location (country, continent), this option will clean you data given a grouping variable)"),
                             selectInput(inputId = 'groupGBIF',label = 'Select the grouping variable',choices = names(datasetGBIF)[1]),
                             selectInput(inputId = 'groupLevelsGBIF',label = 'Select the ids you want to clean',choices = NULL,multiple = TRUE),
                             br(),
                             actionButton(inputId = 'clean_dup_gbif_group',label = 'Clean duplicates by group',styleclass="primary"),
                             br(),
                             h4("Download your clean data"),
                             downloadButton(outputId="downGBIF",label="Download Data")),
                             mainPanel(dataTableOutput("gbif_table")))
luismurao/nichetoolbox documentation built on May 21, 2017, 3:42 p.m.