server.r

require(shiny)

shinyServer(function(input, output){
  
  theData <- reactive( {
    require(rbison)
    
    print("enterData")
    print(input$common)
    print(input$species)
    if (is.null(input$species)) return(NULL)
    #   if (input$common=="") return(NULL)
    print(input$species)
    df.init <- bison(species = input$species, type = "scientific_name", start = 0, count = 20) # big numbers cause errors
    df <- bison(species = input$species, type = "scientific_name", start = 0, count =  df.init$georeferenced)
    #      print("df")
    #      print(head(df))
    print("extractgeo")
    geo <- bison_data(df, "data_df")
    #      print("geo")
    #      print(geo)
    geo$latitude <- as.numeric(as.character(geo$latitude))
    geo$longitude <- as.numeric(as.character(geo$longitude))
    geo$latlong <- paste0(geo$latitude,":",geo$longitude)
    #print("looks good")
    # print(geo)
    
    # state info
    print(df$counties$total)
    if (df$counties$total >0) {
      states <- bison_data(df, datatype = "counties")
      # print(states)
      states$total <- as.integer(states$total)
      # there are ties for max so cannot do ddply on matching - transform and then take first for
      # each on ordered
      states.summary <- ddply(states,"state", transform, tot=sum(total),max=max(total))
      states.summary <- arrange(states.summary,desc(total))
      temp <- ddply(states.summary,"state", function(x) c(county_name=x$county_name[1]) )
      #prob a simpler way but can then do merge
      
      df.states <- merge(temp,states.summary,by=c("state","county_name"),all.x=TRUE)[,c(1,5,2,4)]
      df.states <- arrange(df.states,desc(tot))
      # print(df.states)
      colnames(df.states) <- c('State','Total','Top','County')
    } else {
      df.states <- data.frame(State="No Data",Total=0,Top=0,County="")
    }
    print("dfstates")
    print(df.states)
    
    ## sighting methods get rid of centroid
    method <- bison_data(df)
    method["centroid"] <- NULL
    print(method)
    #plotHeight=200
    
    info=list(df=df,geo=geo,df.states=df.states,method=method) #plotHeight=plotHeight
    return(info)
    print("info returned")
  })
  
  output$locationPlot <- renderPlot( {
    if (is.null(input$species)) return(NULL)
    if (theData()$df$georeferenced==0) return(NULL)
    # print(theData()$df)
    bisonmap(theData()$df)  
  })
  
})

ui.r

require(shiny)

shinyUI(pageWithSidebar(
  
  headerPanel(""),
  
  
  sidebarPanel(    
#     tags$head(
#       tags$link(rel = 'stylesheet', type = 'text/css', href = 'styles.css'),
#       tags$link(rel = 'stylesheet', type = 'text/css', href = 'appStyles.css') # yet to get working
#       
#     ),
    p("The",  a('rOpenSci initiative', href='http://ropensci.org/', id="link"),"  have developed an easy method to access 
", a('US Geological Survey', href='http://bison.usgs.ornl.gov/', id="link")," records for 
             more than 70,000 species of flora and fauna in the USA"),
    p("Enter a common name, press the button, select from the
             options provided and re-press"),
    p("Be as precise as possible e.g 'Black bear' gives 4 
             alternatives, 'bear' more than 800"),
    textInput("common", "Enter Common Name (can be slow response)"),
    uiOutput("selection"),
    submitButton("Go"),
    # actionButton("goButton","Go"),
    p(),
    
    
    htmlOutput("image"),
    uiOutput("imageText")
  ),
  
  
  mainPanel(
    tabsetPanel(
      tabPanel("State Map",
               h4(textOutput("stateCaption")),
               plotOutput("statePlot"),
               h5(textOutput("stateInfo")),
               value = 1),
      tabPanel("Tables",
               
               tableOutput("method"),
               tableOutput("summary"),
               
               
               value=2),
      tabPanel("County Map (be patient!)",
               h4(textOutput("countyCaption")),
               plotOutput("countyPlot"),
               h5(textOutput("countyInfo")),
               value = 3),
      tabPanel("Location (inc. Alaska)",
               h4(textOutput("locationCaption")),
               plotOutput("locationPlot"),
               h5(textOutput("locationInfo")),
               value = 4),
      tabPanel("Google Map (inc. Alaska)",
               h4(textOutput("gvisCaption")),
               htmlOutput("gvisPlot"),
               h5(textOutput("gvisInfo")),
               value = 5),
      tabPanel("Notes",
               # img(src="blankMap.png"), testing and oes work
               
               HTML("<h5>Definitions</h5
                        <ul>
                       <li>Fossil: Petrified evidence of a species occurrence in geological time </li>
                       <li>Specimen: The species or a part of it has been collected from this location and preserved in a formal collection</li>
                       <li>Germplasm: Living tissue from which new organisms can be grown </li>
                      <li>Literature: Assertion in a scientific publication of an occurrence </li>
                      <li>Living: Organism kept in captivity at the given location </li>
                       <li>Observation: A free-living species occurrence that does not produce a specimen or germplasm </li>
                       </ul>
                       <br>
                       Data may have been collected over many decades
                Scientific studies in a particular region may bias results
                       <br><br>
                       R packages used: shiny, rbison, taxize_, rjson, XML, googleVis, plyr, stringr
                  <br><br>
                    Special thanks to Scott Campbell of OpenSci
                    "),
               
               value = 6),
      id="tabs1")    
  ) 
  
))