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A Shiny web application for plotting rainforest tree species on a map with googleVis and rgbif::gbifmap. Data by Rainforest Foundation Norway and Global Biodiversity Information Facility
############################################################################################
#
# 12.1.2014 Tuija Sonkkila
#
# Shiny web application for plotting rainforest tree species on a map
# with googleVis and rgbif::gbifmap
#
# Data by Rainforest Foundation Norway and Global Biodiversity Information Facility
#
# http://www.regnskog.no/no/bevisst-forbruker/tropisk-t%C3%B8mmer/oversikt-tropiske-treslag
# http://www.gbif.org/
#
# Rainforest Foundation Norway data scraped by Scraper
#
# GBIF API query with the rgbif wrapper by rOpenSci
#
###########################################################################################
library(shiny)
library(ggplot2)
library(RColorBrewer)
library(rgbif)
library(googleVis)
library(RCurl)
# Scraped with Scraper from http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
countrydata <- getURL("https://docs.google.com/spreadsheets/d/1GS1MrfozPCvQ1VLBZMBt_wlHtD1M7_paA1stDrr_rd4/pub?output=csv",
.encoding="UTF-8",
ssl.verifypeer = FALSE)
cdata <- read.csv(text = countrydata)
# Columns to continue with
cols <- c("name","longitude", "latitude", "country")
if(file.exists("Extinct.Rda")){
load("Extinct.Rda")
Extinct <- Extinct[ ,cols]
Extinct <- merge(Extinct, cdata, by.x="country", by.y="Acronym")
}
if(file.exists("Critically_Endangered.Rda")){
load("Critically_Endangered.Rda")
Critically_Endangered <- Critically_Endangered[ ,cols]
Critically_Endangered <- merge(Critically_Endangered, cdata, by.x="country", by.y="Acronym")
}
if(file.exists("Endangered.Rda")){
load("Endangered.Rda")
Endangered <- Endangered[ ,cols]
Endangered <- merge(Endangered, cdata, by.x="country", by.y="Acronym")
}
if(file.exists("Vulnerable.Rda")){
load("Vulnerable.Rda")
Vulnerable <- Vulnerable[ ,cols]
Vulnerable <- merge(Vulnerable, cdata, by.x="country", by.y="Acronym")
}
if(file.exists("Near_Threatened.Rda")){
load("Near_Threatened.Rda")
Near_Threatened <- Near_Threatened[ ,cols]
Near_Threatened <- merge(Near_Threatened, cdata, by.x="country", by.y="Acronym")
}
if(file.exists("Other.Rda")){
load("Other.Rda")
Other <- Other[ ,cols]
Other <- merge(Other, cdata, by.x="country", by.y="Acronym")
}
statuses <- character()
for(i in c("Extinct", "Critically_Endangered", "Endangered", "Vulnerable", "Near_Threatened", "Other")) {
if(exists(i)) {
statuses <- c(statuses, i)
}
}
############################################
#
# 12.1.2014 Tuija Sonkkila
#
# The function modifies rgbif::gbifmap
# by adding an alpha argument
#
# rgbif by rOpenSci
#
###########################################
mygbifmap <- function(input = NULL, mapdatabase = "world", region = ".",
geom = geom_point, jitter = NULL, alpha = 0.4, customize = NULL)
{
long = NULL
lat = NULL
group = NULL
longitude = NULL
latitude = NULL
name = NULL
# if(!is.gbiflist(input))
# stop("Input is not of class gbiflist")
tomap <- input[complete.cases(input$latitude, input$latitude), ]
tomap <- tomap[!tomap$longitude==0 & !tomap$latitude==0,]
tomap <- input[-(which(tomap$latitude <=90 || tomap$longitude <=180)), ]
tomap$name <- as.factor(gbif_capwords(tomap$name, onlyfirst=TRUE))
if(length(unique(tomap$name))==1){ theme2 <- theme(legend.position="none") } else
{ theme2 <- NULL }
world <- map_data(map=mapdatabase, region=region)
message(paste("Rendering map...plotting ", nrow(tomap), " points", sep=""))
ggplot(world, aes(long, lat)) +
geom_polygon(aes(group=group), fill="white", color="gray40", size=0.2) +
geom(data=tomap, aes(longitude, latitude, colour=name),
alpha=alpha, size=3, position=jitter) +
scale_color_brewer("", type="qual", palette=6) +
labs(x="", y="") +
theme_bw(base_size=14) +
theme(legend.position = "bottom", legend.key = element_blank()) +
guides(col = guide_legend(nrow=2)) +
blanktheme() +
theme2 +
customize
}
############################################################################################
#
# 12.1.2014 Tuija Sonkkila
#
# Shiny web application for plotting rainforest tree species on a map
# with googleVis and rgbif::gbifmap
#
# Data by Rainforest Foundation Norway and Global Biodiversity Information Facility
#
# http://www.regnskog.no/no/bevisst-forbruker/tropisk-t%C3%B8mmer/oversikt-tropiske-treslag
# http://www.gbif.org/
#
# Rainforest Foundation Norway data scraped by Scraper
#
# GBIF API query with the rgbif wrapper by rOpenSci
#
###########################################################################################
shinyServer(function(input, output) {
rdata <- reactive({
if (is.null(input$c))
return(NULL)
if (exists(input$c))
get(input$c)
})
output$gvis <- renderGvis({
myData <- rdata()
# gVis needs a lat:lon column
myData$Loc <- paste(myData$latitude, myData$longitude, sep=":")
# A number showing how many occurrences there are of this species on this location
# Used in deciding the size of the markers
# http://stackoverflow.com/questions/7450600/how-do-i-count-aggregate-values-from-a-data-frame-and-reincorporate-them-into-th
myData$Count <- ave(myData$Loc, myData[ ,"Loc"], FUN=length)
# Pasting country name to tooltip
myData$Text <- paste(myData$name, " (", myData$Name, ")", sep = "")
gvisGeoChart(myData,
locationvar="Loc",
sizevar="Count",
hovervar="Text",
options=list(displayMode="Markers",
colorAxis="{colors: ['#e7711c', '#4374e0']}",
markerOpacity=0.6,
height=600)
)
})
output$gbifmap <- renderPlot({
if (is.null(rdata()))
return(NULL)
library(RColorBrewer)
# http://novyden.blogspot.fi/2013/09/how-to-expand-color-palette-with-ggplot.html
colourCount = length(unique(rdata()$name))
getPalette = colorRampPalette(brewer.pal(9, "Set1"))
source("mygbifmap.R")
p <- mygbifmap(rdata(),
alpha = 0.8,
customize = list(scale_colour_manual(values = getPalette(colourCount)),
guides(col = guide_legend(ncol=4))))
print(p)
})
output$data <- renderTable({
if (is.null(rdata()))
return(NULL)
rdata()
}, include.rownames = FALSE)
})
############################################################################################
#
# 12.1.2014 Tuija Sonkkila
#
# Shiny web application for plotting rainforest tree species on a map
# with googleVis and rgbif::gbifmap
#
# Data by Rainforest Foundation Norway and Global Biodiversity Information Facility
#
# http://www.regnskog.no/no/bevisst-forbruker/tropisk-t%C3%B8mmer/oversikt-tropiske-treslag
# http://www.gbif.org/
#
# Rainforest Foundation Norway data scraped by Scraper
#
# GBIF API query with the rgbif wrapper by rOpenSci
#
###########################################################################################
shinyUI(pageWithSidebar(
headerPanel("Red-listed rainforest tree species"),
sidebarPanel(
selectInput(inputId = "c",
label = "Choose status:",
choices = statuses,
selected = c("Endangered"))
),
mainPanel(
tabsetPanel(
tabPanel("Map", htmlOutput("gvis"),
br(), br(),
a(href = "http://www.regnskog.no/no/bevisst-forbruker/tropisk-t%C3%B8mmer/oversikt-tropiske-treslag", target = "_blank", "Species by Rainforest Foundation Norway"),
br(),
a(href = "http://www.gbif.org/", target = "_blank", "Location data by Global Biodiversity Information Facility (GBIF)"),
br(), br(),
a(href = "http://tts2.blogspot.fi/2014/01/mapping-red-listed-rainforest-tree.html", target = "_blank", "See blog post")),
tabPanel("Static map", plotOutput("gbifmap", height = "700px", width = "auto")),
tabPanel("Data", tableOutput("data"))
)
)
))
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