ggmap.md

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ggmap

author: Etienne Low-Décarie

Creating maps

class: small-code

if(!require(ggmap)) {install.packages("ggmap")}
require(ggmap)
if(!require(maptools)) {install.packages("maptools")}
require(maptools)

Basic world map

class: small-code

map <- ggplot()+borders("world", 
                        colour="gray50",
                        fill="gray50")
print(map)

Resource

Cheatsheet: https://www.nceas.ucsb.edu/~frazier/RSpatialGuides/ggmap/ggmapCheatsheet.pdf

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Pretty world map

bounding box lowerleftlon, lowerleftlat, upperrightlon, upperrightlat (a little glitchy for google maps)

myLocation <- with(coord, c(min(LON),
                            min(LAT), 
                            max(LON), 
                            max(LAT)))

myLocation <- c(-179,-89,179,89)
myMap <- get_map(location=myLocation, 
                 source="stamen", 
                 maptype="watercolor",
                 crop=FALSE) 

myMap <- ggmap(myMap)
print(myMap)

Load geo-referenced coral bleaching data

Coral bleaching data from ReefBase http://www.reefbase.org

coord <- read.csv("./Data/CoralBleaching_cleaned.csv")

Extract bleaching events

coord <- coord[coord$BLEACHING_SEVERITY %in% c("Low","Medium","HIGH"),]
coord$BLEACHING_SEVERITY <- factor(coord$BLEACHING_SEVERITY, levels=levels(coord$BLEACHING_SEVERITY)[c(2,3,1)])

Add the data to the map

map <- map+geom_point(data=coord,aes(x=LON,
                                     y=LAT,
                                     colour=BLEACHING_SEVERITY),
                      alpha=0.5)
print(map)

Fine tuning: Scales

map <- map+
  scale_colour_manual(values = c("Low"="yellow",
                                 "Medium"="orange",
                                 "HIGH"="red"))+
  guides(colour = guide_legend(override.aes = list(alpha = 1))) #+
  #facet_grid(YEAR~.)

print(map)

Fine tuning: Facets

print(map+facet_wrap(~YEAR))

Exercise 1

Create a coordinate file with the location of your house and the location of the house of your friends

Produce maps from the data in Henry P, Le Lay G, Goudet J, Guisan A, Jahodová S, Besnard G (2009) Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps. Molecular Ecology 18: 2819-2831. paper data

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