ggmap.Rpres

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ggmap
========================================================
author: Etienne Low-Décarie



Creating maps
===
class: small-code

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

Basic world map
===
class: small-code

```{r fig.width=8, fig.height=3,echo=T}
map <- ggplot()+borders("world", 
                        colour="gray50",
                        fill="gray50")
print(map)
```

Resource
===

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

<iframe src="https://www.nceas.ucsb.edu/~frazier/RSpatialGuides/ggmap/ggmapCheatsheet.pdf" width="1000" height="800">
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Pretty world map
===

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

```{r fig.width=8, fig.height=3,echo=T, eval=F}
myLocation <- with(coord, c(min(LON),
                            min(LAT), 
                            max(LON), 
                            max(LAT)))
```

```{r fig.width=8, fig.height=3,echo=T}
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
```{r}
coord <- read.csv("./Data/CoralBleaching_cleaned.csv")
```

Extract bleaching events

```{r}
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
===

```{r fig.width=8, fig.height=3,echo=T}
map <- map+geom_point(data=coord,aes(x=LON,
                                     y=LAT,
                                     colour=BLEACHING_SEVERITY),
                      alpha=0.5)
print(map)
```

Fine tuning: Scales
===

```{r fig.width=8, fig.height=3,echo=T}
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
===

```{r fig.width=8, fig.height=6,echo=T}
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](http://dx.doi.org/10.1111/j.1365-294X.2009.04237.x)
[data](http://datadryad.org/resource/doi:10.5061/dryad.1237)


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var myCountdown1 = new Countdown({
    							time: 300, 
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									rangeHi:"minute"	// <- no comma on last item!
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