Important spatial packages

Preparation

GBRMP shapefiles

GBRMP shapefiles

GBRMP shapefiles

Preparation

Important spatial packages

> library(sp)
> library(raster)
> library(mapdata)
> library(maptools)
> library(rgeos)
> library(ggplot2)
> library(ggmap)
> library(dplyr)
> library(ggrepel)
> 
> source('../Rscripts/spatialFunctions.R')

Spatial data

• Vectors - points, lines
  • sp package
• Rasters - pixels
  • raster package

Vectors

Importing spatial data

mapdata - hi-res world maps

> library(mapdata)
> aus <- map("worldHires","Australia", fill=TRUE)

Importing spatial data

mapdata - hi-res world maps

> library(mapdata)
> aus <- map("worldHires","Australia", fill=TRUE, xlim=c(110,160), 
+             ylim=c(-45,-5), mar=c(0,0,0,0))

Importing spatial data

mapdata - hi-res world maps

> library(mapdata)
> library(maptools)
> library(sp)
> library(ggplot2)
> aus <- map("worldHires","Australia", fill=TRUE, xlim=c(110,160), 
+             ylim=c(-45,-5), mar=c(0,0,0,0), plot=FALSE)
> aus.sp <- map2SpatialPolygons(aus, IDs=aus$names,
+                               proj4string=CRS("+proj=longlat"))
> library(broom)
> ggplot(tidy(aus.sp), aes(y=lat, x=long, group=group)) + geom_polygon()

Importing spatial data

mapdata - hi-res world maps

> ggplot(tidy(aus.sp), aes(y=lat, x=long, group=group)) +
+     geom_polygon(fill='gray60', color='black') +
+     coord_map(xlim=c(146.65,147), ylim=c(-19.35,-19))

Importing spatial data

mapdata - hi-res world maps

Cropping

> library(rgeos)
> x <- c(146.65,147,147,146.65)
> y <- c(-19.35,-19.35,-19,-19)
> reg=SpatialPolygons(list(Polygons(list(Polygon(cbind(x,y))),ID=1)))
> proj4string(reg) <- CRS('+proj=longlat')
> aus.sp.crop <- gIntersection(aus.sp, reg)
> ggplot(tidy(aus.sp.crop), aes(y=lat, x=long, group=group)) +
+     geom_polygon(fill='gray60', color='black') +
+     coord_map()

Importing spatial data

Shapefiles

> gbr.sp<- readShapeSpatial(
+     "Great Barrier Reef Features/Great_Barrier_Reef_Features.shp",
+     proj4string = CRS('+proj=longlat +ellps=WGS84'),
+     repair=TRUE,force_ring=T,verbose=TRUE)
> plot(gbr.sp)

Importing spatial data

Shapefiles and ggplot

> names(gbr.sp) 

 [1] "OBJECTID"   "SORT_GBR_I" "LABEL_ID"   "SUB_NO"     "CODE"       "UNIQUE_ID"  "FEATURE_C" 
 [8] "GBR_NAME"   "FEAT_NAME"  "QLD_NAME"   "X_LABEL"    "GBR_ID"     "LOC_NAME_S" "LOC_NAME_L"
[15] "X_COORD"    "Y_COORD"    "Area_HA"    "GlobalID"   "Shape_STAr" "Shape_STLe"

> levels(gbr.sp$FEAT_NAME)

[1] "Cay"      "Island"   "Mainland" "Reef"     "Rock"     "Sand"    

Importing spatial data

Shapefiles and ggplot

> gbr.df <- tidy(gbr.sp, region='FEAT_NAME')
> ggplot(gbr.df, aes(y=lat, x=long, fill=id, group=group)) +
+     scale_x_continuous('', expand=c(0,0)) +
+     scale_y_continuous('', expand=c(0,0)) +
+     geom_polygon() + coord_map() + theme_classic() +
+         theme(panel.background=element_rect(fill=NA,color='black')) 

Importing spatial data

Shapefiles - cropping

> #gbr.sp.crop <- gIntersection(gbr.sp, reg, byid=TRUE) # does not honor data frame
> gbr.sp.crop <- raster:::intersect(gbr.sp, reg)
> gbr.tsv.df <- tidy(gbr.sp.crop, region='FEAT_NAME')
> ggplot(gbr.tsv.df, aes(y=lat, x=long, fill=id, group=group)) +
+     scale_x_continuous('', expand=c(0,0)) +
+     scale_y_continuous('', expand=c(0,0)) +
+     geom_polygon() + coord_map() + theme_classic() +
+     theme(panel.background=element_rect(fill=NA,color='black')) 

Importing spatial data

Shapefiles - cropping

> ggplot(gbr.tsv.df, aes(y=lat, x=long, fill=id, group=group)) +
+     scale_x_continuous('', expand=c(0,0)) +
+     scale_y_continuous('', expand=c(0,0)) +
+     geom_polygon() + coord_map() + theme_classic() +
+         theme(panel.background=element_rect(fill=NA,color='black'),
+               legend.position=c(0,0), legend.justification=c(0,0)) 

Data frame

> cots <- read.csv("../data/uthicke.csv",strip.white=T)
> summary(cots)

    Station      Latitude        Longitude         Larvae      
 COT002 : 1   Min.   :-19.10   Min.   :145.5   Min.   : 0.000  
 COT003 : 1   1st Qu.:-16.98   1st Qu.:145.6   1st Qu.: 0.000  
 COT004 : 1   Median :-15.92   Median :145.8   Median : 4.450  
 COT005 : 1   Mean   :-16.43   Mean   :145.9   Mean   : 8.964  
 COT006 : 1   3rd Qu.:-15.64   3rd Qu.:146.2   3rd Qu.:11.400  
 COT012 : 1   Max.   :-15.55   Max.   :146.9   Max.   :55.300  
 (Other):22                                                    

Mapping data

> ggplot(cots, aes(y=Latitude,x=Longitude)) + 
+     geom_point() + theme_classic() +
+         theme(panel.background=element_rect(fill=NA, color='black'))

Mapping data

> ggplot(cots, aes(y=Latitude,x=Longitude)) +
+     geom_polygon(data=gbr.df, aes(y=lat, x=long, fill=id, group=group)) +
+     geom_point() + theme_classic() +
+         theme(panel.background=element_rect(fill=NA, color='black'))

Mapping data

> bb = as(raster:::extent(cbind(cots$Longitude,cots$Latitude))+1,
+     "SpatialPolygons")
> gbr.cots.sp <- raster:::intersect(gbr.sp, bb)
> gbr.cots.df <- tidy(gbr.cots.sp, region='FEAT_NAME')
> ggplot(cots, aes(y=Latitude,x=Longitude)) +
+  geom_polygon(data=gbr.cots.df, aes(y=lat, x=long, fill=id, group=group)) +
+  geom_point() +
+  geom_rect(aes(ymin=-Inf, xmin=-Inf, ymax=Inf, xmax=Inf),
+               fill=NA, color='black')+
+  scale_x_continuous('', expand=c(0,0)) +
+  scale_y_continuous('', expand=c(0,0)) +
+  theme_classic() +
+  theme(legend.position=c(0,0), legend.justification=c(0,0))

Mapping data

> bb = as(raster:::extent(cbind(cots$Longitude,cots$Latitude))+1,
+     "SpatialPolygons")
> gbr.cots.sp <- raster:::intersect(gbr.sp, bb)
> gbr.cots.df <- tidy(gbr.cots.sp, region='FEAT_NAME')
> ggplot(cots, aes(y=Latitude,x=Longitude)) +
+  geom_polygon(data=gbr.cots.df, aes(y=lat, x=long, fill=id, group=group)) +
+  geom_point() +
+  geom_text(aes(label=Station),hjust=-0.1) + 
+  geom_rect(aes(ymin=-Inf, xmin=-Inf, ymax=Inf, xmax=Inf),
+               fill=NA, color='black')+
+  scale_x_continuous('', expand=c(0,0)) +
+  scale_y_continuous('', expand=c(0,0)) +
+  theme_classic() +
+  theme(legend.position=c(0,0), legend.justification=c(0,0))

Mapping data

Mapping data

> ggplot(cots, aes(y=Latitude,x=Longitude)) + 
+     geom_point(aes(size=Larvae), pch=21) +
+         theme(panel.background=element_rect(fill=NA, color='black'))

Mapping data

> cots = cots %>% mutate(Present=ifelse(Larvae==0,'N','Y'))
> ggplot(cots, aes(y=Latitude,x=Longitude)) + 
+   geom_point(aes(size=Larvae, fill=Present), pch=21) +
+   scale_fill_manual(values=c('red','green'),guide=FALSE)+
+   guides(size=guide_legend(override.aes=list(fill=c('red',rep('green',5))))) +
+   theme(plot.background=element_rect(fill=NA,color='black'),
+         panel.background=element_rect(fill=NA, color='black'),
+         legend.position=c(0,0),legend.justification=c(0,0)) 

Mapping data

Rasters

> library(ggmap)
> terrain <- get_map(location=c(146,-17.5), zoom=7, maptype="terrain")
> ggmap(terrain) +
+     geom_point(data=cots, aes(y=Latitude,x=Longitude))

Rasters

> library(ggmap)
> satellite <- get_map(location=c(146,-17.5), zoom=7, maptype="satellite")
> ggmap(satellite) +
+     geom_point(data=cots, aes(y=Latitude,x=Longitude), color='red')

Rasters

> library(ggmap)
> map <- get_googlemap(center=c(146,-17.5), scale=2,zoom=7, maptype="roadmap",
+   style='feature:road|visibility:off&style=element:labels|visibility:off')
> ggmap(map) +
+   geom_point(data=cots, aes(y=Latitude,x=Longitude), color='red')

Rasters

Rasters

> library(ggmap)
> ggmap(terrain) + 
+     geom_point(data=cots, aes(y=Latitude,x=Longitude), color='red')+
+         geom_rect(aes(ymin=-Inf, xmin=-Inf, ymax=Inf, xmax=Inf),
+                   fill=NA, color='black')+
+             scale_x_continuous('',expand=c(0,0))+
+                     scale_y_continuous('',expand=c(0,0))+          
+             coord_map(xlim=c(144.956, 147.363), ylim=c(-19.601, -15.0455)) +
+                 theme_classic()

Rasters

Rasters