R/oldScripts/GIS_source.R

In kimberly-bastille/sin-cat: Synthetic Indicator Catalogue

#tech-doc GIS sourcing

#Libraries
library(raster)
library(ncdf4)
library(rgdal)
library(maps)
library(mapdata)
library(dplyr)


#Colors for SST anomalies
colors <- colorRampPalette(c("darkblue",'blue', 'white', 'firebrick1',"firebrick4"))  
color_levels=100   

#GIS Directory
gis.dir <- here::here("gis")

#Data directory
data.dir <- here::here("data")

#Projection
map.crs <- CRS("+proj=longlat +lat_1=35 +lat_2=45 +lat_0=40 +lon_0=-77 +x_0=0
               +y_0=0 +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0")

#Bathymetry
bathy <- raster(paste0(gis.dir,"/NES_bathymetry.tif"))
e  <- extent(-78.5, -64, 33, 45)
bathy <- crop(bathy, e)

#Coastline
coast <- readOGR(gis.dir, 'NES_LME_coast', verbose = F)
coast <- spTransform(coast,map.crs)

#Extent for SST anomaly function
e  <- extent(-77.2, -64.2, 35, 48)

#Extent for thermal habitat
th_extent <-extent(-77,-65,35,45) 

#crop bathymetry
th <- crop(bathy,th_extent)

#projections
projection(th) <- map.crs
projection(bathy) <- map.crs

#get strata files to clip thermal habitat projections
strata <- readOGR(gis.dir,"strata", verbose = F)
strata@proj4string <- map.crs