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GenerateEnvtForcingFields.r
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##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
## GENERAL SETTINGS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
args <- commandArgs(trailingOnly = TRUE)
general <- list()
if (length(args) < 2) {
if(.Platform$OS.type == "windows") {
general$application <- "minitest" # ...or myfish
general$main_path_gis <- file.path("C:","Users","fbas","Documents","GitHub",paste("DISPLACE_input_gis_", general$application, sep=""))
general$main.path.ibm <- file.path("C:","Users","fbas","Documents","GitHub", paste("DISPLACE_input_", general$application, sep=''))
general$igraph <- 0 # caution: should be consistent with existing objects already built upon a given graph
do_plot <- TRUE
}
} else {
general$application <- args[1]
general$main_path_gis <- args[2]
general$main.path.ibm <- args[3]
general$igraph <- args[4] # caution: should be consistent with existing objects already built upon a given graph
do_plot <- FALSE
}
if(general$application=="testexample") name_GIS_file <- "habitat_landscapes" # this name used by the Objects Editor ui
if(general$application=="myfish") name_GIS_file <- "EUNIS_codes_Combined_ICES_FAO9_clipped" # this name used by the Objects Editor ui
if(general$application=="BalticSea") name_GIS_file <- "EUNIS_codes_Combined_ICES_FAO9_clipped" # this name used by the Objects Editor ui
if(general$application=="minitest") name_GIS_file <- "EUNIS_codes_Combined_ICES_FAO9_clipped" # this name used by the Objects Editor ui
##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
## THe ROUTINE !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!##
cat(paste("START \n"))
# load the DISPLACE graph
coord <- read.table(file=file.path(general$main_path_gis, "GRAPH",
paste("coord", general$igraph, ".dat", sep=""))) # build from the c++ gui
coord <- as.matrix(as.vector(coord))
coord <- matrix(coord, ncol=3)
coord <- cbind(coord, 1:nrow(coord))
colnames(coord) <- c('x', 'y', 'harb', 'pt_graph')
if(do_plot) plot(coord[,1], coord[,2])
graph <- read.table(file=file.path(general$main_path_gis , "GRAPH",
paste("graph", general$igraph, ".dat", sep=""))) # build from the c++ gui
graph <- as.matrix(as.vector(graph))
graph <- matrix(graph, ncol=3)
if(do_plot) segments(coord[graph[,1]+1,1], coord[graph[,1]+1,2], coord[graph[,2]+1,1], coord[graph[,2]+1,2], col=4)
# CAUTION: +1, because c++ to R
cat(paste("Read the graph....done\n"))
# adding initial values and vector fields per environmental forcing variable
# code_area / landscape / sst / salinity / wind / Nitrogen / Phosphorus / Oxygen / DissolvedCarbon
## CODE AREA (-10 if outside)
code_area <- 0 # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, code_area=code_area)
if(FALSE){
#------------------
# RASTER-----------
#------------------
library(maptools)
library(raster)
polPath <- file.path(general$main_path_gis, "HABITATS")
anf <- function(x) as.numeric(as.character(x))
#sh_coastlines <- readShapePoly(file.path(polPath,"francois_EU"))
## use point-raster overlay.......
library(raster)
landscapes <- raster(file.path(polPath, "habitat_landscapes.tif")) # probably need an update of rgdal here....
coord <- cbind(x=anf(coord[,'x']), y=anf(coord[,'y']))
# convert to UTM
library(sp)
library(rgdal)
SP <- SpatialPoints(cbind(as.numeric(as.character(coord[,'x'])), as.numeric(as.character(coord[,'y']))),
proj4string=CRS("+proj=longlat +datum=WGS84"))
coord <- cbind.data.frame(coord,
spTransform(SP,
CRS(paste("+proj=utm +zone=34 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0", sep=''))))
# convert to UTM
dd <- extract (landscapes, coord[,3:4]) # get the landscape on the coord points!
coord <- cbind(coord, landscapes_code=dd) # look at “Towards a representative MPA network in the Baltic Sea”.
} # end FALSE
if(TRUE){
#------------------
# RASTER-----------
#------------------
extractNodesOnRaster <- function (coord=coord,
general=general,
filename=file.path("Input_of_nutrients_Total_nitrogen", "Total nitrogen1.tif"),
namefield="nitrogen"){
library(maptools)
library(raster)
anf <- function(x) as.numeric(as.character(x))
#sh_coastlines <- readShapePoly(file.path(polPath,"francois_EU"))
## use point-raster overlay.......
library(raster)
raster_var <- raster(file.path(filename)) # probably need an update of rgdal here....
coord <- cbind(x=anf(coord[,'x']), y=anf(coord[,'y']))
# convert to UTM
library(sp)
library(rgdal)
SP <- SpatialPoints(cbind(as.numeric(as.character(coord[,'x'])), as.numeric(as.character(coord[,'y']))),
proj4string=CRS("+proj=longlat +datum=WGS84"))
coord <- cbind.data.frame(coord,
spTransform(SP,
CRS(paste(attributes(raster_var)$crs))))
dd <- extract (raster_var, coord[,3:4]) # get the landscape on the coord points!
coord <- cbind(coord, raster_var=dd) # look at “Towards a representative MPA network in the Baltic Sea”.
colnames(coord)[ncol(coord)] <- namefield
return(coord)
}
# calls
polPath <- file.path(general$main_path_gis, "HABITATS")
filename <- file.path(polPath, "Input_of_nutrients_Total_nitrogen", "Total nitrogen1.tif") # HELCOM HOLAS II Total nitrogen as µmol / l
dd <- extractNodesOnRaster (coord=coord, general=general, filename=filename, namefield="nitrogen")
nitrogen <- dd [,"nitrogen"]
nitrogen <- replace(nitrogen, is.na(nitrogen), 0)
polPath <- file.path(general$main_path_gis, "HABITATS")
filename <- file.path(polPath, "Input_of_nutrients_Total_phosphorus", "Total phosphorus1.tif") # HELCOM HOLAS II Total phosphorus as µmol / l
dd <- extractNodesOnRaster (coord=coord, general=general, filename=filename, namefield="phosphorus")
phosphorus <- dd [,"phosphorus"]
phosphorus <- replace(phosphorus, is.na(phosphorus), 0)
polPath <- file.path("D:","FBA")
filename <- file.path(polPath, "Bathy_GEBCO_1_min", "GRIDONE_1D.nc") # GRIDONE_1D
dd <- extractNodesOnRaster (coord=coord, general=general, filename=filename, namefield="bathymetry")
bathymetry <- dd [,"bathymetry"]
bathymetry <- replace(bathymetry, is.na(bathymetry), 0)
# check
plot(coord[,c(1,2)], col=cut(bathymetry, breaks=c(-10000,-1000, -200, -100, -50, -20, 10000)))
polPath <- file.path(general$main_path_gis, "SHIPPING")
filename <- file.path(polPath, "CargoPlusTank.tif") # HELCOM 2016
dd <- extractNodesOnRaster (coord=coord, general=general, filename=filename, namefield="shippingdensity")
shippingdensity <- dd [,"shippingdensity"]
shippingdensity <- replace(shippingdensity, is.na(shippingdensity), 0)
# check
plot(coord[,c(1,2)], col=cut(shippingdensity, breaks=c(-1,1000, 2000, 10000)))
polPath <- file.path(general$main_path_gis, "HABITATS")
filename <- file.path(polPath, "oxygen", "hypoxia_only_on_Figure8.tif") # from Gogina et al., Mapping hypoxia area only
dd <- extractNodesOnRaster (coord=coord, general=general, filename=filename, namefield="oxygen")
oxygen <- dd [,"oxygen"]
oxygen <- replace(oxygen, is.na(oxygen), 0)
} # end FALSE
if(TRUE){
## FROM A SHAPE FILE
#------------------
# SHAPE-----------
#------------------
library(maptools)
anf <- function(x) as.numeric(as.character(x))
## load shape.......
landscapes <- readShapePoly(file.path(general$main_path_gis, "HABITATS", name_GIS_file),
proj4string=CRS("+proj=longlat +datum=WGS84") ) # probably need an update of rgdal here....
cat(paste("Read GIS shape file (this one must include a hab_code field)...done\n"))
coords <- cbind(x=anf(coord[,'x']), y=anf(coord[,'y']))
# convert to UTM
library(sp)
library(rgdal)
spo <- SpatialPoints(cbind(as.numeric(as.character(coords[,'x'])), as.numeric(as.character(coords[,'y']))),
proj4string=CRS("+proj=longlat +datum=WGS84"))
# use the magic 'over' function to see in which polygon it is located
idx <- over(spo, landscapes); #print(idx)
coord <- cbind.data.frame(as.data.frame(coord), landscapes_code=NA)
coord$landscapes_code <- as.character(idx$hab_code)
cat(paste("overlay...done\n"))
# assign 0 to the NA code
coord[is.na(coord$landscapes_code), 'landscapes_code'] <- 0
# a visual check
if(do_plot) plot(coord[,1], coord[,2], col=coord[,'landscapes_code'])
} # end TRUE
## LANSCAPE (BENTHOS)
#landscape_code <- 0 # TODO: use input data to overlay a spatialPoints on a polygon shape
landscape_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
landscape_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
#coord <- cbind(coord, landscapes_code=landscape_code)
coord <- cbind(coord, landscape_norm=landscape_norm)
coord <- cbind(coord, landscape_alpha=landscape_alpha)
## wind speed
wind <- 12 # TODO: use input data to overlay a spatialPoints on a polygon shape
wind_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
wind_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, wind=wind)
coord <- cbind(coord, wind_norm=wind_norm)
coord <- cbind(coord, wind_alpha=wind_alpha)
## SST
sst <- 12 # TODO: use input data to overlay a spatialPoints on a polygon shape
sst_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
sst_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, sst=sst)
coord <- cbind(coord, sst_norm=sst_norm)
coord <- cbind(coord, sst_alpha=sst_alpha)
## salinity
salinity <- 20 # TODO: use input data to overlay a spatialPoints on a polygon shape
salinity_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
salinity_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, salinity=salinity)
coord <- cbind(coord, salinity_norm=salinity_norm)
coord <- cbind(coord, salinity_alpha=salinity_alpha)
## Nitrogen
#nitrogen <- 1 # TODO: use input data to overlay a spatialPoints on a polygon shape
nitrogen_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
nitrogen_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, nitrogen=nitrogen)
coord <- cbind(coord, nitrogen_norm=nitrogen_norm)
coord <- cbind(coord, nitrogen_alpha=nitrogen_alpha)
## Phosphorus
#phosphorus <- 1 # TODO: use input data to overlay a spatialPoints on a polygon shape
phosphorus_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
phosphorus_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, phosphorus=phosphorus)
coord <- cbind(coord, phosphorus_norm=phosphorus_norm)
coord <- cbind(coord, phosphorus_alpha=phosphorus_alpha)
## Oxygen
#oxygen <- 1 # Hypoxia area added from a raster file.....
oxygen_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
oxygen_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, oxygen=oxygen)
coord <- cbind(coord, oxygen_norm=oxygen_norm)
coord <- cbind(coord, oxygen_alpha=oxygen_alpha)
## DissolvedCarbon
dissolvedcarbon <- 1 # TODO: use input data to overlay a spatialPoints on a polygon shape
dissolvedcarbon_norm <- rlnorm(nrow(coord), meanlog=log(0.05),sdlog=log(1.5))
dissolvedcarbon_alpha <- rnorm(nrow(coord),90,sd=40) # TODO: use input data to overlay a spatialPoints on a polygon shape
coord <- cbind(coord, dissolvedcarbon=dissolvedcarbon)
coord <- cbind(coord, dissolvedcarbon_norm=dissolvedcarbon_norm)
coord <- cbind(coord, dissolvedcarbon_alpha=dissolvedcarbon_alpha)
## bathymetry
bathymetry <- bathymetry # using input data to overlay a spatialPoints on a raster
coord <- cbind(coord, bathymetry=bathymetry)
## Shippingdensity
shippingdensity <- shippingdensity # using input data to overlay a spatialPoints on a raster
coord <- cbind(coord, shippingdensity=shippingdensity)
if(ncol(coord) !=31) stop("check to get 31 fields!")
# colnames(coord)
#[1] "x" "y" "harb" "pt_graph" "code_area" "landscapes_code" "landscape_norm"
#[8] "landscape_alpha" "wind" "wind_norm" "wind_alpha" "sst" "sst_norm" "sst_alpha"
#[15] "salinity" "salinity_norm" "salinity_alpha" "nitrogen" "nitrogen_norm" "nitrogen_alpha" "phosphorus"
#[22] "phosphorus_norm" "phosphorus_alpha" "oxygen" "oxygen_norm" "oxygen_alpha" "dissolvedcarbon" "dissolvedcarbon_norm"
#[29] "dissolvedcarbon_alpha" "bathymetry", "shippingdensity"
# export
write.table(coord,
file=file.path(general$main.path.ibm, "graphsspe", paste0('environment_on_coord',general$igraph,'.dat')),
row.names=FALSE, col.names=TRUE, sep= ",", quote=FALSE)