emissv

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This package provides tools to create emissions (with a focus on vehicular emissions) for use in numeric air quality models such as WRF-Chem.

Installation

System dependencies

EmissV import functions from ncdf4 for reading model information, raster and sf to process grinded/geographic information and units. These packages need some aditional libraries:

To Ubuntu

The following steps are required for installation on Ubuntu:

  sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes
  sudo apt-get --yes --force-yes update -qq
  # netcdf dependencies:
  sudo apt-get install --yes libnetcdf-dev netcdf-bin
  # units/udunits2 dependency:
  sudo apt-get install --yes libudunits2-dev
  # sf dependencies (without libudunits2-dev):
  sudo apt-get install --yes libgdal-dev libgeos-dev libproj-dev

To Fedora

The following steps are required for installation on Fedora:

  sudo dnf update
  # netcdf dependencies:
  sudo yum install netcdf-devel
  # units/udunits2 dependency:
  sudo yum install udunits2-devel
  # sf dependencies (without libudunits2-dev):
  sudo yum install gdal-devel proj-devel proj-epsg proj-nad geos-devel

To Windows

No additional steps for windows installation.

Detailed instructions can be found at netcdf, libudunits2-dev and sf developers page.

conda (miniconda / anaconda)

First create a new environment called rspatial (or a better name):

  conda create -n rspatial -y
  conda activate rspatial

and to install some requisites:

  conda install -c conda-forge r-sf -y
  conda install -c conda-forge r-rgdal -y
  conda install -c conda-forge r-lwgeom -y

Package installation

To install the CRAN version (0.665.5.2):

install.packages("EmissV")

To install the development version (0.665.5.3) using remotes:

require("remotes")
remotes::install_github("atmoschem/EmissV")

or to install the development version (0.665.5.3) using devtools:

require("devtools")
devtools::install_github("atmoschem/EmissV")

Using `EmissV` with EDGAR 5.0 emissions

EmissV can be used to process emissions of atmospheric pollutants and green house gases from inventories such as EDGAR, RCP, GAINS and other datasets in NetCDF format, the GEIA-ACCENT and ECCAD emission data portal makes available some of these inventories. You can verify the supported format with:

EmissV::read()

To generate a simple emission it’s a straightforward process in 4 steps:

library(EmissV)
### 1. download the EDGAR Netcdf using the function get_edgar from the eixport R-package 
### or from the http://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/EDGAR/datasets/v50_AP/ 
### EDGAR 5.0 website and unzip inside a temporary directory
# create the temporary directory to download the data
dir.create(file.path(tempdir(), "EDGAR"))
# download the total emissions of NOx from EDGAR v50_AP for 2015
eixport::get_edgar(dataset = "v50_AP",
                   pol     = 'NOx',
                   sector  = "TOTALS",
                   year    = 2015,
                   type    = 'nc', ask = FALSE, copyright = FALSE,
                   destpath = file.path(tempdir(), "EDGAR"))
# unzip the file
unzip(zipfile = paste0(file.path(tempdir(), "EDGAR"),'/v50_NOx_2015.0.1x0.1.zip'),
      exdir   = paste0(file.path(tempdir(), "EDGAR")))

### 2. read the emissions (using the spec argument to split NOx into NO and NO2)
NOx <- read(paste0(file.path(tempdir(), "EDGAR"),'/v50_NOx_2015.0.1x0.1.nc'),
            version = 'EDGAR',
            spec    = c(E_NO  = 0.9 ,   # optional, 90% of NOx used to NO
                        E_NO2 = 0.1 ))  # optional, 10% of NOx uset to NO2

### 3. get the information from a WRF grid from a initial conditions file (wrfinput)
g   <- gridInfo(paste(system.file("extdata", package = "EmissV"),"/wrfinput_d01",sep=""))

### 4. calculate the emissions for grid g
NO  <- emission(grid = g, inventory = NOx$E_NO, pol = "NO", mm = 30.01,   plot = T)
NO2 <- emission(grid = g, inventory = NOx$E_NO2,pol = "NO2",mm = 46.0055, plot = T)

The next step is to save the emission in a emission file, the next example show how to save emissions using the eixport R-package:

library(eixport)
### create a temporary folder for emissions
dir.create(file.path(tempdir(), "EMISSION"))

### create the emision file
wrf_create(wrfinput_dir = system.file("extdata", package = "EmissV"),
           wrfchemi_dir = file.path(tempdir(), "EMISSION"),
           domains      = 1)
           
### get the file path of the emission file
emis_file <- list.files(path = file.path(tempdir(), "EMISSION"),
                        pattern = "wrfchemi_d01",
                        full.names = TRUE)

### save the emission
wrf_put(NO,  file = emis_file, name = "E_NO",  verbose = TRUE)
wrf_put(NO2, file = emis_file, name = "E_NO2", verbose = TRUE)

Check the wrf_create, wrf_put and to_wrf to more information and customize for your application.

NOTE: The emission file must be compatible with the WRF-Chem options (many arguments are the same as the namelist.input from WRF) check the eixport R-Package documentation and the WRF-Chem manual for more information.

Other R-packages are available to write netcdf such as ncdf4, RNetCDF, tidync are available on CRAN. Other languages such as NCL leanguage and the Python package wrf-python, and preprocessor anthro_emiss are aternative to write NetCDF files.

Using `EmissV` to estimate vehicular emissions

In EmissV the vehicular emissions are estimated by a top-down approach, i.e. the emissions are calculated using the statistical description of the fleet at avaliable level (National, Estadual, City, etc).The following steps show an example workflow for calculating vehicular emissions, these emissions are initially temporally and spatially disaggregated, and then distributed spatially and temporally.

I. Total: emission of pollutants is estimated from the fleet, use and emission factors and for the interest area (cities, states, countries, etc).

library(EmissV)

fleet <- vehicles(example = T)
# using a example of vehicles (DETRAN 2016 data and SP vahicle distribution):
#                              Category   Type Fuel      Use       SP ...
# Light Duty Vehicles Gasohol   LDV_E25    LDV  E25  41 km/d 11624342 ...
# Light Duty Vehicles Ethanol  LDV_E100    LDV E100  41 km/d   874627 ...
# Light Duty Vehicles Flex        LDV_F    LDV FLEX  41 km/d  9845022 ...
# Diesel Trucks               TRUCKS_B5 TRUCKS   B5 110 km/d   710634 ...
# Diesel Urban Busses           CBUS_B5    BUS   B5 165 km/d   792630 ...
# Diesel Intercity Busses       MBUS_B5    BUS   B5 165 km/d    21865 ...
# Gasohol Motorcycles          MOTO_E25   MOTO  E25 140 km/d  3227921 ...
# Flex Motorcycles               MOTO_F   MOTO FLEX 140 km/d   235056 ...

fleet <- fleet[,c(-6,-8,-9)] # dropping RJ, PR and SC

EF     <- emissionFactor(example = T)
# using a example emission factor (values calculated from CETESB 2015):
#                                     CO          PM
# Light duty Vehicles Gasohol  1.75 g/km 0.0013 g/km
# Light Duty Vehicles Ethanol 10.04 g/km 0.0000 g/km
# Light Duty Vehicles Flex     0.39 g/km 0.0010 g/km
# Diesel trucks                0.45 g/km 0.0612 g/km
# Diesel urban busses          0.77 g/km 0.1052 g/km
# Diesel intercity busses      1.48 g/km 0.1693 g/km
# Gasohol motorcycles          1.61 g/km 0.0000 g/km
# Flex motorcycles             0.75 g/km 0.0000 g/km

TOTAL  <- totalEmission(fleet,EF,pol = c("CO"),verbose = T)
# Total of CO : 1128297.0993334 t year-1

II. Spatial distribution: The package has functions to read information from tables, georeferenced images (tiff), shapefiles (sh), OpenStreet maps (osm), global inventories in NetCDF format (nc) to calculate point, line and area sources.

raster <- raster::raster(paste(system.file("extdata", package = "EmissV"),
                         "/dmsp.tiff",sep=""))

grid   <- gridInfo(paste(system.file("extdata", package = "EmissV"),
                   "/wrfinput_d02",sep=""))
# Grid information from: .../EmissV/extdata/wrfinput_d02

shape  <- raster::shapefile(paste(system.file("extdata", package = "EmissV"),
                            "/BR.shp",sep=""),verbose = F)[12,1]
Minas_Gerais <- areaSource(shape,raster,grid,name = "Minas Gerais")
# processing Minas Gerais area ...
# fraction of Minas Gerais area inside the domain = 0.0145921494236101

shape  <- raster::shapefile(paste(system.file("extdata", package = "EmissV"),
                            "/BR.shp",sep=""),verbose = F)[22,1]
Sao_Paulo <- areaSource(shape,raster,grid,name = "Sao Paulo")
# processing Sao Paulo area ...
# fraction of Sao Paulo area inside the domain = 0.474658563750987

sp::spplot(raster::merge(drop_units(TOTAL$CO[[1]]) * Sao_Paulo, 
                         drop_units(TOTAL$CO[[2]]) * Minas_Gerais),
           scales = list(draw=TRUE),ylab="Lat",xlab="Lon",
           main=list(label="Emissions of CO [g/d]"),
           col.regions = c("#031638","#001E48","#002756","#003062",
                           "#003A6E","#004579","#005084","#005C8E",
                           "#006897","#0074A1","#0081AA","#008FB3",
                           "#009EBD","#00AFC8","#00C2D6","#00E3F0"))

<em>Figure 1</em> - Emissions of CO using nocturnal lights.

III. Emission calculation: calculate the final emission from all different sources and converts to model units and resolution.

CO_emissions <- emission(TOTAL,"CO",list(SP = Sao_Paulo, MG = Minas_Gerais),grid,mm=28, plot = T)
# calculating emissions for CO using molar mass = 28 ...

<em>Figure 2</em> - CO emissions ready for use in air quality model.

IV. Temporal distribution: the package has a set of hourly profiles that represent the mean activity for each day of the week calculated from traffic counts of toll stations located in São Paulo city.

data(perfil)
names(perfil)

The package has additional functions for read netcdf data, create line and point sources (with plume rise) and to estimate the total emissions of of volatile organic compounds from exhaust (through the exhaust pipe), liquid (carter and evaporative) and vapor (fuel transfer operations).

Functions:

read: read global inventories in netcdf format
vehicles: tool to set-up vehicle data.table
emissionFactor: tool to set-up emission factors data.table
gridInfo: read grid information from a NetCDF file
pointSource: emissions from point sources
plumeRise: calculate plume rise
rasterSource: distribution of emissions by a georeferenced image
lineSource: distribution of emissions by line vectors
streetDist: distribution by OpenStreetnMap street (in progress)
areaSource: distribution of emissions by region
totalEmission: total emissions
emission: Emissions to atmospheric models
speciation: Speciation of emissions in different compounds

Sample datasets:

Species: species mapping tables
Perfil: vehicle counting profile for vehicular activity
Sample of an image of persistent lights of the Defense Meteorological Satellite Program (DMSP)
CETESB 2015 emission factors as emissionFactor(example=T)
DETRAN 2016 data and SP vahicle distribution as vehicles(example=T)
Shapefiles for Brazil states

Contributing

Bug reports, suggestions, and code contributions are all welcome. Please see CONTRIBUTING.md for details. Note that this project adopt the Contributor Code of Conduct and by participating in this project you agree to abide by its terms.