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Observation and Modeling","monthly_downloads":336,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# EmissV \u003cimg src=\"man/figures/logo.png\" align=\"right\" alt=\"\" width=\"140\" /\u003e\n\u003c!-- badges: start --\u003e\n[![Licence:MIT](https://img.shields.io/github/license/hyperium/hyper.svg)](https://opensource.org/licenses/MIT) \n[![codecov](https://codecov.io/github/atmoschem/EmissV/graph/badge.svg?token=SDUpHzwgBh)](https://codecov.io/github/atmoschem/EmissV)\n[![R build status](https://github.com/atmoschem/EmissV/workflows/R-CMD-check/badge.svg)](https://github.com/atmoschem/EmissV/actions)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/EmissV)](http://cran.r-project.org/web/packages/EmissV)\n[![cran checks](https://badges.cranchecks.info/worst/EmissV.svg)](https://cran.r-project.org/web/checks/check_results_EmissV.html)\n[![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/EmissV)](https://cran.r-project.org/package=EmissV)\n[![metacran downloads](https://cranlogs.r-pkg.org/badges/EmissV)](https://cran.r-project.org/package=EmissV)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1451027.svg)](https://doi.org/10.5281/zenodo.1451027) \n[![status](http://joss.theoj.org/papers/071d027997ac93d8992099cb5010a044/status.svg)](http://joss.theoj.org/papers/071d027997ac93d8992099cb5010a044)\n\u003c!-- badges: end --\u003e  \n\nEmissV is a R-package that provides tools to create emissions for use in numeric air quality models such as [WRF-Chem](https://ruc.noaa.gov/wrf/wrf-chem/). The package can read inputs from global fluxes from inventories in Netcdf Format **[1]** or estimate the emissions using top-down approach for point/line/area sources **[2]**.\n\n**[1]** _Schuch D, Ibarra-Espinosa S, Dias de Freitas E, Andrade M (2018). “EmissV: A preprocessor for WRF-Chem model.” **Journal of Atmospheric Science Research**, 5, [doi:10.30564/jasr.v1i1.347](https://doi.org/10.30564/jasr.v1i1.347)_.\n\n**[2]** _Schuch D, Ibarra-Espinosa S, Dias de Freitas E (2018). “EmissV: An R package to create vehicular and other emissions by Top-down methods to air quality models.” **The Journal of Open Source Software**, 6, [doi:10.21105/joss.00662](https://doi.org/10.21105/joss.00662)_.\n\n## Installation\n\n### System dependencies \n\nEmissV import functions from [ncdf4](http://cran.r-project.org/package=ncdf4) for reading model information, [raster](http://cran.r-project.org/package=raster) and [sf](https://cran.r-project.org/web/packages/sf/index.html) to process grinded/geographic information and [units](https://github.com/edzer/units/). These packages need some aditional libraries: \n\n### To Ubuntu\nThe following steps are required for installation on Ubuntu:\n```bash\n  sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes\n  sudo apt-get --yes --force-yes update -qq\n  # netcdf dependencies:\n  sudo apt-get install --yes libnetcdf-dev netcdf-bin\n  # units/udunits2 dependency:\n  sudo apt-get install --yes libudunits2-dev\n  # sf dependencies (without libudunits2-dev):\n  sudo apt-get install --yes libgdal-dev libgeos-dev libproj-dev\n```\n\n### To Fedora\nThe following steps are required for installation on Fedora:\n```bash\n  sudo dnf update\n  # netcdf dependencies:\n  sudo yum install netcdf-devel\n  # units/udunits2 dependency:\n  sudo yum install udunits2-devel\n  # sf dependencies (without libudunits2-dev):\n  sudo yum install gdal-devel proj-devel proj-epsg proj-nad geos-devel\n```\n\n### To Windows\nNo additional steps for windows installation.\n\nDetailed instructions can be found at [netcdf](https://www.unidata.ucar.edu/software/netcdf/), [libudunits2-dev](https://r-quantities.github.io/units/) and [sf](https://r-spatial.github.io/sf/#installing) developers page.\n\n### To [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) (miniconda / anaconda)\n\nFirst create a new environment called rspatial *(or a better name)*:\n```bash\n  conda create -n rspatial -y\n  conda activate rspatial\n```\n\nand to install some requisites:\n```bash\n  conda install -c conda-forge r-sf -y\n  conda install -c conda-forge r-rgdal -y\n  conda install -c conda-forge r-lwgeom -y\n  conda install -c conda-forge r-raster -y\n```\n\n### Package installation\nTo install the *[CRAN](https://cran.r-project.org/package=EmissV) version*:\n\n```r\ninstall.packages(\"EmissV\")\n```\n\nTo install the *development version* using [remotes](https://CRAN.R-project.org/package=remotes):\n```r\nrequire(\"remotes\")\nremotes::install_github(\"atmoschem/EmissV\")\n```\nor to install the *development version* using [devtools](https://CRAN.R-project.org/package=devtools):\n```r\nrequire(\"devtools\")\ndevtools::install_github(\"atmoschem/EmissV\")\n```\n\n## Using `EmissV` with EDGAR 8.1 emissions\n\n`EmissV` can be used to process emissions of [atmospheric pollutants](https://en.wikipedia.org/wiki/Air_pollution#Sources) and [green house gases](https://en.wikipedia.org/wiki/Greenhouse_gas) from inventories such as [EDGAR](https://data.europa.eu/doi/10.2904/JRC_DATASET_EDGAR), [RCP](https://tntcat.iiasa.ac.at/RcpDb/dsd?Action=htmlpage\u0026page=welcome#), [GAINS](https://iiasa.ac.at/web/home/research/researchPrograms/air/GAINS.html) and other datasets in [NetCDF](https://www.unidata.ucar.edu/software/netcdf/) format, the [GEIA-ACCENT](http://accent.aero.jussieu.fr/database_table_inventories.php) and [ECCAD](https://eccad3.sedoo.fr/) emission data portal makes available some of these inventories. You can verify the supported format with:\n\n```r\nEmissV::read()\n```\n\nTo generate a simple emission it's a straightforward process in 4 steps:\n\n```r\nlibrary(EmissV)\n### 1. download the EDGAR 8.1 Netcdf flux file using R or from \n### https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/EDGAR/datasets\n# create the temporary directory to download the data\nfolder \u003c- file.path(tempdir(), \"EDGARv8.1\")\ndir.create(folder)\n# download the total emissions of NOx from EDGAR v50_AP for 2015\nurl     \u003c- \"https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/EDGAR/datasets\"\ndataset \u003c- \"v81_FT2022_AP_new/NOx/TOTALS/flx_nc\"\nfile    \u003c- \"v8.1_FT2022_AP_NOx_2022_TOTALS_flx_nc.zip\"\ndownload.file(paste0(url,\"/\",dataset,\"/\",file), paste0(folder,\"/\",file))\n# unzip the file\nunzip(paste0(folder,\"/\",file),exdir = folder)\n\n### 2. read the emissions (using the spec argument to split NOx into NO and NO2)\nnox  \u003c- read(file    = dir(path=folder, pattern=\"flx\\\\.nc\", full.names=TRUE),\n             version = \"EDGARv8\",\n             spec    = c(E_NO  = 0.9 ,   # 90% of NOx is NO\n                         E_NO2 = 0.1 ))  # 10% of NOx is NO2\n\n### 3. get the information from a WRF grid from a initial conditions file (wrfinput)\ng   \u003c- gridInfo(paste(system.file(\"extdata\", package = \"EmissV\"),\"/wrfinput_d01\",sep=\"\"))\n\n### 4. calculate the emissions for grid g\nNO  \u003c- emission(grid = g, inventory = NOx$E_NO, pol = \"NO\", mm = 30.01,   plot = T)\nNO2 \u003c- emission(grid = g, inventory = NOx$E_NO2,pol = \"NO2\",mm = 46.0055, plot = T)\n```\nThe next step is to save the emission in a emission file, the next example show how to save emissions using the [eixport](https://github.com/atmoschem/eixport) R-package:\n\n```r\nlibrary(eixport)\n### create a temporary folder for emissions\ndir.create(file.path(tempdir(), \"EMISSION\"))\n\n### create the emision file\nwrf_create(wrfinput_dir = system.file(\"extdata\", package = \"EmissV\"),\n           wrfchemi_dir = file.path(tempdir(), \"EMISSION\"),\n           domains      = 1)\n           \n### get the file path of the emission file\nemis_file \u003c- list.files(path = file.path(tempdir(), \"EMISSION\"),\n                        pattern = \"wrfchemi_d01\",\n                        full.names = TRUE)\n\n### save the emission\nwrf_put(NO,  file = emis_file, name = \"E_NO\",  verbose = TRUE)\nwrf_put(NO2, file = emis_file, name = \"E_NO2\", verbose = TRUE)\n```\n\nCheck the [wrf_create](https://atmoschem.github.io/eixport/reference/wrf_create.html), [wrf_put](https://atmoschem.github.io/eixport/reference/wrf_put.html) and [to_wrf](https://atmoschem.github.io/eixport/reference/to_wrf.html) to more information and customize for your application.\n\n**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](https://atmoschem.github.io/eixport/reference/wrf_create.html) R-Package documentation and the [WRF-Chem manual](https://ruc.noaa.gov/wrf/wrf-chem/Users_guide.pdf) for more information.\n\nOther R-packages are available to write netcdf such as [ncdf4](https://CRAN.R-project.org/package=ncdf4), [RNetCDF](https://CRAN.R-project.org/package=RNetCDF), [tidync](https://CRAN.R-project.org/package=tidync) are available on [CRAN](https://cran.r-project.org/). Other languages such as [NCL leanguage](https://www.ncl.ucar.edu/) and the Python package [wrf-python](https://wrf-python.readthedocs.io/en/latest/), and preprocessor [anthro_emiss](https://www2.acom.ucar.edu/wrf-chem/wrf-chem-tools-community) are aternative to write NetCDF files.\n\n## Using `EmissV` to estimate vehicular emissions\n\nIn 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.\n\n**I.** Total: emission of pollutants is estimated from the fleet, use and emission factors and for the interest area (cities, states, countries, etc).\n\n``` r\nlibrary(EmissV)\n\nfleet \u003c- vehicles(example = T)\n# using a example of vehicles (DETRAN 2016 data and SP vahicle distribution):\n#                              Category   Type Fuel      Use       SP ...\n# Light Duty Vehicles Gasohol   LDV_E25    LDV  E25  41 km/d 11624342 ...\n# Light Duty Vehicles Ethanol  LDV_E100    LDV E100  41 km/d   874627 ...\n# Light Duty Vehicles Flex        LDV_F    LDV FLEX  41 km/d  9845022 ...\n# Diesel Trucks               TRUCKS_B5 TRUCKS   B5 110 km/d   710634 ...\n# Diesel Urban Busses           CBUS_B5    BUS   B5 165 km/d   792630 ...\n# Diesel Intercity Busses       MBUS_B5    BUS   B5 165 km/d    21865 ...\n# Gasohol Motorcycles          MOTO_E25   MOTO  E25 140 km/d  3227921 ...\n# Flex Motorcycles               MOTO_F   MOTO FLEX 140 km/d   235056 ...\n\nfleet \u003c- fleet[,c(-6,-8,-9)] # dropping RJ, PR and SC\n\nEF     \u003c- emissionFactor(example = T)\n# using a example emission factor (values calculated from CETESB 2015):\n#                                     CO          PM\n# Light duty Vehicles Gasohol  1.75 g/km 0.0013 g/km\n# Light Duty Vehicles Ethanol 10.04 g/km 0.0000 g/km\n# Light Duty Vehicles Flex     0.39 g/km 0.0010 g/km\n# Diesel trucks                0.45 g/km 0.0612 g/km\n# Diesel urban busses          0.77 g/km 0.1052 g/km\n# Diesel intercity busses      1.48 g/km 0.1693 g/km\n# Gasohol motorcycles          1.61 g/km 0.0000 g/km\n# Flex motorcycles             0.75 g/km 0.0000 g/km\n\nTOTAL  \u003c- totalEmission(fleet,EF,pol = c(\"CO\"),verbose = T)\n# Total of CO : 1128297.0993334 t year-1\n```\n\n**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.\n\n``` r\nraster \u003c- raster::raster(paste(system.file(\"extdata\", package = \"EmissV\"),\n                         \"/dmsp.tiff\",sep=\"\"))\n\ngrid   \u003c- gridInfo(paste(system.file(\"extdata\", package = \"EmissV\"),\n                   \"/wrfinput_d02\",sep=\"\"))\n# Grid information from: .../EmissV/extdata/wrfinput_d02\n\nshape  \u003c- raster::shapefile(paste(system.file(\"extdata\", package = \"EmissV\"),\n                            \"/BR.shp\",sep=\"\"),verbose = F)[12,1]\nMinas_Gerais \u003c- areaSource(shape,raster,grid,name = \"Minas Gerais\")\n# processing Minas Gerais area ...\n# fraction of Minas Gerais area inside the domain = 0.0145921494236101\n\nshape  \u003c- raster::shapefile(paste(system.file(\"extdata\", package = \"EmissV\"),\n                            \"/BR.shp\",sep=\"\"),verbose = F)[22,1]\nSao_Paulo \u003c- areaSource(shape,raster,grid,name = \"Sao Paulo\")\n# processing Sao Paulo area ...\n# fraction of Sao Paulo area inside the domain = 0.474658563750987\n\nsp::spplot(raster::merge(drop_units(TOTAL$CO[[1]]) * Sao_Paulo, \n                         drop_units(TOTAL$CO[[2]]) * Minas_Gerais),\n           scales = list(draw=TRUE),ylab=\"Lat\",xlab=\"Lon\",\n           main=list(label=\"Emissions of CO [g/d]\"),\n           col.regions = c(\"#031638\",\"#001E48\",\"#002756\",\"#003062\",\n                           \"#003A6E\",\"#004579\",\"#005084\",\"#005C8E\",\n                           \"#006897\",\"#0074A1\",\"#0081AA\",\"#008FB3\",\n                           \"#009EBD\",\"#00AFC8\",\"#00C2D6\",\"#00E3F0\"))\n```\n![*Figure 1* - Emissions of CO using nocturnal lights.](https://raw.githubusercontent.com/atmoschem/EmissV/master/CO_all.png)\n\n**III.** Emission calculation: calculate the final emission from all different sources and converts to model units and resolution.\n``` r\nCO_emissions \u003c- emission(total = TOTAL,\n                         pol   = \"CO\",\n                         area  = list(SP = Sao_Paulo, MG = Minas_Gerais),\n                         grid  = grid,\n                         mm    = 28, \n                         plot  = T)\n# calculating emissions for CO using molar mass = 28 ...\n```\n![*Figure 2* - CO emissions ready for use in air quality model.](https://raw.githubusercontent.com/atmoschem/EmissV/master/CO_final.png)\n\n**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.\n``` r\ndata(perfil)\nnames(perfil)\n```\n\nThe 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).\n\nFunctions:\n\n- [read](https://atmoschem.github.io/EmissV/reference/read.html): read global inventories in netcdf format\n- [vehicles](https://atmoschem.github.io/EmissV/reference/vehicles.html): tool to set-up vehicle data.table\n- [emissionFactor](https://atmoschem.github.io/EmissV/reference/emissionFactor.html): tool to set-up emission factors data.table\n- [gridInfo](https://atmoschem.github.io/EmissV/reference/gridInfo.html): read grid information from a NetCDF file\n- [pointSource](https://atmoschem.github.io/EmissV/reference/pointSource.html): emissions from point sources\n- [plumeRise](https://atmoschem.github.io/EmissV/reference/plumeRise.html): calculate plume rise\n- [rasterSource](https://atmoschem.github.io/EmissV/reference/rasterSource.html): distribution of emissions by a georeferenced image\n- [lineSource](https://atmoschem.github.io/EmissV/reference/lineSource.html): distribution of emissions by line vectors\n- [areaSource](https://atmoschem.github.io/EmissV/reference/areaSource.html): distribution of emissions by region\n- [totalEmission](https://atmoschem.github.io/EmissV/reference/totalEmission.html): total emissions\n- [emission](https://atmoschem.github.io/EmissV/reference/emission.html): Emissions to atmospheric models\n- [speciation](https://atmoschem.github.io/EmissV/reference/speciation.html): Speciation of emissions in different compounds\n\nSample datasets:\n\n- [Species](https://atmoschem.github.io/EmissV/reference/species.html): species mapping tables\n- [Perfil](https://atmoschem.github.io/EmissV/reference/perfil.html): vehicle counting profile for vehicular activity\n- Sample of an image of persistent lights of the Defense Meteorological Satellite Program (DMSP)\n- CETESB 2015 emission factors as ```emissionFactor(example=T)```\n- DETRAN 2016 data and SP vahicle distribution as ```vehicles(example=T)```\n- Shapefiles for Brazil states\n\n\n### Contributing\n\nBug reports, suggestions, and code contributions are all welcome. Please see [CONTRIBUTING.md](https://github.com/atmoschem/EmissV/blob/master/CONTRIBUTING.md) for details. Note that this project adopt the [Contributor Code of Conduct](https://github.com/atmoschem/EmissV/blob/master/CONDUCT.md) and by participating in this project you agree to abide by its terms.\n\n\n### License\n\nEmissV is published under the terms of the [MIT License](https://opensource.org/licenses/MIT). Copyright [(c)](https://raw.githubusercontent.com/atmoschem/emissv/master/LICENSE) 2018 Daniel Schuch.\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.1451027","https://doi.org/10.30564/jasr.v1i1.347)_","https://doi.org/10.21105/joss.00662)_"],"works":{"https://doi.org/10.5281/zenodo.1451027":null},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["atmoschem","atmospheric-sciences","emissions-model","vehicular-emissions-inventories","vein","exporting-emissions","wrf"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/81461","html_url":"https://ost.ecosyste.ms/projects/81461"}