Paper 😃 Accepted 😃 on GMD 🎉🎉!

Our paper was just accepted on GMD

https://www.geosci-model-dev-discuss.net/gmd-2017-193/

Vein Package

Vehicular Emissions INventory (VEIN) model.

Please read the documentation.

System requirements

vein imports functions from spatial packages listed below. In order to install these packages, firstly the user must install the requirements mentioned here.

Packages needed

After installing system dependencies, you need these packages:

In order to run the demo, this package is also needed:

ggplot2

Installation

VEIN can be installed via CRAN or github

library(devtools) 
install_github("atmoschem/vein")
library(vein)
demo(VEIN)

install.packages("vein")
library(vein)
demo(VEIN)

What is VEIN

Vehicular Emissions Inventories. An R package to estimate vehicular emissions. It currently covers the following pollutants in speed functions:

Criteria: “CO”, “NOx”, “HC”, “PM”, “CH4”, “NMHC”, “CO2”, “SO2”, “Pb”, “FC” (Fuel Consumption).
PAH and POP: “indeno(1,2,3-cd)pyrene”, “benzo(k)fluoranthene”, “benzo(b)fluoranthene”, “benzo(ghi)perylene”, “fluoranthene”, “benzo(a)pyrene”, “pyrene”, “perylene”, “anthanthrene”, “benzo(b)fluorene”, “benzo(e)pyrene”, “triphenylene”, “benzo(j)fluoranthene”, “dibenzo(a,j)anthacene”, “dibenzo(a,l)pyrene”, “3,6-dimethyl-phenanthrene”, “benzo(a)anthracene”, “acenaphthylene”, “acenapthene”, “fluorene”, “chrysene”, “phenanthrene”, “napthalene”, “anthracene”, “coronene”, “dibenzo(ah)anthracene”
Dioxins and Furans: “PCDD”, “PCDF”, “PCB”.
Metals: “As”, “Cd”, “Cr”, “Cu”, “Hg”, “Ni”, “Pb”, “Se”, “Zn”.
NMHC:
ALKANES: “ethane”, “propane”, “butane”, “isobutane”, “pentane”, “isopentane”, “hexane”, “heptane”, “octane”, “TWO_methylhexane”, “nonane”, “TWO_methylheptane”, “THREE_methylhexane”, “decane”, “THREE_methylheptane”, “alcanes_C10_C12”, “alkanes_C13”.
CYCLOALKANES: “cycloalcanes”.
ALKENES: “ethylene”, “propylene”, “propadiene”, “ONE_butene”, “isobutene”, “TWO_butene”, “ONE_3_butadiene”, “ONE_pentene”, “TWO_pentene”, “ONE_hexene”, “dimethylhexene”.
ALKYNES:“ONE_butine”, “propine”, “acetylene”.
ALDEHYDES: “formaldehyde”, “acetaldehyde”, “acrolein”, “benzaldehyde”, “crotonaldehyde”, “methacrolein”, “butyraldehyde”, “isobutanaldehyde”, “propionaldehyde”, “hexanal”, “i_valeraldehyde”, “valeraldehyde”, “o_tolualdehyde”, “m_tolualdehyde”, “p_tolualdehyde”.
KETONES: “acetone”, “methylethlketone”.
AROMATICS: “toluene”, “ethylbenzene”, “m_p_xylene”, “o_xylene”, “ONE_2_3_trimethylbenzene”, “ONE_2_4_trimethylbenzene”, “ONE_3_5_trimethylbenzene”, “styrene”, “benzene”, “C9”, “C10”, “C13”.

Also, somre Brazilian emission factors and speciations for WRF-Chem, mechanisms:

e_eth e_hc3 e_hc5 e_hc8 e_ol2 e_olt e_oli e_iso e_tol e_xyl e_c2h5oh e_ald e_hcho e_ch3oh e_ket E_SO4i E_SO4j E_NO3i E_NO3j E_MP2.5i E_MP2.5j E_ORGi E_ORGj E_ECi E_ECj H2O

What is new?

I decided to jump into a new ‘minor’ version because it brings lots of cool improvements.

vein imports sf functions.
R packages -raster-, -rgdal- and -rgeos- not needed anymore.
vein now imports data-table.
Add class GriddedEmissionsArray.
Fix #28, data.table imported in emis_grid. Now it is very fast!
Fix #49: Documentation in inventory est.
Fix #50: Fix repetition of x_DF.
Fix #51: deparse text.
Fix #52: separate objects in rm with ‘,’
Fix #55.
Minor fix on demo(VEIN).
emis and emis_cold adjust length of ef by length of columns of first element of the list of data-frames.
Revised all examples.
returns sf in temp_fact, netspeed and emis_post! (0.3.17)

Check the NEWS

future steps

Add more support to sf.
Estimation of evaporative emissions with Copert Tier 3.
More speciations.
A book (hopefully released in 2018).

How does it work?

VEIN consist of: “Elaboration of vehicular emissions inventories, consisting in four stages, 1) pre-processing activity data, 2) preparing emissions factors, 3) estimating the emissions and 4) post-processing of emissions in maps and databases.”

This implies the use of several functions in a coordinates ans structured way, therefore it is added the new function inventory which creates a structured set of directories and scripts to run VEIN. Please, open the file ‘main.R’ and run each line to understand VEIN. Remember, if you have doubts with any function, just type ‘?’ with the name of the function. For intance: ?inventory.

library(vein)
inventory(name = file.path(tempdir(), "YourCity"), show.dir = T,
          show.scripts = T)

## files at /tmp/RtmpiGkKOE/YourCity

## Directories:
##  [1] "/tmp/RtmpiGkKOE/YourCity"             
##  [2] "/tmp/RtmpiGkKOE/YourCity/ef"          
##  [3] "/tmp/RtmpiGkKOE/YourCity/emi"         
##  [4] "/tmp/RtmpiGkKOE/YourCity/emi/BUS_01"  
##  [5] "/tmp/RtmpiGkKOE/YourCity/emi/HGV_01"  
##  [6] "/tmp/RtmpiGkKOE/YourCity/emi/LCV_01"  
##  [7] "/tmp/RtmpiGkKOE/YourCity/emi/MC_01"   
##  [8] "/tmp/RtmpiGkKOE/YourCity/emi/PC_01"   
##  [9] "/tmp/RtmpiGkKOE/YourCity/est"         
## [10] "/tmp/RtmpiGkKOE/YourCity/images"      
## [11] "/tmp/RtmpiGkKOE/YourCity/network"     
## [12] "/tmp/RtmpiGkKOE/YourCity/post"        
## [13] "/tmp/RtmpiGkKOE/YourCity/post/df"     
## [14] "/tmp/RtmpiGkKOE/YourCity/post/grids"  
## [15] "/tmp/RtmpiGkKOE/YourCity/post/streets"
## [16] "/tmp/RtmpiGkKOE/YourCity/profiles"    
## [17] "/tmp/RtmpiGkKOE/YourCity/veh"         
## Scripts:
## [1] "est/BUS_01_input.R" "est/HGV_01_input.R" "est/LCV_01_input.R"
## [4] "est/MC_01_input.R"  "est/PC_01_input.R"  "main.R"            
## [7] "post.R"             "traffic.R"

Please, read the examples in the documentation of each function and run the demo.

1) Examples with traffic data:

age functions

data("net")
PC_E25_1400 <- age_ldv(x = net$ldv, name = "PC_E25_1400")

## Average age of PC_E25_1400 is 11.17

## Number of PC_E25_1400 is 1946.95 * 10^3 veh

plot(PC_E25_1400, xlab = "age of use")

## 
## Average =  11.17

If you want to know the vehicles per street and by age of use, just add the net. Age functions now returns ‘sf’ objects if the net argument is present.

PC_E25_1400net <- age_ldv(x = net$ldv, name = "PC_E25_1400", net = net)

## Average age of PC_E25_1400 is 11.17

## Number of PC_E25_1400 is 1946.95 * 10^3 veh

sp::spplot(as(PC_E25_1400net, "Spatial"),
       c("PC_E25_1400_1", "PC_E25_1400_9"),
       main = "PC by age of use", scales = list(draw = T),
       col.regions = rev(cptcity::cpt()))

temporal factors and netspeed

data("net")
data("pc_profile")
pc_week <- temp_fact(net$ldv+net$hdv, pc_profile)
dfspeed <- netspeed(pc_week, net$ps, net$ffs, net$capacity, net$lkm, alpha = 1.5)
class(dfspeed)

## [1] "Speed"      "data.frame"

plot(dfspeed, xlab = "Hours", ylab = "Speed [km/h]")

If you want ot check the speed at different hours by street, just add net:

dfspeednet <- netspeed(pc_week, net$ps, net$ffs, net$capacity, net$lkm,
                       alpha = 1.5, net = net)
sp::spplot(as(dfspeednet, "Spatial"),
       c("S1", "S9"), scales = list(draw = T),
       col.regions = rev(cptcity::cpt()))

2) Emission Factors

V <- 0:150
ef1 <- ef_ldv_speed(v = "PC",t = "4S", cc = "<=1400", f = "G", eu = "PRE",
p = "CO")
efs <- EmissionFactors(ef1(1:150))
plot(Speed(1:150), efs, xlab = "speed[km/h]", type = "b", pch = 16)

3) Estimation of emissions

euro <- c(rep("V", 5), rep("IV", 5), rep("III", 5), rep("II", 5),
          rep("I", 5), rep("PRE", 15))
lef <- lapply(1:40, function(i) {
ef_ldv_speed(v = "PC", t = "4S", cc = "<=1400", f = "G",
          eu = euro[i], p = "CO", show.equation = FALSE) })
E_CO <- emis(veh = PC_E25_1400, lkm = net$lkm, ef = lef, speed = dfspeed,
             profile = pc_profile)

## Number of columns of 'veh' is different than length of 'ef'

## adjusting length of ef to the number of colums of 'veh'

## 139727.29 kg emissions in 24 hours and 7 days

plot(E_CO, xlab = "Hours", ylab = "[g/h]")

4) Post Emissions

E_CO_STREETS <- emis_post(arra = E_CO, pollutant = "CO", by = "streets_wide")

make a grid. If you plan to run WRF, use:

when spobj is “character”, it is a path to wrfinput file and then runs eixport::wrf_grid to create a grid based on a wrf_input file.

Create a grid using make_grid.The spobj is the spatial net
spobj is “character”, it is a path to wrfinput file and the grid will have the size of the wrf_input.

data(net)
E_CO_STREETSnet <- emis_post(arra = E_CO, pollutant = "CO", by = "streets_wide",
                             net = net)
g <- make_grid(net, 1/102.47/2) #500m in degrees

## Number of lon points: 23
## Number of lat points: 19

E_CO_g <- emis_grid(spobj = E_CO_STREETSnet, g = g, sr= 31983)

## Transforming spatial objects to 'sr'

## Sum of street emissions 139727288.63
## Sum of gridded emissions 139727288.63

sp::spplot(as(E_CO_g, "Spatial"),
       c("V1", "V9"), scales = list(draw = T),
       col.regions = rev(cptcity::cpt()))

Creating a WRFChem Input file using eixport:

If you created a grid using a wrfinput file and then ran emis_gris to grid your emissions, create a GriddedEmissionsArray and then use

eixport::wrf_create to create a wrfchem input file with 0.
eixport::wrf_put to the wrfchem input file.

eixport::wrf_create(wrfinput_dir = "PathToWrfInput", wrfchemi_dir = "OutputPathWrfChemInput")
gwrf <- eixport::wrf_grd("PathToWrfInput")
E_CO_gwrf <- emis_grid(spobj = E_CO_STREETSnet, g = gwrf)
gr <- GriddedEmissionsArray(E_CO_gwrf, rows = 19, cols = 23, times = 168, T)
eixport::wrf_put(file = "PathToWRFChemInputFile, name = "E_CO", POL = gr)

If you created a grid using a spatial net, use vein::wmis_wrf or eixport::as4wrf and get the NCL script AS4WRF.ncl from the developer.

Thanks and enjoy VEIN!

Citation

If you use VEIN, please, cite it:

Ibarra-Espinosa, S., Ynoue, R., O’Sullivan, S., Pebesma, E., Andrade, M. D. F., and Osses, M. (2017). VEIN v0.2.2: an R package for bottom-up Vehicular Emissions Inventories Geosci. Model Dev. Discus, https://doi.org/10.5194/gmd-2017-193, in accepted, 2017.

https://doi.org/10.5194/gmd-2017-193

Communications, doubts etc

There is a group about this VEIN here https://groups.google.com/forum/#!forum/veinmodel
Eventually you can ask on Eart Science Stackoverflow,

Issues

If you encounter any issues while using VEIN, please submit your issues to: https://github.com/atmoschem/vein/issues/

If you have any suggestions just let me know to sergio.ibarra@usp.br.

Contributing

Please, read this guide. Contributions of all sorts are welcome, issues and pull requests are the preferred ways of sharing them. When contributing pull requests, please follow the Google’s R Style Guide. This project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

VEIN model

Sergio Ibarra-Espinosa

19 de Octubre de 2016