WRF/Chem: Editing NetCDF (wrfchemi files) for own emissions
You can try the R package eixport, with wrf_put

# example
# Read the array emissions,
CO &lt;- wrf_get(file = "Path_to_WRFCHEMI", name = "E_CO")
# Change the values, here you should use your data
CO[] = rnorm(length(CO))
# Inyect your emissions into the wrfchemi
wrf_put(file = "Path_to_WRFCHEMI", name = "E_CO", POL = CO)



  How to deal with the speciation (my shapefile has only PM10 and
  PM2.5). where exactly do I place this in the new emissions file (the
  edited wrfchemi)I want. There are many pm species there (like pm2.5
  nucleation mode, pm, etc). I am not sure what weights to put on these.


You need to know the speciation for your local. At my department at Uni. of São Paulo, we use the following speciation of PM 2.5 (g/h/km^2)

e_so4i = 0.0077, e_so4j = 0.0623, e_no3i = 0.00247, e_no3j = 0.01053, e_pm2.5i = 0.1, e_pm2.5j = 0.3, e_orgi = 0.0304, e_orgj = 0.1296, e_eci = 0.056, e_ecj = 0.024, h2o = 0.277

Check this


  My emissions are not time dependent, and what do I do when I edit the
  wrfchemi file for this. (the wrfchemi files I have now are also not
  time dependent)


You need to first edit the namelist.wps and namelist.input to the desired length of time. Then, after running  ./real.exe you will have the wrfinput_d0x. At this stage you can use wrf_create which creates a wrfchemi file with 0. Read the manual to see if you want two 0-12z 12-0z files or one file with the length for all hours. Then you can use wrf_put. Just follow the example and read the manual.

You might also try the R package EmissV

References:


Ibarra-Espinosa et al., (2018). eixport: An R package to export
emissions to atmospheric models. Journal of Open Source Software,
3(24), 607, https://doi.org/10.21105/joss.00607 Schuch et al.,
(2018). 
EmissV: an R package to create vehicular and other emissions
for air quality models. Journal of Open Source Software, 3(30), 662,
https://doi.org/10.21105/joss.00662