Skip to contents

Process atmospheric composition data

Source: R/process.R
process_geos.Rd

The process_geos() function imports and cleans raw atmospheric composition data, returning a single SpatRaster object.

Usage

process_geos(
  date = c("2018-01-01", "2018-01-10"),
  variable = NULL,
  path = NULL,
  extent = NULL,
  daily_agg = FALSE,
  fun = "mean",
  ...
)

Arguments

date

character(1 or 2). Date (1) or start and end dates (2). Format YYYY-MM-DD (ex. September 1, 2023 = "2023-09-01").

variable

character(1). GEOS-CF variable name(s). See Notes for collection-specific variable-name guidance.

path

character(1). Directory with downloaded netCDF (.nc4) files.

extent

numeric(4) or SpatExtent giving the extent of the raster if NULL (default), the entire raster is loaded

daily_agg

logical(1). If TRUE, aggregate sub-daily layers to daily values using fun. Default FALSE preserves the original hourly output. Aggregation groups layers by variable/level and date so that pressure-level structure is preserved. Not meaningful for collections that are already daily.

fun

character(1). Aggregation function passed to terra::tapp() (e.g. "mean", "max", "min", "sum"). Ignored when daily_agg = FALSE.

...

Placeholders.

Value

a SpatRaster object;

Details

GEOS-CF netCDF collections currently supported by download_geos() are: "aqc_tavg_1hr_g1440x721_v1", "chm_tavg_1hr_g1440x721_v1", "met_tavg_1hr_g1440x721_x1", "xgc_tavg_1hr_g1440x721_x1", "chm_inst_1hr_g1440x721_p23", and "met_inst_1hr_g1440x721_p23".

Note

Layer names of the returned SpatRaster object contain the variable, pressure level, date, and hour when daily_agg = FALSE (default). When daily_agg = TRUE, layer names contain the variable, pressure level, and date only, and terra::time() is set to midnight UTC of each date.

Collection-specific variable names accepted by variable:

CollectionVariables
aqc_tavg_1hr_g1440x721_v1no2, co, so2, pm25_rh35_gcc, o3
chm_tavg_1hr_g1440x721_v1ocpi, bcpo, pm25soa_rh35_gc, dst4, prpe, macr, pm25ss_rh35_gcc, hno4, ch4, nh3, h2o2, rcho, hno3, dst1, pan, pm25oc_rh35_gcc, c3h8, soas, no, tolu, mvk, xyle, isop, noy, sala, so2, co, n2o5, eoh, o3, acet, c2h6, mek, nit, benz, soap, alk4, ocpo, ald2, hcho, pm25_rh35_gocar, dst3, pm25su_rh35_gcc, pm25_rh35_gcc, pm25ni_rh35_gcc, pm25bc_rh35_gcc, dst2, pm25du_rh35_gcc, bcpi, no2, salc, nh4
met_tavg_1hr_g1440x721_x1zl, zpbl, ps, v2m, v, q2m, u, t2m, troppb, q, t, v10m, t10m, u2m, q10m, ts, slp, cldtt, phis, tprec, u10m, rh
xgc_tavg_1hr_g1440x721_x1wetdepflx_nh4, aod550_dst6, wetdepflx_dst1, tropcol_io, totcol_o3, tropcol_hcho, drydepflx_bcpi, aod550_cloud, aod550_dst5, wetdepflx_hcho, aod550_salc, aod550_dust, wetdepflx_so2, wetdepflx_salc, wetdepflx_dst3, drydepflx_nit, wetdepflx_so4, aod550_sala, aod550_dst1, tropcol_co, wetdepflx_bcpi, drydepflx_sala, wetdepflx_nh3, tropcol_no2, wetdepflx_nit, aod550_sulfate, wetdepflx_ocpi, drydepflx_hcho, drydepflx_dst4, tropcol_so2, drydepflx_ocpi, tropcol_o3, drydepflx_nh4, aod550_dst7, totcol_co, totcol_so2, totcol_io, drydepflx_nh3, wetdepflx_sala, wetdepflx_dst4, drydepflx_o3, drydepflx_hno3, aod550_dst4, aod550_oc, totcol_no2, drydepflx_dst2, tropcol_bro, wetdepflx_bcpo, drydepflx_bcpo, wetdepflx_dst2, drydepflx_dst1, aod550_dst2, aod550_bc, aod550_dst3, wetdepflx_ocpo, drydepflx_dst3, drydepflx_salc, wetdepflx_hno3, drydepflx_ocpo, drydepflx_no2, totcol_hcho, totcol_bro
chm_inst_1hr_g1440x721_p23pm25soa_rh35_gc, pm25ss_rh35_gcc, so2, co, o3, pm25oc_rh35_gcc, pm25du_rh35_gcc, noy, no2, pm25ni_rh35_gcc, pm25bc_rh35_gcc, pm25_rh35_gcc, pm25su_rh35_gcc
met_inst_1hr_g1440x721_p23omega, t, eth, q, epv, rh, slp, airdens, ps, h, th, v, u, airvol_chem

variable matching is case-insensitive (for example, "o3" matches "O3").

Reference: NASA GEOS-CF OpenDAP catalog https://opendap.nccs.nasa.gov/dods/gmao/geos-cf/assim.

Author

Mitchell Manware

Examples

## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
##       amount of data which is not included in the package.
if (FALSE) { # \dontrun{
geos <- process_geos(
  date = c("2024-01-01", "2024-01-10"),
  variable = "O3",
  path = "./data/aqc_tavg_1hr_g1440x721_v1"
)
## daily mean across all sub-daily layers per variable/level
geos_daily <- process_geos(
  date = c("2024-01-01", "2024-01-10"),
  variable = "O3",
  path = "./data/aqc_tavg_1hr_g1440x721_v1",
  daily_agg = TRUE,
  fun = "mean"
)
} # }