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Set arguments for the calculation process

Source: R/set_arguments.R
set_args_calc.Rd

This function sets the arguments for the calculation process. It takes several parameters including site ID, time ID, time period, extent, user email, export path, and input path.

Usage

set_args_calc(
  char_siteid = "site_id",
  char_timeid = "time",
  char_period = c("2018-01-01", "2022-10-31"),
  num_extent = c(-126, -62, 22, 52),
  char_user_email = paste0(Sys.getenv("USER"), "@nih.gov"),
  export = FALSE,
  path_export = "inst/targets/calc_spec.qs",
  char_input_dir = "input",
  nthreads_nasa = 14L,
  nthreads_tri = 5L,
  nthreads_geoscf = 10L,
  nthreads_gmted = 4L,
  nthreads_narr = 24L,
  nthreads_groads = 3L,
  nthreads_population = 3L,
  nthreads_append = 8L,
  nthreads_impute = 64L
)

Arguments

char_siteid

Character string specifying the site ID. Default is "site_id".

char_timeid

Character string specifying the time ID. Default is "time".

char_period

Character vector specifying the time period. Default is c("2018-01-01", "2022-10-31").

num_extent

Numeric vector specifying the extent. Default is c(-126, -62, 22, 52).

char_user_email

Character string specifying the user email. Default is the current user's email with nih.gov domain.

export

logical(1). If TRUE, the list for the calculation process is exported to path_export. Default is FALSE.

path_export

Character string specifying the export path. Default is "inst/targets/calc_spec.qs".

char_input_dir

Character string specifying the input path. Default is "input".

nthreads_nasa

integer(1). Number of threads for NASA data. Default is 14L.

nthreads_tri

integer(1). Number of threads for TRI data. Default is 5L.

nthreads_geoscf

integer(1). Number of threads for GEOSCF data. Default is 10L.

nthreads_gmted

integer(1). Number of threads for GMTED data. Default is 4L.

nthreads_narr

integer(1). Number of threads for NARR data. Default is 24L.

nthreads_groads

integer(1). Number of threads for GROADS data. Default is 3L.

nthreads_population

integer(1). Number of threads for population data. Default is 3L.

nthreads_append

integer(1). Number of threads for appending data. Default is 8L.

nthreads_impute

integer(1). Number of threads for imputing data. Default is 64L.

Value

A list of arguments for common use in the calculation process. A *.qs or *.rds file defined in path_export is saved if export is TRUE.

  • char_siteid: Character string specifying the site ID.

  • char_timeid: Character string specifying the time ID.

  • char_period: Character vector specifying the time period.

  • num_extent: Numeric vector specifying the extent.

  • char_user_email: Character string specifying the user email.

  • char_input_dir: Character string specifying the input path.

  • nthreads_nasa: Number of threads for NASA data.

  • nthreads_tri: Number of threads for TRI data.

  • nthreads_geoscf: Number of threads for GEOS-CF data.

  • nthreads_gmted: Number of threads for GMTED data.

  • nthreads_narr: Number of threads for NARR data.

  • nthreads_groads: Number of threads for SEDAC Groads data.

  • nthreads_population: Number of threads for population data.

  • nthreads_append: Number of threads for appending data.

  • nthreads_impute: Number of threads for imputing data.

Note

The number of threads used is fixed as 1L otherwise specified in nthreads_* arguments. path_input should contain the following subdirectories:

  • modis/raw/61/MOD11A1

  • modis/raw/61/MOD06_L2

  • modis/raw/61/MOD09GA

  • modis/raw/61/MCD19A2

  • modis/raw/61/MOD13A2

  • modis/raw/5000/VNP46A2

  • aqs

  • nlcd

  • geos/aqc_tavg_1hr_g1440x721_v1

  • geos/chm_tavg_1hr_g1440x721_v1

  • HMS_Smoke/data

  • gmted

  • nei

  • narr

  • HMS_Smoke

  • koppen_geiger

  • ecoregions

  • sedac_groads

  • sedac_population

Author

Insang Song