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Crash-Resilient Wrapper for get_soil()

Source: R/env_data_collection_src.R
get_soil_resumable.Rd

Downloads SoilGrids properties one environment at a time with the same checkpointing scheme as get_weather_resumable: each result is written to disk immediately and recorded in an append-only log, so a crashed run resumes with restart_from_log.

SoilGrids is rate-limited and slower than NASA POWER, which makes long soil jobs the most frequent victims of a mid-run failure.

Usage

get_soil_resumable(
  env.id = NULL,
  lat = NULL,
  lon = NULL,
  variables.names = "clay",
  depths = c("0-5cm", "5-15cm", "15-30cm", "30-60cm", "60-100cm", "100-200cm"),
  stat = c("mean", "q_5", "q_50", "q_95", "uncertainty"),
  dir.path = NULL,
  run.id = "soil_run",
  sleep = 20,
  tries = 3L,
  resume = TRUE,
  verbose = TRUE
)

Arguments

env.id, lat, lon, variables.names, depths, stat

Passed to get_soil.

dir.path

character. Parent directory. Default getwd().

run.id

character. Run directory name. Default "soil_run".

sleep

numeric. Seconds between environments. Default 20, matching get_soil; lowering it much invites throttling by ISRIC.

tries

integer. Retry attempts per environment. Default 3.

resume

logical. Skip environments already logged ok. Default TRUE.

verbose

logical. Print progress. Default TRUE.

Value

A data.frame of soil properties (wide by default), with attributes run.dir, n_ok, n_failed and failed.

Details

Results are stored long on disk, one row per property-depth, and reshaped to wide only at assembly. Storing long is what makes resumption safe: parts fetched at different times still stack correctly, whereas pre-widened parts could have mismatched columns.

See get_weather_resumable for the full checkpoint design.

See also

restart_from_log, read_progress_log, get_soil

Examples

if (FALSE) { # \dontrun{
## Long-running download job requiring access to SoilGrids.
grid <- data.frame(env = paste0("P", 1:200),
                   lat = runif(200, -13, -12),
                   lon = runif(200, -56, -55))

soil <- get_soil_resumable(
  env.id = grid$env, lat = grid$lat, lon = grid$lon,
  variables.names = c("clay", "sand", "silt", "soc", "phh2o"),
  run.id = "zoning_grid")

## After a crash, in a new session:
soil <- restart_from_log(run.id = "zoning_grid")

## Points in the ocean never resolve -- keep the successes
soil <- restart_from_log(run.id = "zoning_grid", retry.failed = FALSE)
} # }