diff --git a/docs/configuration.md b/docs/configuration.md index def764a..2c9577b 100644 --- a/docs/configuration.md +++ b/docs/configuration.md @@ -72,17 +72,17 @@ str(receptors) ### Model control -| Arg | Description | -| --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `n_hours` | Number of hours to run each simulation; negative indicates backward in time | -| `numpar` | number of particles to be run; defaults to 200 | -| `rm_dat` | Logical indicating whether to delete `PARTICLE.DAT` after each simulation. Default to TRUE to reduce disk space since all of the trajectory information is also stored in `STILT_OUTPUT.rds` alongside the calculated upstream influence footprint | -| `run_foot` | Logical indicating whether to produce footprints. If FALSE, `run_trajec` must be TRUE. This can be useful when calculating trajectories separate from footprints | -| `run_trajec` | Logical indicating whether to produce new trajectories with `hycs_std`. If FALSE, will try to load the previous trajectory outputs. This is often useful for regridding purposes | -| `trajec_fmt` | File extension for trajectory output files. Defaults to `rds` (serialized R data). Can be set to `parquet` for cross-platform output or as an empty string `''` to disable writing trajectory outputs | -| `simulation_id` | Unique identifier for each simulation; defaults to NA which determines a unique identifier for each simulation by hashing the time and receptor location | -| `timeout` | number of seconds to allow `hycs_std` to complete before sending SIGTERM and moving to the next simulation; defaults to 3600 (1 hour) | -| `varsiwant` | character vector of 4-letter `hycs_std` variables. Defaults to the minimum required variables including `'time', 'indx', 'long', 'lati', 'zagl', 'foot', 'mlht', 'dens', 'samt', 'sigw', 'tlgr'`. Can optionally include options listed below. | +| Arg | Description | +| --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `n_hours` | Number of hours to run each simulation; negative indicates backward in time | +| `numpar` | number of particles to be run; defaults to 200 | +| `rm_dat` | Logical indicating whether to delete `PARTICLE.DAT` after each simulation. Default to TRUE to reduce disk space since all of the trajectory information is also stored in `STILT_OUTPUT.rds` alongside the calculated upstream influence footprint | +| `run_foot` | Logical indicating whether to produce footprints. If FALSE, `run_trajec` must be TRUE. This can be useful when calculating trajectories separate from footprints | +| `run_trajec` | Logical indicating whether to produce new trajectories with `hycs_std`. If FALSE, will try to load the previous trajectory outputs. This is often useful for regridding purposes | +| `trajec_fmt` | File extension for trajectory output files. Defaults to `rds` (serialized R data). Can be set to `parquet` for cross-platform output or as an empty string `''` to disable writing trajectory outputs. The `arrow` package must be manually installed to write `parquet` output | +| `simulation_id` | Unique identifier for each simulation; defaults to NA which determines a unique identifier for each simulation by hashing the time and receptor location | +| `timeout` | number of seconds to allow `hycs_std` to complete before sending SIGTERM and moving to the next simulation; defaults to 3600 (1 hour) | +| `varsiwant` | character vector of 4-letter `hycs_std` variables. Defaults to the minimum required variables including `'time', 'indx', 'long', 'lati', 'zagl', 'foot', 'mlht', 'dens', 'samt', 'sigw', 'tlgr'`. Can optionally include options listed below. | #### Optional `varsiwant` arguments