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add note about installing arrow
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jmineau committed Sep 20, 2024
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Expand Up @@ -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

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