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Change from bash to console.
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mmcdermott committed Aug 11, 2024
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Expand Up @@ -82,19 +82,18 @@ By following these steps, you can seamlessly transform your dataset, define nece
processed in parallel. You can easily re-shard your input MEDS cohort in the environment into which this
package is installed with the following command:

```bash
```console
# Re-shard pipeline
# $MIMICIV_MEDS_DIR is the directory containing the input, MEDS v0.3 formatted MIMIC-IV data
# $MEDS_TAB_COHORT_DIR is the directory where the re-sharded MEDS dataset will be stored, and where your model
# will store cached files during processing by default.
# $N_PATIENTS_PER_SHARD is the number of patients per shard you want to use.
#
MEDS_transform-reshard_to_split \
input_dir="$MIMICIV_MEDS_DIR" \
cohort_dir="$MEDS_TAB_COHORT_DIR" \
'stages=["reshard_to_split"]' \
stage="reshard_to_split" \
stage_configs.reshard_to_split.n_patients_per_shard=$N_PATIENTS_PER_SHARD
input_dir="$MIMICIV_MEDS_DIR" \
cohort_dir="$MEDS_TAB_COHORT_DIR" \
'stages=["reshard_to_split"]' \
stage="reshard_to_split" \
stage_configs.reshard_to_split.n_patients_per_shard=$N_PATIENTS_PER_SHARD
```

1. **`meds-tab-describe`**: This command processes MEDS data shards to compute the frequencies of different code types. It differentiates codes into the following categories:
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