From 5eb32aedf2e2e4bf770653c3ff8f3b7b138fb294 Mon Sep 17 00:00:00 2001 From: Matthew McDermott Date: Sun, 11 Aug 2024 16:25:28 -0400 Subject: [PATCH] Change from bash to console. --- README.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index c752d6e..838081a 100644 --- a/README.md +++ b/README.md @@ -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: