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Snt25 412 - clean up reporting rate pipeline #57

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dca0515
refactor(pipeline): update routine data choice parameters and streaml…
claude-marie Mar 19, 2026
bc87c40
test
claude-marie Mar 20, 2026
0390973
update for outliers imputation
claude-marie Mar 20, 2026
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3,288 changes: 1,644 additions & 1,644 deletions pipelines/snt_dhis2_incidence/code/snt_dhis2_incidence.ipynb
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3,288 changes: 1,644 additions & 1,644 deletions pipelines/snt_dhis2_incidence/country_specific/snt_dhis2_incidence_NER.ipynb
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3,062 changes: 1,530 additions & 1,532 deletions pipelines/snt_dhis2_incidence/reporting/snt_dhis2_incidence_report.ipynb
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2,380 changes: 1,189 additions & 1,191 deletions ...ines/snt_dhis2_reporting_rate_dataelement/code/snt_dhis2_reporting_rate_dataelement.ipynb
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14 changes: 9 additions & 5 deletions pipelines/snt_dhis2_reporting_rate_dataset/code/snt_dhis2_reporting_rate_dataset.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -51,17 +51,21 @@
"\n",
"### Pipeline parameters\n",
"\n",
"- **Outliers detection method**: Specify which method was used to detect outliers in routine data. Choose \"Routine data (Raw)\" to use raw routine data.\n",
" \n",
"- **Use routine with outliers removed**: Toggle this on to use the routine data after outliers have been removed (using the outliers detection method selected above). Else, this pipeline will use either the imputed routine data (to replace the outlier values removed) or the raw routine data if you selected \"Routine data (Raw)\" as your choice of “Outlier processing method”."
"- **Routine data source**: Select the routine dataset variant used for reporting rate computation.\n",
"\n",
"- **`raw`**: Loads routine data from the formatted dataset.\n",
"\n",
"- **`imputed`**: Loads routine data from the outliers dataset using imputed values.\n",
"\n",
"- **`outliers_removed`**: Loads routine data from the outliers dataset after outliers removal."
]
},
{
"cell_type": "markdown",
"id": "064495be-24e5-4b76-a91f-7ac3d1a27a5a",
"metadata": {
"papermill": {
"duration": 0.000092,
"duration": 9.2e-05,
"end_time": "2025-12-19T10:21:50.273573",
"exception": false,
"start_time": "2025-12-19T10:21:50.273481",
Expand Down Expand Up @@ -1189,7 +1193,7 @@
"input_path": "/home/hexa/workspace/pipelines/snt_dhis2_reporting_rate_dataset/code/snt_dhis2_reporting_rate_dataset.ipynb",
"output_path": "/home/hexa/workspace/pipelines/snt_dhis2_reporting_rate_dataset/papermill_outputs/snt_dhis2_reporting_rate_dataset_OUTPUT_2025-12-19_102148.ipynb",
"parameters": {
"ROUTINE_FILE": "NER_routine_outliers-mean_imputed.parquet",
"ROUTINE_FILE": "NER_routine_outliers_imputed.parquet",
"SNT_ROOT_PATH": "/home/hexa/workspace"
},
"start_time": "2025-12-19T10:21:48.422273",
Expand Down
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