explorer to teva

aphp · Apr 23, 2024 · b440c6f · b440c6f
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diff --git a/...ities/omop-explorer/configuration-omop.md → ...onalities/omop-teva/configuration-omop.md b/...ities/omop-explorer/configuration-omop.md → ...onalities/omop-teva/configuration-omop.md
@@ -1,16 +1,16 @@
-# OMOP Explorer - Config
+# OMOP Teva - Config
 
 ## Table configuration
 
-All plots generated by ```eds_scikit.plot.generate_omop_explorer``` are based on the configuration file ```eds_scikit.plot.default_omop_explorer_config```. 
+All plots generated by ```eds_scikit.plot.generate_omop_teva``` are based on the configuration file ```eds_scikit.plot.default_omop_teva_config```. 
 
 A table configuration is defined by :
 
 - category columns list
 - date column
 - category columns mapping
 
-=== "Default condition explorer configuration"
+=== "Default condition teva configuration"
 
     ```python
     "condition_occurrence": {
@@ -33,7 +33,7 @@ A table configuration is defined by :
     },
     ```
 
-=== "Custom diabete condition explorer configuration"
+=== "Custom diabete condition teva configuration"
 
     ```python
     "condition_occurrence": {
@@ -59,27 +59,27 @@ A table configuration is defined by :
 
 ## Specifying table configuration
 
-To specify configuration, simply update ```default_omop_explorer_config``` and pass it to ```generate_omop_explorer```.
+To specify configuration, simply update ```default_omop_teva_config``` and pass it to ```generate_omop_teva```.
 
 ```python
-from eds_scikit.plot import generate_omop_explorer
-from eds_scikit.io.omop_explorer_default_config import default_omop_explorer_config
+from eds_scikit.plot import generate_omop_teva
+from eds_scikit.io.omop_teva_default_config import default_omop_teva_config
 
-omop_explorer_config = default_omop_explorer_config
+omop_teva_config = default_omop_teva_config
 
 condition_mapper = {
     "condition_source_value": {"has_diabete": r"^E10|^E11|^E12|^E13|^E14|O24"}
 }
 
-omop_explorer_config["condition_occurrence"]["mapper"].update(condition_mapper)
+omop_teva_config["condition_occurrence"]["mapper"].update(condition_mapper)
 
 start_date, end_date = "2021-01-01", "2021-12-01"
-generate_omop_explorer(data=data, 
+generate_omop_teva(data=data, 
                        start_date=start_date,
                        end_date=end_date,
-                       explorer_config=omop_explorer_config)
+                       teva_config=omop_teva_config)
 ```
 
-!!! warning "Adding a new table in default_omop_explorer_config"
-    For now, if you want to generate a dashboard for a table which do not exists in default_omop_explorer_config you must redefine and update ```generate_omop_explorer```.
+!!! warning "Adding a new table in default_omop_teva_config"
+    For now, if you want to generate a dashboard for a table which do not exists in default_omop_teva_config you must redefine and update ```generate_omop_teva```.
 
diff --git a/...nalities/omop-explorer/custom-explorer.md → .../functionalities/omop-teva/custom-teva.md b/...nalities/omop-explorer/custom-explorer.md → .../functionalities/omop-teva/custom-teva.md
@@ -1,6 +1,6 @@
-# Custom Explorer
+# Custom Teva
 
-OMOP-explorer module can also be applied to any dataframe. User must use ```reduce_table``` and ```visualize_table``` from ```eds_scikit.plot.table_viz```.
+OMOP-Teva module can also be applied to any dataframe. User must use ```reduce_table``` and ```visualize_table``` from ```eds_scikit.plot.table_viz```.
 
 !!! warning "Make sure to specify categorical columns with less then 50 values."
     Use the function ```eds_scikit.plot.table_viz.map_column``` to reduce columns volumetry.

diff --git a/docs/functionalities/omop-explorer/index.md → docs/functionalities/omop-teva/index.md b/docs/functionalities/omop-explorer/index.md → docs/functionalities/omop-teva/index.md
@@ -1,6 +1,7 @@
-# OMOP Explorer
+# OMOP Teva
 
-The OMOP Explorer module of [eds-scikit](https://github.com/aphp/eds-scikit) supports data scientists working on OMOP data. Its main objective is to allow quick OMOP tables exploration by displaying __cartesian product values volumetry__ over time.
+The OMOP Teva module of [eds-scikit](https://github.com/aphp/eds-scikit) supports data scientists working on OMOP data.
+OMOP Teva generates an interactive dashboard for each OMOP table, allowing timely visualization of the volumes associated with each combination of values. This provides a general overview of the possible values, their relative importance and allows to detect quickly possible bias.
 
 ```vegalite
 {
@@ -866,46 +867,46 @@ The OMOP Explorer module of [eds-scikit](https://github.com/aphp/eds-scikit) sup
   }
 ```
 
-<!-- --8<-- [start:omop-explorer] -->
+<!-- --8<-- [start:omop-teva] -->
 
-=== card {: href=/functionalities/omop-explorer/quick-use-omop }
+=== card {: href=/functionalities/omop-teva/quick-use-omop }
 
     :fontawesome-solid-file-medical:
-    **OMOP Explorer - Quick use**
+    **OMOP Teva - Quick use**
 
     ---
 
     Quick use for OMOP dataset exploration.
 
-=== card {: href=/functionalities/omop-explorer/configuration-omop }
+=== card {: href=/functionalities/omop-teva/configuration-omop }
 
     :fontawesome-solid-gears:
-    **OMOP Explorer - Config**
+    **OMOP Teva - Config**
 
     ---
 
     See how your can configurate your own OMOP dashboards .
 
-=== card {: href=/functionalities/omop-explorer/custom-explorer }
+=== card {: href=/functionalities/omop-teva/custom-teva }
 
     :fontawesome-solid-file:
-    **Custom Explorer**
+    **Custom Teva**
 
     ---
 
     For any dataframe exploration.
 
-=== card {: href=/functionalities/omop-explorer/omop-explorer-example }
+=== card {: href=/functionalities/omop-teva/omop-teva-example }
 
     :fontawesome-solid-chart-line:
-    **OMOP Explorer - Example**
+    **OMOP Teva - Example**
 
     ---
 
     A toy example of what can be obtained with this module.
 
 
 
-<!-- --8<-- [end:omop-explorer] -->
+<!-- --8<-- [end:omop-teva] -->
 
 See [Adjusting for the progressive digitization of health records](https://www.medrxiv.org/content/10.1101/2023.08.17.23294220v1) for a better understanding about temporal bias in EHR data and [EDS-Teva](https://github.com/aphp/edsteva) for a more complete library on how to handle those bias.
diff --git a/...es/omop-explorer/omop-explorer-example.md → ...ionalities/omop-teva/omop-teva-example.md b/...es/omop-explorer/omop-explorer-example.md → ...ionalities/omop-teva/omop-teva-example.md
@@ -1,6 +1,6 @@
-# OMOP Explorer example
+# OMOP Teva example
 
-OMOP Explorer generates an interactive dashboard for each table, allowing visualization of the volumes associated with each combination of values. This provides a general overview of the possible values, their relative importance and allows to detect quickly possible bias.
+OMOP Teva generates an interactive dashboard for each table, allowing visualization of the volumes associated with each combination of values. This provides a general overview of the possible values, their relative importance and allows to detect quickly possible bias.
 
 The dashboard below provides an example for the __visit_occurrence__ table.
 

diff --git a/...onalities/omop-explorer/quick-use-omop.md → ...nctionalities/omop-teva/quick-use-omop.md b/...onalities/omop-explorer/quick-use-omop.md → ...nctionalities/omop-teva/quick-use-omop.md
@@ -1,8 +1,8 @@
-# Quick use - OMOP Explorer
+# OMOP Teva - Quick use
 
-This tutorial demonstrates how the OMOP explorer module can be quickly used to generate OMOP tables dashboard.
+This tutorial demonstrates how the OMOP teva module can be quickly used to generate OMOP tables dashboard.
 
-Simply apply ```generate_omop_explorer``` function after loading the data. It will create a directory with one HTML per OMOP table.
+Simply apply ```generate_omop_teva``` function after loading the data. It will create a directory with one HTML per OMOP table.
 
 ??? tip "Loading dataset"
 
@@ -27,10 +27,10 @@ Simply apply ```generate_omop_explorer``` function after loading the data. It wi
     ```
 
 ```python
-from eds_scikit.plot import generate_omop_explorer
+from eds_scikit.plot import generate_omop_teva
 
 start_date, end_date = "2021-01-01", "2021-12-01"
-generate_omop_explorer(data=data, start_date=start_date, end_date=end_date)
+generate_omop_teva(data=data, start_date=start_date, end_date=end_date)
 ```
 
 === "Visit occurrence"
@@ -17505,7 +17505,7 @@ generate_omop_explorer(data=data, start_date=start_date, end_date=end_date)
 === "Condition occurrence (diabete)"
 
     !!! warning "In this example ```condition_source_value``` is splited between diabetic and non-diabetic conditions."
-        You can modify dashboard configuration by importing ```eds_scikit.plot.default_omop_explorer_config``` and customizing it. See next section for details on how to do it.
+        You can modify dashboard configuration by importing ```eds_scikit.plot.default_omop_teva_config``` and customizing it. See next section for details on how to do it.
 
     ```vegalite
     {

diff --git a/...scikit/io/omop_explorer_default_config.py → eds_scikit/io/omop_teva_default_config.py b/...scikit/io/omop_explorer_default_config.py → eds_scikit/io/omop_teva_default_config.py
@@ -1,4 +1,4 @@
-default_omop_explorer_config = {
+default_omop_teva_config = {
     "visit_occurrence": {
         "category_columns": [
             "care_site_short_name",

diff --git a/eds_scikit/plot/__init__.py b/eds_scikit/plot/__init__.py
@@ -1,3 +1,3 @@
 from eds_scikit.plot.table_viz import map_column, reduce_table, visualize_table
-from eds_scikit.plot.omop_explorer import generate_omop_explorer
-from eds_scikit.io.omop_explorer_default_config import default_omop_explorer_config
+from eds_scikit.plot.omop_teva import generate_omop_teva
+from eds_scikit.io.omop_teva_default_config import default_omop_teva_config
diff --git a/eds_scikit/plot/omop_explorer.py → eds_scikit/plot/omop_teva.py b/eds_scikit/plot/omop_explorer.py → eds_scikit/plot/omop_teva.py
@@ -3,28 +3,28 @@
 from loguru import logger
 
 from eds_scikit.io import HiveData
-from eds_scikit.io.omop_explorer_default_config import default_omop_explorer_config
+from eds_scikit.io.omop_teva_default_config import default_omop_teva_config
 from eds_scikit.plot.table_viz import reduce_table, visualize_table
 
 
-def generate_omop_explorer(
+def generate_omop_teva(
     data: HiveData,
     start_date: str,
     end_date: str,
-    explorer_config: dict = default_omop_explorer_config,
-    output_dir="omop_explorer",
+    teva_config: dict = default_omop_teva_config,
+    output_dir="omop_teva",
 ):
-    """Generate OMOP explorer folder.
+    """Generate OMOP teva folder.
 
     Parameters
     ----------
     data : HiveData
     start_date : str
     end_date : str
-    explorer_config : dict, optional
-        OMOP explorer configuration, by default default_omop_explorer_config
+    teva_config : dict, optional
+        OMOP teva configuration, by default default_omop_teva_config
     output_dir : str, optional
-        Output directory path, by default "omop_explorer"
+        Output directory path, by default "omop_teva"
     """
 
     if not os.path.exists(f"{output_dir}/"):
@@ -38,7 +38,7 @@ def generate_omop_explorer(
     visit_occurrence = visit_occurrence.merge(
         data.care_site[["care_site_id", "care_site_short_name"]], on="care_site_id"
     )
-    config = explorer_config["visit_occurrence"]
+    config = teva_config["visit_occurrence"]
     visit_columns = [
         *config["category_columns"],
         config["date_column"],
@@ -69,7 +69,7 @@ def generate_omop_explorer(
     logger.info("Starting procedure_occurrence processing.")
 
     procedure_occurrence = data.procedure_occurrence
-    config = explorer_config["procedure_occurrence"]
+    config = teva_config["procedure_occurrence"]
     procedure_occurrence = procedure_occurrence.merge(
         visit_occurrence, on="visit_occurrence_id", how="left"
     )
@@ -100,7 +100,7 @@ def generate_omop_explorer(
     logger.info("Starting condition_occurrence processing.")
 
     condition_occurrence = data.condition_occurrence
-    config = explorer_config["condition_occurrence"]
+    config = teva_config["condition_occurrence"]
     condition_occurrence = condition_occurrence.merge(
         visit_occurrence, on="visit_occurrence_id", how="left"
     )
@@ -131,7 +131,7 @@ def generate_omop_explorer(
     logger.info("Starting notes processing.")
 
     note = data.note
-    config = explorer_config["note"]
+    config = teva_config["note"]
     note = note.merge(visit_occurrence, on="visit_occurrence_id", how="left")
     note["visit_occurrence_id"] = note["visit_occurrence_id"].astype(str)
 
@@ -154,7 +154,7 @@ def generate_omop_explorer(
     logger.info("Starting drug exposure prescription processing.")
 
     drg_exposure = data.drug_exposure_prescription
-    config = explorer_config["drug_exposure_prescription"]
+    config = teva_config["drug_exposure_prescription"]
     drg_exposure = drg_exposure.merge(
         visit_occurrence, on="visit_occurrence_id", how="left"
     )
@@ -183,7 +183,7 @@ def generate_omop_explorer(
     logger.info("Starting drug exposure administration processing.")
 
     drg_exposure = data.drug_exposure_administration
-    config = explorer_config["drug_exposure_administration"]
+    config = teva_config["drug_exposure_administration"]
     drg_exposure = drg_exposure.merge(
         visit_occurrence, on="visit_occurrence_id", how="left"
     )

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -46,14 +46,14 @@ nav:
       - Emergency Units: functionalities/patients-course/is_emergency.md
       - Visit merging: functionalities/patients-course/visit_merging.md
       - Consultation dates: functionalities/patients-course/consultation_dates.md
-    - OMOP explorer:
-      - functionalities/omop-explorer/index.md
-      - functionalities/omop-explorer/quick-use-omop.md
-      # - functionalities/omop-explorer/quick-use-general.md
-      - functionalities/omop-explorer/configuration-omop.md
-      - functionalities/omop-explorer/custom-explorer.md
-      - functionalities/omop-explorer/omop-explorer-example.md
-      # - functionalities/omop-explorer/detailed-use-omop.md
+    - OMOP Teva:
+      - functionalities/omop-teva/index.md
+      - functionalities/omop-teva/quick-use-omop.md
+      # - functionalities/omop-teva/quick-use-general.md
+      - functionalities/omop-teva/configuration-omop.md
+      - functionalities/omop-teva/custom-teva.md
+      - functionalities/omop-teva/omop-teva-example.md
+      # - functionalities/omop-teva/detailed-use-omop.md
     - Biology:
       - functionalities/biology/index.md
       - functionalities/biology/quick-use.md