Update readme.md

readme.md

@@ -4,7 +4,7 @@ Below are the instructions to create a valid configuration file.
 
 ## Configuration File Structure
 
-The configuration file should be in YAML format (.config file) and follow the structure outlined below:
+The configuration file should be in YAML format (.config file) and follow the structure outlined below for **ICU Data**:
 
 ```yaml
 disease_label: <disease_label> mandatory only if the prediction task is Phenotype
@@ -20,7 +20,7 @@ proc: <proc>
 meds: <meds>
 disease_filter: <disease_filter>
 icu_no_icu: <icu_no_icu>
-groupingICD: <groupingICD>
+groupingDiag: <groupingDiag>
 select_diag: <select_diag>
 select_med: <select_med>
 select_proc: <select_proc>
@@ -31,6 +31,33 @@ outlier: <outlier>
 left_outlier: <left_outlier>
 ```
 
+The configuration file should be in YAML format (.config file) and follow the structure outlined below for **Non-ICU Data**:
+
+```yaml
+disease_label: <disease_label> mandatory only if the prediction task is Phenotype
+timePrediction: <timePrediction>
+timeWindow: <timeWindow>
+timebucket: <timebucket>
+radimp: <radimp>
+predW: <predW>
+diagnosis: <diagnosis>
+lab: <lab>
+proc: <proc>
+meds: <meds>
+disease_filter: <disease_filter>
+icu_no_icu: <icu_no_icu>
+groupingDiag: <groupingDiag>
+groupingProc: <groupingProc>
+groupingMed: <groupingMed>
+select_diag: <select_diag>
+select_med: <select_med>
+select_proc: <select_proc>
+select_lab: <select_lab>
+outlier_removal: <outlier_removal>
+outlier: <outlier>
+left_outlier: <left_outlier>
+```
+
 Replace the `<variable>` placeholders with the corresponding values specific to your use case. Detailed explanations of each variable and their valid values are provided in the next section.
 
 ## Variable Definitions and Valid Values
@@ -60,11 +87,15 @@ Replace the `<variable>` placeholders with the corresponding values specific to
   - CAD
   - No Disease Filter
 - `icu_no_icu` (string): Specifies the dataset type. Valid values: ICU.
-- `groupingICD` (string): Specifies the grouping ICD option. Valid values:
+- `groupingDiag` (string): Specifies the grouping ICD option for diagnosis. Valid values:
   - Convert ICD-9 to ICD-10 and group ICD-10 codes
   - Keep both ICD-9 and ICD-10 codes
   - Convert ICD-9 to ICD-10 codes
-- `select_diag`, `select_med`, `select_proc`, `select_out`, `select_chart` (boolean): Specifies whether to do features selection as describe in https://github.com/healthylaife/MIMIC-IV-Data-Pipeline benchmark. Valid values: True or False.
+- `groupingMed`: Specifies if grouping Medication codes should be done to use Non propietary names : Valid values : Yes, No
+- `groupingProc` : Specifies the ICD codes version to perform grouping for procedures : Valid values :
+  - ICD-9 and ICD-10
+  - ICD-10
+- `select_diag`, `select_med`, `select_proc`, `select_out`, `select_chart`,`select_lab` (boolean): Specifies whether to do features selection as describe in https://github.com/healthylaife/MIMIC-IV-Data-Pipeline benchmark. Valid values: True or False.
 - `outlier_removal` (string): Specifies the outlier removal method. Valid values:
   - No outlier detection
   - Impute Outlier (default:98)
@@ -74,7 +105,7 @@ Replace the `<variable>` placeholders with the corresponding values specific to
 
 ## Example Configuration File
 
-Here's an example of a valid configuration file:
+Here's an example of a valid configuration file for **ICU Data**:
 
 ```yaml
 disease_label: CAD
@@ -100,6 +131,31 @@ outlier_removal: Impute Outlier (default:98)
 outlier: 98
 left_outlier: 0
 ```
+Here's an example of a valid configuration file for **Non-ICU Data**:
+
+```yaml
+timePrediction: 0
+timeWindow: First 48 hours
+timebucket: 2
+radimp: forward fill and mean
+predW: 2
+diagnosis: True
+lab: True
+proc: False
+meds: False
+disease_filter: CKD
+icu_no_icu: ICU
+groupingDiag: Convert ICD-9 to ICD-10 and group ICD-10 codes
+select_diag: False
+select_med: False
+select_proc: False
+select_lab: False
+outlier_removal: Impute Outlier (default:98)
+outlier: 98
+left_outlier: 0
+groupingMed: Yes
+groupingProc: ICD-10
+```
 
 Feel free to modify the values to fit your specific requirements.