c-harmonise-data.md

@@ -25,7 +25,7 @@ Just like regular tables, views can be created by using a dictionary. In this ca
 
   <img src="uploads/create_view_1.png" alt="create_view_1" width="700"/>  
 
-* **2.2.** Type in a name for the view (e.g. epice-pt_data_harmonised)  
+* **2.2.** Type in a name for the view (e.g. EPICE-PT_Perinatal_harmonised_WP7_demo)  
 * **2.3.** In the table references, select the table from which the variables will be derived (the table you created in [step 2](b-import-data#2-import-data-into-your-node) of Part B of the tutorial) and click `Add`  
 * **2.4.** Click `Browse` and select the harmonisation dictionary  
 * **2.5.** Click `Save`  
@@ -35,23 +35,55 @@ Just like regular tables, views can be created by using a dictionary. In this ca
 The view you have created contains the target variables in the harmonisation dictionary and also a reference to the original table. It does not yet contain any data because no data has yet been pulled and transformed from the original table (this will be done in [step 4](#4-harmonise-each-variable)).  
 
 ## 3. Grant the Central Node and the Analysis Team Access to the Harmonised View
-Before you actually start harmonising the variables, you should allow both the central node and the analysis team to retrieve the data dictionary and summary statistics from the view you created. This is done by granting the `central_node` and `wp7_demo` accounts (created in [Part A](a-create-accounts) of this tutorial) a specific level of access to your view.
+Before you actually start harmonising the variables, you should allow both the central node and the analysis team to retrieve the data dictionary and summary statistics from the view you created. This is done by granting the `central-node` and `wp7-demo` accounts (created in [Part A](a-create-accounts) of this tutorial) a specific level of access to your view.
 
 * **3.1.** Click on the view you created in the previous section.  
 * **3.2.** In the `Permissions` tab, click on `Add Permission` > `Add user permission`  
-    ![add_user_perm_1](uploads/add_user_perm_1.png)  
+    ![add_user_perm_1](uploads/add_user_perm_view.png)  
 
-* **3.3.** Type in `central_node` for the name and select `View dictionary and summaries` for the level of access the central node will have to the view.  
+* **3.3.** Type in `central-node` for the name and select `View dictionary and summaries` for the level of access the central node will have to the view.  
     ![add_user_perm_2](uploads/add_user_perm_2.png)  
 * **3.4.** Click `Save`.  
-* **3.5.** Repeat steps 3.1-3.4, this time using `wp7_demo` as the name.  
+* **3.5.** Repeat steps 3.1-3.4, this time using `wp7-demo` as the name.  
 
 The central node and the analysis team will now be able to retrieve the data dictionary and summary statistics from your view.  
-In order to allow the analysis team to also use DataSHIELD to perform analysis, you also need to explicitly grant the `wp7_demo` permission to use DataSHIELD on your node:
+In order to allow the analysis team to also use DataSHIELD to perform analysis, you also need to explicitly grant the `wp7-demo` account permission to use DataSHIELD on your node:
 
 * **3.6.** In the top bar, click on `Administration`.  
 * **3.7.** Click on `DataSHIELD` and scroll down to the `Permissions` section.  
 * **3.8.** Click on `Add Permission` > `Add user permission`.  
-* **3.9.** Type in `wp7_demo` and click `Save`.  
+* **3.9.** Type in `wp7-demo` and click `Save`.  
 
 ## 4. Harmonise Each Variable
+To pull and transform the original variables from the original table, you need to individually harmonise each target variable in the view.  
+The harmonisation approach for each target variable depends on whether it is a categorical variable or not. For categorical target variables, continue reading below. For continuos target variables, got to [4.2](#harmcontinuous).
+
+* **4.1. The target variable is categorical**  
+For categorical target variables you can use the graphical web interface:
+
+  * **4.1.1.** Click on a categorical variable in the view
+    > NOTE  
+    If you know that you will not be able to harmonise any of your original variables to this variable, skip to 4.1.6.
+  * **4.1.2.** Click on `Derive` > `Categorize another variable to this`  
+      <img src="uploads/harmonise_categorical_1.png" alt="harmonise_categorical_1" width="700"/>  
+  * **4.1.3.** Select the variable from which values will be derived (a variable from the original table) and click `Next`  
+  * **4.1.4.** Map the original values to the new values defined in the harmonisation dictionary  
+      <img src="uploads/harmonise_categorical_2.png" alt="harmonise_categorical_2" width="450"/>  
+      In the image above, we are taking a variable from the original table and harmonising it to the `delmode_bin` variable in our view. The `delmode_bin` variable has three categories:
+      * 1 - vaginal
+      * 2 - caesarean section
+      * 9 - missing
+
+    So in this example, we are mapping the original categories "Vaginal" and "Instrumental" to 1 and "Caesarean" to 2.  
+    We are also mapping missing, empty or any other values to 9 and tagging them as missing.
+  * **4.1.5.** Click `Next`. In this window, you will be able to see a preview of what the resulting harmonised variable will look like. Click on `Full summary` to see summary statistics or on the `Values` tab to see a fragment of the resulting values.  
+  This preview, gives you a chance to assess if the resulting values will be in line with what you intended. If not, you can go back by clicking on `Previous`, then change the mappings and try again.
+  
+  * **4.1.5.** Click `Finish`  
+  * **4.1.6.** Before you move on to another variable, you must set the harmonisation status of this one. On the variable page, click on `Edit Annotation` > `Apply annotation`.
+  * **4.1.7.** Select `Harmonization` > `Harmonization Status` and then select 
+
+
+<div name="harmcontinuous"></div>
+
+* **The Target variable is continuous**
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