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docs/doc/en/3.4.-Attributes.md

@@ -1,4 +1,3 @@
-
 # Attributes
 
 Attributes are variables associated with files, cases or journals. They can be useful to add context when interpeting your analysis. Open the Manage Attributes dialog. You can add, delete, rename and add memo notes to attributes.

docs/doc/en/4.2.-AI-Assisted-Coding.md

@@ -1,6 +1,7 @@
 ## Introduction
 
 QualCoder’s built-in AI features (version 3.6 and up) can assist the coding process in various ways:
+
 - **AI Search:** Leverage the AI's ability to quickly analyze large amounts of text to find and explore specific topics or concepts within your corpus.
 - **Search for concepts, not keywords:** QualCoder uses a combination of semantic search technologies and Large Language Models like GPT-4. As a result, you don’t need to enter exact keywords but can also search for much more abstract concepts, e.g. "changing gender roles" or "recognition in the workplace". 
 - **Interpret your data interactively with the AI:** The AI not only suggests relevant data but also provides interpretation, offering a different perspective that can enrich your understanding of the data.

docs/doc/en/5.1.-AI-chat-based-analysis.md

@@ -1,3 +1,5 @@
+# 5.1 AI Chat based analysis
+
 The AI Chat tab in the main window allows you to discuss certain aspects of your analysis with the AI. QualCoder provides four different types of chats:
 
 <img src="https://github.com/user-attachments/assets/faddc4da-e281-48f9-816e-97c5bad45108" width=270em alt="Screenshot New Chat">
@@ -59,6 +61,7 @@ If you want to **define your own types of text analysis**, you can do so by addi
 <img src="https://github.com/user-attachments/assets/64423034-a9f8-4e7f-ab99-f50853b155b3" width=750em alt="Screenshot code analysis chat">
 
 From the AI Chat tab, click "New > New Code Analysis Chat". In the following window, select a code or a category you want to analyze, and choose between several analytic prompts:
+
 - **Code summary** will give you an overview of the data associated with the selected code
 - **Analyze unexpected** will look for the most interesting, unexpected insights in you coded data
 - **Analyze differences** will examine whether there are significant differences between your empirical cases/documents with regard to the selected code. 

docs/doc/en/5.2.-Journals.md

@@ -4,6 +4,7 @@ Journals can be exported as a single journal or all journal text can be collated
 Journals can be deleted. Journals can have attributes.
 
 There is a search option to search through journal text. The search uses regex symbols for more flexibility.
+
 * A dot '.' is used as a wild card, e.g. '.ears' will match ‘bears’ and 'years'
 * A '?' after a character will match one or none times that character, e.g. 'bears?' will match 'bear' and 'bears'
 * A '*' after a character will match zero or more times. 

docs/doc/en/5.3.-Reports.md

@@ -1,4 +1,5 @@
 # Reports menu options
+
 * Coding reports (the main reporting function)
 * Coding comparison - for text files (compares 2 coders)
 * Coding comparison by file - for text files (compares 2 coders)
@@ -27,7 +28,7 @@ Coding results can be narrowed down by using the File selection, Case selection
 If text is entered into the Search text field, only codings which contain the matching text will be presented. 
 The search text also looks for matching text in memos for coded image areas and coded audio/video segments. The search text function must be used in combination with File selection, Case selection or Attribute selection.
 
-** Important coded text, images, segments
+## Important coded text, images, segments
 There is a tick box to select only the Important codings. This is useful for quickly finding those important exemplars that you may use in a written report.
 
 ## Attribute selection in reports
@@ -102,7 +103,7 @@ Disagree % shows the percentage of all the coded and non-coded text that did not
 
 Agree coded only % shows the percentage of all the dual coded text divided by single plus dual coded text.
 
-Cohen’s Kappa is calculated based on the information in Wikipedia https://en.wikipedia.org/wiki/Cohen%27s_kappa
+Cohen’s Kappa is calculated based on the information in  [Wikipédia](https://en.wikipedia.org/wiki/Cohen%27s_kappa).
 
 <img width="1060" height="472" alt="Code comparisons table" src="https://github.com/user-attachments/assets/07e5ef6c-4e84-411b-a432-3f0ceac69b61" />
 
@@ -247,6 +248,7 @@ Apply SQL Statements to query the data.
 This window contains three panes. The top pane is where SQL statements are entered and the bottom pane contains the results of queries. The left pane contains tables and field names. Double-clicking on a field name adds it to the SQL statement. Results can be exported to a delimited file. If you are not familiar with SQL take care as you will be able to update and delete the data as well as select data. Note: Some Unicode symbols are not converted to plain text and are ignored.
 
 There are several prepared statements listed:
+
 * Case text
 * Coded text using a case attribute selection (v3.6+)
 * Codes fileid and coded text

docs/doc/en/6.1.-Imports-and-Exports.md

@@ -1,18 +1,20 @@
+# 6.1 Imports and exports
 Project menu
+
 * Exports
 * Imports
 
-#  Codebook export
+##  Codebook export
 
 This is an option under the Project Menu > Exports.
 
 A codebook is a list of your codes. Each code memo should detail the reasons for the purpose of each code. The codebook can be exported to a text file. The codebook also shows the frequency of the codes used (from all coders). As codes and categories are put in a tree like structure the double minus ‘–‘ indicates the subordinate codes and categories within a category.
 
-# Codebook import
+## Codebook import
 
 Import a codebook as a plain text (.txt) file or as a .csv file. Use two greater than symbols to separate category and code.
 
-## Plain text
+### Plain text
 
 Use the tab to then add a memo.
 
@@ -24,7 +26,7 @@ category1>>code3
 
 category3>>code4
 
-## CSV
+### CSV
 
 The categories and codes are in the first column. Any code memos are in the second column.
 
@@ -34,8 +36,8 @@ category1>>category2>>code2
 
 category3>>code3
 
-#  REFI-QDA
-The Rotterdam Exchange Format Initiative (REFI) is an open standard for exporting and importing codebooks and projects from and to different computer-aided qualitative data analysis software. The website for the exchange initiative is www.qdasoftware.org
+##  REFI-QDA
+[Rotterdam Exchange Format Initiative (REFI)](https://www.qdasoftware.org)  is an open standard for exporting and importing codebooks and projects from and to different computer-aided qualitative data analysis software.
 
 Currently, QualCoder is able to export and import a codebook. 
 
@@ -51,14 +53,14 @@ If no coded data is visible, you may need to change the current coder's name in
 
 This is now old (Feb 2021), but a user tested the importation of a REFI-QDA project file generated by QualCoder and imported into MAXQDA, Quirkos, Atlas.ti. Only text and Images were tested. A PDF of the test results is here: [Testing importation of REFI-QDA Project files into Atlas, MAXQDA, Quirkos PDF](https://qualcoder.files.wordpress.com/2021/02/refi-qda-project-import-quirkos-maxqda-atlas.pdf)
 
-# RQDA
-Projects made with RQDA (http://rqda.r-forge.r-project.org/) can be directly imported. All data except for file categories are imported.
+## RQDA
+Projects made with [RQDA](http://rqda.r-forge.r-project.org/) can be directly imported. All data except for file categories are imported.
 
 Close any opened project. Then in the Main Menu under Project click on RQDA Project import. You will be asked to create a new project- so enter a name. Then you will be asked to select the RQDA project file. QualCoder will then import the data.
 
 If no coded data is visible, you may need to change the current coder's name in Settings. Try the drop down coder name box.
 
-# Survey import
+## Survey import
 
 This requires a CSV or Excel (xlsx format) file. You can try importing the survey.csv file in the Examples folder.
 
@@ -88,7 +90,7 @@ The default option, is that each qualitative response for each row, will be stor
 
 When you click on the OK button, the cases and their attributes will be added. 
 
-## Older versions of QualCoder, e.g. QualCoder 3.5.
+### Older versions of QualCoder, e.g. QualCoder 3.5.
 Each qualitative question answer was appended to ONE text file. Preceding the answer was additional QualCoder added text, to show which case the answer was relevant to. 
 
 In this format: _[unique id] The qualitative text._
@@ -98,7 +100,7 @@ Open Manage Files, then View that file, and you will see the case assigned text
 ![image](https://github.com/user-attachments/assets/5c05347a-731b-40d8-943f-921409447403)
 
 
-# Bibliography import
+## Bibliography import
 
 Import a bibliography. This must be in RIS formatted plain text. The file can have endings of .txt or .ris
 
@@ -117,19 +119,20 @@ In here there will be four new attribute columns: Ref_Authors, Ref_Title, Ref_Ty
 
 Files link to references will have details in those columns.
 
-# Help - Special Functions
+## Help - Special Functions
 
-## Dynamic update text content
+### Dynamic update text content
 
 This is useful for updating text files such as blog post extract that change over time. Update a text file while attempting to keep the existing coded text segments. Select the text file that needs to be replaced and select the replacement file. Click the cogs button to run the update. This function works by finding the identical matching text in the replacement file, as it parses through the file text. It may produce erroneous  coded segments.
 
-## Merge QualCoder Projects
+### Merge QualCoder Projects
 
 Select a QualCoder project to merge (source project) into the currently opened project (destination project), then click the _Run merge projects_, cogs button. **Before performing the merge, make a backup of the destination project.**
 
 Caution: If each project to be merged has the same coder name, e.g. 'default' then these will merge as such, and you will not be able to separate out which coder performed their own coding. This may or may not be an important consideration to your final merged project.
 
 The following occurs:
+
 * Copies unmatched files from source project folders to destination project folders.
 * Adds new (unmatched) source categories to destination database.
 * Adds new (unmatched) source code names to destination database.

docs/doc/en/6.2.-AI-Prompt-Library.md

@@ -15,6 +15,7 @@ This is the basic structure:
 <img src="https://github.com/user-attachments/assets/b77df95d-f5b3-4ffa-8d3a-a511c82ef9ab" width=500em>
 
 This structure consists of 
+
 - **fixed elements** (shown here in white on blue) that are defined in the source code of the application,
 - **contextual information** (here in green) that you enter at various places in QualCoder's user interface, such as code names and memos, or the project memo with important information about your research,
 - **empirical data** (here in yellow), selected in various ways, and
@@ -39,13 +40,9 @@ The prompts are divided into several categories:
     - **User** prompts are defined by the user and stored on their computer. They are available to any project opened on that computer.
     - **Project** specific prompts are stored with the project files. If you or someone else opens the same project on a different computer, these prompts will be available there as well.
 
-3) **Prompt name and description**
-
-    These are displayed in several places in the user interface where you can select an analytic prompt. The names must be unique within each scope. 
-
-4) **Prompt text**
+3) **Prompt name and description**: These are displayed in several places in the user interface where you can select an analytic prompt. The names must be unique within each scope. 
 
-    These are the actual instructions that will be sent to the AI (the orange box in the image above). If you want to share your prompt with someone else, this is the most important information you will need to send over.
+4) **Prompt text**: These are the actual instructions that will be sent to the AI (the orange box in the image above). If you want to share your prompt with someone else, this is the most important information you will need to send over.
 
 
 ## A Note About Languages

docs/doc/en/7.3.-QualCoder-Development.md

@@ -22,9 +22,11 @@ Some potential plans for the future are to add functionality:
 ### Reports: 
 
 **Look at alternative ways to visualise codes:**
+
 * Display code frequency in a comparative way - e.g. compare female versus males for the code frequencies using bar charts or other plots
 
 **Look at timeline reporting:**
+
 * Maybe add in a way to display coding from documents in a timeline - drawing from a file data attribute that is created by the end user.
 
 ### General: