I have edited your question title as it seems from your question description that you are writing a master's thesis or dissertation and want to know what to include in the methodology chapter. I am not very sure about what the norm is in your field, but generally speaking, the methodology section should include a description of the research questions and/or hypotheses to be investigated and relevant methods of investigation, along with a justification for why you think these methods are the most appropriate for the research question(s). You should discuss not only the benefits of the methods used, but also the disadvantages or limitations, and how you overcame them. Ethical issues are also usually discussed in this section, with an explanation of how they were dealt with. Regarding the sections and subsections, you can, I think use these based on the content you are including. However, this is a generic approach, and it would be a good idea to discuss with an expert from your field of study, as thesis writing conventions may differ across fields.
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