The essentials of a methods sections include a clear and precise description of:

1. The rationale for the choice of methods
The choice of methods are based upon the scientific aim of the project. All scientific projects aim to solve a problem and the methods describe how that problem might be solved. Different researchers may choose different methods to solve the same problem, which is why the methods of any study should be critiqued as closely as the results and the conclusions.

 
2. The features of a study design
-The study plan that addresses the aim the study, research questions and hypotheses.
-The materials and study subjects – how they were selected and manipulated.
-Any experimental procedures including the hypotheses being tested.

 
3. How the study was conducted
Describe what was done and why. What was observed, what interventions were employed and how the data was collected. When outlining the data collection process, include the variables measured and all measuring instruments. If existing data sets were used, cite the data sources and outline what subsets of this data were included in your study.

4. How the data was analysed
Describe how the data was prepared for analysis and how it was analysed. Include the name of tests, software and tools, using citation where appropriate. Describe any additional variables that were created for analysis; for example, if measuring the age of an organism, you may wish to allocate this data into age classes.

How the methods section is structured may depend upon personal preference and the type of study. A typical structure outlined by Azevedo et al. (2011) is:
1. Study design;
2. Selection of participants — selection criteria and selection methods;
3. Data collection — variables, methods and instruments and
4. Data analysis.

The level of detail required
Enough detail should be provided so that someone else can repeat the same methods. For example, given my research background, if I read the following: ‘Presence/absence of ‘species X’ plant specimens were counted within 100 1x1 meter quadrats. These quadrats were randomly selected from within a 50 x 50 meter grid’, I would be able to replicate this method. An example of too much detail in this instance, would be to describe exactly how observers moved from quadrat to quadrat.

If the method used is common practice, then limited information is needed. If common methods are modified, then these modifications need to be described along with the rationale for modifying this method.

If you have developed a new method you must describe it in full. If appropriate, consider publishing a separate methods paper, then you need only cite this paper in your original research paper methods section.

Also consider:
Make sure you receive appropriate legal and ethical approval when working with animal and human subjects. Universities and government institutions will have their own frameworks to follow.

 
A different way of thinking about what to include in a method section is to consider following the standard ‘who, what, where, when, why and how’ approach.
-Who did the work?
-What was done to achieve the results? How, exactly, was the work carried out?
-Where was the work conducted?
-Why were the actions chosen and why were things conducted in a certain way?

Ask a colleague with a similar scientific background to review a late draft for errors.