Chapter 7 Writing & Publishing
7.1 Tools
7.1.1 latex
Latex is a software to write text. You can find thousands of tutorials online. If you want to work with latex on shared documents, consider overleaf.
7.2 Writing Papers
Here some general tips for structuring and writing a manuscript.
7.2.1 Structuring the manuscript
Find a journal of interest, check the author guidelines and follow the instructions. A list of journals of interest can be found in the internal folder of the github.
The manuscript needs to have page and line numbers, double spaced lines
Abstract:
Normally abstracts are around 300 words. For a better abstract, structure it in small sections, much like manuscript itself: Introduction, Methods, Results, Discussion and conclusions.
No references in the abstract
Introduction:
A ideal introduction has a simple structure without subheaders, but with generally 4-5 paragraphs:
First paragraph: Present the key challenge of the manuscript, general importance of this challenge for science and open questions
Second paragraph: Details on what people has already found out about the main challenge.
Third paragraph: what is the best study system, why and open questions
Fourth paragraph: what is the best tool or method strategy and why. This paragraph may be merged with the third one if study system and tool are too intertwined
Fifth paragraph: Aims, specific study questions and hypotheses, experimental design, expectations. It will help the paper structure if you explicitly list with numbers very specific questions or hypotheses to be addressed by the experiment and analyses.
General suggestion: every paragraph must have the first sentence presenting the topic of the paragraph and everything related to it must be in the same paragraph. If the paragraph is in the introduction, the last sentence may be related to an open question that will be targeted in your study. If the paragraph is in the discussion, the last sentence must be a strong concluding sentence with a take-home message based in your findings.
Methods
must have one general, but small paragraph telling what was the main methodological approach.
Then the methods must be structured in subsections. Typically, these are:
‚Study system’ or ‚empirical data’ if empirical or ‚Model description’ is modelling manuscript (with many sub-subsections):
‚Experimental design’: this must explain what experiments were carrying out to answer i) all the questions; ii) particular questions. Normally you have one figure illustrating the scenarios.
‚Analyses’: Start with a general paragraph explaining what model output you used for analyses, whether you did further calculations and manipulations for analyses that are relevant for all study questions. Thereafter, then follow the structure of the hypotheses and create one paragraph for study question and explain what analyses were carried out to answer explicitly each specific study question.
Results:
- Start explaining general overall findings, then structure according to the study questions/hypotheses. Normally you have one Figure for each question.
Discussion:
- This is where you discuss the findings in relation to one another and tot he literature. It is useful to start discussing the results in a section per study question. Then add a section on implications to theory and conservation. Another section to limitations and perspectives. Finally a conclusion.
7.2.2 Language Tips
‚in order’ can be always excluded to save words
Avoid synonyms, define terms at first mention, preferentially in the introduction and stick to that term throughout the text! You can add a couple of synonyms early in the introduction to increase findability of the manuscript in search engines when it gets publish. However, for most part of the paper use only one term for a given concept.
You need to edit each sentence. This make sentences simple and direct. Prefer only one verb per sentence.
You cannot use the conjunction ‚On the other hand," without having used ‚On the one hand,’ right before
In written English, the sentences should always have a noun!!!
- Example: Wrong: „For plants, some traits do this, others do that." Correct: „For plants, some traits do this, other traits do that."
In this regard, in any given sentence, there should be only one subject to avoid confusion with the verbs.
- Example: Wrong: „Plants have traits and some do this." (some plants or some traits?) Correct: „Plants have traits. Some traits do this."
7.4 Reviewing Papers
A template of a review feedback letter:
Comments to MS-ID
For editor [This section should be cut and pasted onto the part of the review form online that is confidential to the editor, i.e. not visible to the authors, and should NOT be retained in this file if you decide to upload the comments as a file.]:
[here you talk in brief your general opinion on the paper and justify your recommendation, while mentioning in the aspects, like statistics, that you cannot comment with much confidence. Stress what you think from all your concerns listed below, which are the most critical, those that the authors MUST clarify]
For authors [From this section to the end of the file you can upload to the online review form, normally only necessary when the comments are too extensive.]:
[Here you explain in 1-3 sentences what the paper does and finds (important for the editor). Explain your general assessment on the language and style. Whether the authors can substantiate their claims, whether you see potential in the manuscript, that you may have concerns and what is your general recommendation. Key recommendations are: reject (even if the authors tackle the issues, the manuscript might not fit the scope of the journal, or would remain too trivial and non-original); reject and invite for resubmission (the manuscript has a potential for a good contribution to the field if the major points are correctly addressed, particularly if major points involve re-doing analyses, which mean potentially changed content after revision); major revision (when there are major points, but the authors just need to do some re-writing and/or re-analysing); minor revision (when there is no major point, just minor corrections); accept (everything is at contempt). Be always polite and encouraging.]
Major points:
[Here you list the points that you find critical, which may implicit mean the authors will need to 1) rewrite; 2) re-analyse; 3) re-do experiments. Critical points: big flaws in the rationale; non-adequate experiment or analyses; wrong conclusions; missing analyses; missing key literature; poor structure. These points can be general and not necessarily addressed to a particular line or sentence. Be always polite and encouraging; if you have any critic, you must provide a solution or a suggestion. Do not criticize just for the sake of it.]
Minor points:
[These are points that you can locate specifically to a line, sentence, paragraph, table or figure. Normally these are unclear statements, typos, errors, missing information, poor design, formatting issues. These can be normally quickly solved.]
References
Grimm, Volker, Jacqueline Augusiak, Andreas Focks, Béatrice M. Frank, Faten Gabsi, Alice S.A. Johnston, Chun Liu, et al. 2014. “Towards Better Modelling and Decision Support: Documenting Model Development, Testing, and Analysis Using Trace.” Ecological Modelling 280 (May): 129–39. https://doi.org/10.1016/j.ecolmodel.2014.01.018.
Grimm, Volker, Uta Berger, Donald L. DeAngelis, J. Gary Polhill, Jarl Giske, and Steven F. Railsback. 2010. “The Odd Protocol: A Review and First Update.” Ecological Modelling 221 (23): 2760–8. https://doi.org/10.1016/j.ecolmodel.2010.08.019.