Example: The following entry was created using this method:
David Lilja (2017) has suggested a step by step approach of linear regression using R \cite{Lilja2017}
So, we have covered the following items:
- How to write and format paragraphs in Authorea to write academic documents
- How to insert lists, tables, and figures
- How to insert citations to validate your work
In general, when you use citations and referencing, you should either use verbatim comments or you should paraphrase the content of the paper or source from where you have obtained the information. Now that we have covered the basic elements of writing using Authorea, let's turn to the mechanics of writing a grant application and what to include. Remember the basic rules:
- Start with a title
- Write an outline
- Fill the outline with paragraphs of text
- Insert lists, tables, and figures where appropriate and label them.
- Use citations for all facts you present unless they are self-evident or widely accepted and does not normally require a citation
Part II: About writing a research proposal
Write a title of your proposal: rules of writing a title
As I wrote already, you will see that your proposals can be self-initiated, i.e., you will write on your own and propose your research. This happens when you write a Master or a doctoral thesis research proposal as a student, or when you write a research proposal to an agency or funding organisation such as the HRC or the Marsden. In other situations, you 'respond' to the call for proposals when the donor agency would put up information and seek specific proposals. In any case, you start with an expressive title that serves to register your proposal. The title should be written in a way that makes it obvious as to what you are planning to propose. So at the least include an idea of the research you want to do and the outcome you seek or the type of study you want to work on. For journal articles, a good idea is to write it like you are tweeting your research. Short, expressive and provides sufficient information for anyone to make sense of what you are proposing. In summary:
- Your title will be the first thing you will write
- Title must be short and expressive
- Write in title case: this means the first letter of the first word is capitalised; unless another word is a proper noun or needs to be capitalised on the first letter, all other words are written using small letters.
Write a summary or short abstract: rules of writing the summary
The next important element of writing a proposal is to write a short summary. However, I recommend that you write the summary as the last thing. Develop the proposal first of all; then write a succinct summary or abstract. The summary can be structured or unstructured. A structured summary includes the headings and short descriptions of the relevant sections of the proposal. For example, a summary might contain 'introduction', 'methods', 'significance' in the short summary or abstract. This is always placed as the first text block. After the summary or short abstract, you should include the background or introduction, and the methods section in that order. But you do not write them in that order.
Write the goals and objectives: what will you include
Write the background after you write the goals, objectives, and the methods sections. Start with the goal and set the objectives. The goal is usually one or two sentences and you should write this in general terms. For example, if you were to propose a research project where you wanted to develop polygenic risk scores for say obesity, you would write the goal as simple as
"The goal of this project is to develop a predictive or prognostic genetic risk score for obesity".
Next, write the objectives of the study. Again, like 'goal', this will be a maximum of three to five objectives. You should write these using the SMART (Specific, Measurable, Achievable, Realistic, and Time bound) acronym. A specific objective means it has to be precise. For example, if you were to write the objectives for the polygenic risk scores, you would be specific by writing something like:
"We will identify genome wide association studies on the risk alleles for obesity from the database of genome wide association studies". Such a statement tells the reader that the researchers will be specifically targeting obesity as a disease, they will identify genome wide association studies, they will identify risk alleles.
Your objectives must be measurable. This means you will be able to assess objectively. For example, for the polygenic risk score proposal, you may write, "We will identify and validate the extent to which additive effects of multiple alleles put together can explain variation in the prevalence of obesity among the studied population".
Your objectives must be achievable and realistic. This still means you can talk about moonshot, but take small bites at a time. Your objectives need to be such that they will not normally incur a cost in terms of time and resources that are untenable. So, in the polygenic risk score proposal, you cannot write that you will conduct your own GWAS studies. That would not support a viable and realistic project.
This is why your objectives need to be time bound. You must include an element of time. A statement might start like this, "Over the first 6 months ....", or "In the x time period ..." (where x is a number)
The goals and objectives must address a problem that you will solve and in writing the objectives, you provide a roadmap. How you will solve them belongs to the methods section.
Write the methods section: what will you include
The methods section is your technical know-how as to how you will solve the problem whose solution you proposed in the goals section. Add sections and subsections to indicate the different methodological steps. You can write 'step by step' and then indicate the steps. Or you can start with a description of the study design you will undertake, the population you will study, the steps or processes of data collection, the validation of instruments you will use, and the statistical data analysis you will conduct. If you will be using a study design where you will collect primary data (this means first hand data from people), then you will need to specify the sample size. You will need to specify your theory, your hypotheses and how you will meet those hypotheses.
Normally, you will not need to estimate sample size for the following situations:
- If you will conduct a secondary data analysis of government or other archival data where all data are already collected and made available to you
- where you will be collecting data from census (as there is no sampling involved)
- where you will be working on census based data provided to you with fixed number of people (for example large surveys where they collect information from thousands of individuals and you will be using all of that data set)
- where you will be conducting systematic review or a meta analysis
As a checklist, you will want to include the following in your methods section:
- Start each section with a relevant reference to the objective that you will meet. So write something like, "Objective 1 will be met by ...." and so on.
- Indicate the study design. If you will use a primary study design, then indicate whether your study design will be a case study, a case series, a cross-sectional survey, a case control study, a cohort study, or an experimental study design or an epidemiological study design that is something like a randomised controlled trial. If you will conduct a secondary data analysis, indicate what type of secondary data analysis. Will you be using government data bases to search for information? Will you conduct a meta-analysis?
- Indicate the population you will study. Who are they? Where will you find them? How will you find them?
- Indicate the exposure variable you will study. If you are proposing an experimental study such as a randomised controlled trial, then indicate the independent variable.
- Indicate how you will obtain data. What data you will seek? Which variables you will study? How will you measure these variables? Are they already collected?
- Examine each of your hypotheses. What difference would be meaningful difference? This will form the basis of your sample size and power calculation.
- If you will use an instrument like a questionnaire, or a survey instrument, then indicate how you will validate such instruments?
- Indicate how you will analyse the data? What steps you will take for preprocessing the data set? What tests will you do?
- What are the limitations of your approach? How can they be improved? What are the advantages?
Now that you have written the methods section, it is time for you to turn to writing the backgrounds or the introduction section. You will write late in the process because you want to focus the attention of your reader to specific points that will have high impact on assessment of your proposal. This is where we turn our attention now.
Write the backgrounds/introduction section
Treat the background writing like storytelling. Convert it into a three-part act:
- In the first part, introduce a problem. Build a crisis point and show what would happen if the problem is not mitigated.
- In the second part, suggest a resolution to the problem and a pathway out of the problem.
- In the third part, state how you propose to solve the problem and why or how your solution adds something 'new' to solving the problem or brings a new perspective that is either different or better than existing solutions.
This is a general framework. What you will write will depend on the nature of the problem you will write about. Some of these are discipline-specific. For example, if you were to propose development of a polygenic risk score for obesity, then your story-line would go something like:
- Obesity is a risk for different diseases downstream. If that problem is not addressed or treated, then this will lead to other serious issues such as heart disease burden, diabetes, and other issues
- Behavioural approach might work in controlling issues around obesity such as exercise, dietary advice, and medication, but focusing only on the environmental aspect of obesity control does not take into account the genetic component. Understanding the genetic contribution to obesity is important but hindered by non-availabilty of genetic data. However, that problem is now addressed with human genome project and other studies looking into genetic contribution of obesity. But it may not be one gene, but an interplay of multiple genes, and identifying and cataloging genes is not enough. How do we add value to that information?
- Now, at that point, jump to propose that you will conduct a polygenic risk score and stratify individuals on their genetic scores on the risk of their obesity and obesity related issues.
This is one approach. Other approaches include starting with what we know about a situation or a problem, what we do not know about the problem, and what difference will your proposed research add to the larger picture, and what will be your contribution to the field. This is useful when you are proposing to write a doctoral or master level thesis proposal.
In summary,
- Start with a problem or a health issue (as you are all health sciences graduates)
- Critique what is known and point out the deficits
- Introduce some solutions
- Offer your own solution and argue how you add value to the existing knowledge base.
In this way, lead your reader to the next stages and walk your way through what steps you will take to address the issue you have raised. Here, jump off to the goals and objectives of your project and then launch on the methods section.
In the third and final part, let's see how we can use Authorea to tie everything together. The rules once again:
- Write a title
- Set up an outline
- Decide on the sections (for a proposal they would be something like summary, introduction, methods; for a journal article the major sections will be abstract, introduction, methods, results, discussion)
- Do your background research and identify the resources you will use (the citation and the literature)
- Identify the graphs and tables (a good idea would be to draw the tables on pen and paper before committing to the computer)
- Plan on the attack using paragraphs of text
At this stage, you are ready to kick the tyres on Authorea.
Part III: Use Authorea to write your proposal
Step by step of using Authorea to write your proposal
Step 1: Get an account on Authorea and start a new document. This should be intuitive. You will see a blank new document
Step 2: Start by creating an outline on Authorea
Step 3: Fill in the tables and figures (see the above sections)
Step 4: Start filling in the sections by writing paragraphs of text and adding lists, other tables, figures and citations as needed.
Once you are done with a first draft, leave it for a day, and then come back to it for revising the re-editing. As in using a washing machine, "rinse and repeat". Repeat till you are satisfied with the draft. You are now ready to export the document from Authorea to other formats.
Exporting an Authorea document to PDF
Click on the export icon or drop down the Document tab and select 'Export'. Export to PDF or Word or LaTeX. Save your paper to a drive on your selected folder and then upload to learn, or distribute the final document using email.
Upload the PDF to Learn for submission
After saving the file on your hard drive of the computer, you will need to log into "learn". Then, upload to Learn using the usual procedures.
Part IV: Advanced topics (to be completed, not included here as these are not immediately necessary for you)
How to share your work from Authorea to journals and preprints
Version control
What is a markdown block and why will you use it
What is a latex block and why will you use it
Intefacing a Jupyter notebook with Authorea
Interfacing a reference manager with Authorea
Anchoring in Authorea