Exercise: Build a Research Diary

Learning Goal

Create a Quarto document for documenting ongoing research activity in a structured, readable way.

The focus is not only on recording what you did. The goal is to make the reasoning, evidence, uncertainty, and next steps clear enough that you or a collaborator could understand the decision later.

Prerequisites

You should be familiar with:

Starter Scenario

Choose one recent decision, comparison, or exploratory step from your own modelling work. This does not need to be a major result.

Examples include:

  • Choosing between two environmental datasets
  • Excluding, transforming, or aggregating observations
  • Changing a parameter value or model setting
  • Comparing alternative model runs
  • Diagnosing unexpected spatial or temporal patterns
  • Deciding whether to trust a model output
  • Recording why a result was not used
  • Noting an assumption that may need to be revisited

Step-By-Step Exercise

  1. Create a new file called notebook.qmd.
  2. Add a YAML header with a title, your name, today’s date, and format: html.
  3. Add a short context section explaining the project, model, dataset, or research question.
  4. Describe the recent data exploration or modelling decision you selected.
  5. List the inputs used, such as datasets, scripts, model versions, parameters, spatial extent, time period, or assumptions.
  6. Summarise the evidence you looked at by including a code chunk that prints relevant information to the html output. This could include a table, figure, map, model run ID, file path, warning message.
  7. State the decision or outcome.
  8. Explain the rationale for the decision.
  9. Note any uncertainty, limitations, or conditions under which the decision should be revisited.
  10. Add one to three concrete next steps.

Suggested Starter Content

---
title: "Restoration Project Notebook"
author: "Your Name"
date: today
format: html
---

## Context

Project, model, dataset, or research question:

## Entry 1: dd/mm/yyyy

Briefly describe the recent modelling decision or data exploration. Explain why this step mattered for the modelling workflow or research question.

## Inputs used

- Dataset(s):
- Script(s) or workflow step(s):
- Model version or settings:
- Spatial extent and time period:
- Key assumptions:

## Evidence

Describe the evidence used to support the decision, using a code chunk to include any relevant data, summary, or visualization. 

## Observations

- What did you notice?
- Were there unexpected patterns, warnings, or inconsistencies?
- What seemed reliable or unreliable?

## Decision or outcome

State what you decided, changed, kept, rejected, or postponed.

## Rationale

Explain why the decision makes sense based on the available evidence.

## Uncertainty and limitations

What remains uncertain? Under what conditions should this decision be revisited?

## Next steps

1.
2.
3.

Advanced tasks

  • Add a callout to highlight an assumption, risk, or issue to revisit.
  • Add caching to the code chunk so that it runs only when the underlying data or code changes.
  • Add a second entry for the next week and add the first entry to a collapsible callout. (works best for HTML output, not PDF)

Expected Outcome

By the end, you should have a Research Diary entry that:

  • renders as a readable HTML document
  • records a real environmental modelling decision or exploration
  • separates context, evidence, decision, rationale, uncertainty, and next steps
  • could help you or a collaborator understand the decision later
  • could be reused as a template for future modelling work

Self-Check

Ask yourself:

  • Would this entry make sense if I read it again in a month?
  • Can another researcher understand why the decision was made?
  • Is the evidence specific enough to locate or reproduce the check?
  • Are uncertainty and next steps recorded clearly?
  • Is the structure simple enough to reuse consistently?