---
title: Class Project Overview 
subtitle: ""
---

::: {.note}
Some of this will only fully make sense once we are a few weeks into
the course. It's nevertheless a good idea to read through it and get an
overall idea before we have discussed all the different tools and
details mentioned. Re-visit/re-read as needed.
:::

# Overview

A semester long data analysis project will be a major method of
assessment for this class. The project should include all the different
components of a data analysis we will cover in this class.

-   Finding a good data - question pair
-   Getting the data
-   Cleaning the data
-   Exploring the data
-   Processing the data
-   Analyzing the data
-   Reporting/communicating your findings
-   Doing everything reproducibly

**You can do the class project either on your own or in a team of two.**

# Timeline

There are several deadlines throughout the course at which time you need
to submit parts of your project

-   Part 1: Have a question/hypothesis & suitable data.
-   Part 2: Part 1 + exploratory analysis.
-   Part 3: Part 2 + start of statistical analysis.
-   Part 4: Part 3 + most of statistical analysis.
-   Part 5: Complete project, ready for peer review.
-   Part 6: Complete final project, updated based on reviewer feedback.

The deadlines are listed in the **Schedule** document (it's unlikely,
but they might change, so keep checking that document).

# Project Requirements

You can pick your project topic and data source pretty much however you
like. The only requirements are:

-   Real world (messy) data.
-   An interesting question.
-   An analysis that has not been done previously.
-   A fully reproducible and automated analysis using the tools we use
    in this class.

# Data sources

You can use data from any source you like, here are some possible ones.

## Your "own" data

If you have data that you are using for some research project(s) you are
doing, you are welcome and encouraged to work on this as part of the
class project. Of course, what you do for this class project needs to be
new work, not a previously done and recycled analysis. Also, since the
analysis needs to be fully reproducible, you need to provide the data at
least within the class (no need to make it publicly available). *I
encourage you to use the class project toward helping you do an analysis
and write a report that can help you with a project you want to publish
as part of your research!*

## Publicly available data

You can use any data you can get access to. Since it needs to be
reproducible, you need to be able to share the data at least with me and
the classmates who will review your project. If you need some ideas for
data, check out this [website I maintain with various links to
resources](https://andreashandel.github.io/research-and-teaching-resources/),
among them is a list with links to various data sources. Of course you
are not limited to data listed there.

*Often, the most interesting questions can be asked by combining data
from more than one source.*


# Logistics and formatting

Each assignment needs to be submitted in a fully reproducible form,
using the tools we cover in the class (R, Quarto, GitHub, etc.). You
should create a Github repository (using the template described below)
which should contain all the files for your project. Name it
`YOURLASTNAME-MADA-project`. The preferred type is a public repository,
if you have data that requires to be kept confidential, you can make it
a private repository. If you need to use a private repository, please
let me know.

The main document should be a Quarto file, which can be turned into a
suitable output format (html or word or pdf). This should have the
structure of a scientific paper. I suggest you use the `manscript.qmd`
file of the template and replace the template content with your content.
I also suggest having the output be a word document, since that is what
most journals want for submission of a scientific paper. The template I
provide is set up for word output. However, if you for instance decide
to include interactive figures or apps (using e.g. Shiny) in your
analysis project, you can also pick html as output. If for some reason
you want/need pdf, that's ok too (then you need a LaTeX system
installed, see the Quarto documentation for how to do that).

Structure your project similar to the provided template (see below),
with data, scripts, results and manuscript in different folders, various
R scripts to perform different bits of the analysis, and a final Rmd
file that pulls everything in and generates the report.

Use a setup that resembles a real research paper. A main manuscript file
in Quarto format should contain text, the main results (figures/tables),
references, etc. A supplementary Quarto file should contain additional
results, such as some of your exploratory analysis findings. Any code
and further results should be in additional Quarto files (with code
either inside the Quarto file, or in separate R files). Overall, your
write-up can be a bit more detailed than what would normally go into a
peer reviewed paper, with the most salient parts shown in the main text,
and the rest in a supplementary file.

For all your submissions, you need to provide everything needed (data,
code, etc.) to allow a full and automated reproduction of your analysis.

References should be included as a bibtex file and cited in the Rmd
file. See the template for an example.

# Project template

I created a [public Github repository called
data-analysis-template](https://github.com/ahgroup/data-analysis-template)
which is meant as a template for doing a data analysis project. It has
different folders for organizing your project. Various readme files are
provided to explain what each folder should contain. The template also
contains several example files to show how the whole project workflow
(or any data analysis workflow for that matter) can work.

Use the provided template as starting point for your project. To do so,
go to its Github repository and follow the instructions to turn it into a new repository for your class
project, call it `YOURLASTNAME-MADA-project`. Once you made the new
repository, follow the usual Github workflow to get it to your local
computer. Then open the readme file and change the text so it states
somewhere "This is YOURNAME class project repository".


Inside the `manuscript` folder, there is a Quarto template file called
`manuscript.qmd` with a suggested outline for the report write-up. I
have also indicated which sections need to be completed/filled for which
part of the project. This template is just a guide, you do not have to
follow exactly that structure, as long as you provide all the requested
parts for the the different submission deadlines and a final, complete,
fully automated and reproducible project, with all files in one GitHub
repository, at the end.

In addition to the Quarto file, there is a bibliography file in bibtex
format which contains the references, and a style file which indicates
reference formatting. You can use it as starting point. Feel free to
switch the reference formatting style. You do need to use a setup and
reference manager that plays nicely with Quarto. I recommend Zotero with the Better Bibtex extension.


# Feedback and Assessment

You will receive feedback from me and/or your classmates after each
submission.

-   I will provide feedback and assess parts 1,2 and 4, mainly checking
    to see that you deliver what you were supposed to and got the
    project to the requested stage.
-   Your classmates will provide peer-review feedback on parts 3 and 5.
    Details on that is provided in the [**Project Review**](/project/project-review.qmd) document.
-   Part 6 is the final submission.

The initial submissions and peer reviews make up 40% of the project
grade. The final submission counts for the remaining 60%.

**More details on what exactly is expected and how it is assessed is
provided in the [**Project Details**](/project/project-details.qmd) document.

# Project communications

Any communication regarding this project should happen in the *Project*
discussion channel. Go there to ask project-specific questions, to post
links to your repository whenever you have a part finished, etc. I will
also post any further or clarifying information there.
