Enough R to write a thesis

From raw data to finished thesis

Published

January 7, 2025

The biostats books, apps, and tutorials are written to give you enough skills to write a thesis.

The books emphasis reproducible research.

Biostats books

Working in R

Learn how to import, manipulate and visualise data with our working in R book. After an introduction to R, this book has a tidyverse flavour, showing how to manipulate data with dplyr and make publishable plots with ggplot2. It includes lots of exercises to hone your skills.

The data life-cycle

Your data are precious. Learn how to take care of them with our data life-cycle book.

Statistics in R

Statistics logo

Coming soon!

Reproducible documents with R

Learn how to write reproducible documents (anything from a course assignment to a thesis or manuscript) in quarto: no more copy-paste nightmares. Quarto is the successor to R markdown . All the biostats books were written in quarto; you can see the source code in our repo on GitHub.

Git and GitHub

Learn how to use version control with our step-by-step guide to setting up and using git and GitHub in RStudio.

Enough targets to Write a Thesis

Learn how to run data analysis pipeline for reproducible and scalable workflows. Our guide to using the targets package will show you how.

Writing an R package

Want to make your code into an R package? Our guide to writing an R package will show you how.

Biostats apps and tutorials

We have developed interactive learnr tutorials for

naming objects
dates and times
string manipulation

and shiny apps to explore some statistical concepts.

These can be installed from biostats apps and learnr tutorials with

# install `remotes` package if you don't have it already
# install.packages("remotes")

remotes::install_github("biostats-r/biostats.tutorials")

Packages

The checker package checks that students have the correct version of R, R packages, RStudio and other dependencies installed, and that the recommended RStudio configuration has been applied. It uses yaml to record the settings.

Courses

Quarto thesis template

Try our thesis template for your MSc thesis to make a fully reproducible thesis.

The Biostats team

These books are a collaboration between the Department of Biological Sciences, University of Bergen and the Department of Mathematical Sciences, University of Trondheim.

This is BioCeed product.

```{r} r_logo <- fontawesome::fa(name = "r-project", fill = "steelblue") ``` The biostats `r r_logo` books, apps, and tutorials are written to give you enough `r r_logo` skills to write a thesis. The books emphasis reproducible research. ## Biostats books ```{=html} <style> a.book:link { color:#eeaa2c; text-decoration:none; font-weight:normal; } a.book:visited { color: #eeaa2c; text-decoration:none; font-weight:normal; } a.book:hover { color: #eeaa2c; text-decoration:underline; font-weight:normal; } a.book:active { color: #eeaa2c; text-decoration:none; font-weight:normal; } </style> ``` ### <a class = "book" href = "workingInR/index.html">Working in R</a> ::: {layout="[[25,75]]"} ```{r} #| label: working-in-r #| fig-link: workingInR/index.html #| echo: false #| fig-alt: "Working in R logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/1_workingR.png") ``` Learn how to import, manipulate and visualise data with our [working in R](workingInR/index.html) book. After an introduction to R, this book has a tidyverse flavour, showing how to manipulate data with `dplyr` and make publishable plots with `ggplot2`. It includes lots of exercises to hone your skills. ::: ### <a class = "book" href = "data_lifecycle/index.html">The data life-cycle</a> ::: {layout="[[25,75]]"} ```{r} #| label: data-lifecycle #| fig-link: data_lifecycle/index.html #| echo: false #| fig-alt: "Data life-cycle book logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/7_data.png") ``` Your data are precious. Learn how to take care of them with our [data life-cycle](data_lifecycle/index.html) book. ::: ### Statistics in R ::: {layout="[[25,75]]"} ```{r} #| label: statistics #| echo: false #| fig-alt: "Statistics logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/2_stats.png") ``` Coming soon! ::: ### <a class = "book" href = "quarto/index.html">Reproducible documents with R</a> ::: {layout="[[25,75]]"} ```{r} #| label: markdown #| fig-link: quarto/index.html #| echo: false #| fig-alt: "Quarto markdown logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/3_quarto.png") ``` Learn how to write reproducible documents (anything from a course assignment to a thesis or manuscript) in [quarto](quarto/index.html): no more copy-paste nightmares. Quarto is the successor to R markdown . All the biostats books were written in quarto; you can see the source code in our [repo](https://github.com/biostats-r/biostats) on GitHub. ::: ### <a class = "book" href = "github/index.html">Git and GitHub</a> ::: {layout="[[25,75]]"} ```{r git, echo = FALSE, fig.alt="git logo", out.width= "25%", out.extra='style="float:left; padding:5px"'} #| label: git #| fig-link: github/index.html #| echo: false #| fig-alt: "Git and GitHub logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/4_git.png") ``` Learn how to use version control with our step-by-step guide to setting up and using [git and GitHub](github/index.html) in RStudio. ::: ### <a class = "book" href = "targets/index.html">Enough targets to Write a Thesis</a> ::: {layout="[[25,75]]"} ```{r} #| label: targets #| fig-link: targets/index.html #| echo: false #| fig-alt: "Targets logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/6_targets.png") ``` Learn how to run data analysis pipeline for reproducible and scalable workflows. Our guide to [using the targets package](targets/index.html) will show you how. ::: ### <a class = "book" href = "package/index.html">Writing an R package</a> ::: {layout="[[25,75]]"} ```{r} #| label: package #| fig-link: package/index.html #| echo: false #| fig-alt: "Writing an R package logo" #| out-width: 300px #| out.extra: 'style="float:left; padding:5px"' knitr::include_graphics("figures/5_package.png") ``` Want to make your code into an R package? Our guide to [writing an R package](package/index.html) will show you how. ::: ## Biostats apps and tutorials We have developed interactive `learnr` tutorials for - naming objects - dates and times - string manipulation and shiny apps to explore some statistical concepts. These can be installed from [biostats apps and `learnr` tutorials](https://github.com/biostats-r/biostats.tutorials) with ```{r} #| label: biostats.tutorials #| echo: true #| eval: false # install `remotes` package if you don't have it already # install.packages("remotes") remotes::install_github("biostats-r/biostats.tutorials") ``` ## Packages The `checker` package checks that students have the correct version of R, R packages, RStudio and other dependencies installed, and that the recommended RStudio configuration has been applied. It uses yaml to record the settings. ## Courses - [Bio101](https://github.com/biostats-r/Bio101_tutorial) - [Bio104](https://github.com/biostats-r/Bio104_tutorial) - [Bio300b](https://biostats-r.github.io/bio300B/index.html) ## Quarto thesis template Try our [thesis template](https://github.com/biostats-r/quartothesis) for your MSc thesis to make a fully reproducible thesis. ## The Biostats team These books are a collaboration between the [Department of Biological Sciences](https://www.uib.no/en/bio), [University of Bergen](https://www.uib.no/en) and the [Department of Mathematical Sciences](https://www.ntnu.edu/imf), [University of Trondheim](https://www.ntnu.edu/). - [Dr Aud Halbritter](https://github.com/audhalbritter) - [Dr Josh Lynn](https://research.manchester.ac.uk/en/persons/joshua.lynn) - [Dr Emily G. Simmonds](https://www.ntnu.edu/employees/emily.g.simmonds) - [Dr Jonathan Soulé](https://www.uib.no/personer/Jonathan.Jean.Cornille.Soul%C3%A9) - [Dr Richard J. Telford](https://github.com/richardjtelford/) This is [BioCeed](https://bioceed.w.uib.no/) product.