Enough R to write a thesis

From raw data to finished thesis

Published

November 15, 2023

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.

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 (our earlier R markdown book is here). All the biostats books were written in R markdown or 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

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.

Dr Aud Halbritter
Dr Josh Lynn
Dr Emily G. Simmonds
Dr Jonathan Soule
Dr Richard J. Telford

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/working.jpg") ``` 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. ::: ### 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/stats.jpg") ``` 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/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 (our earlier [R markdown](rmarkdown/index.html) book is here). All the biostats books were written in R markdown or 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/github.jpg") ``` 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/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/package.jpg") ``` 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 eval = FALSE} # install remotes if you don't have it already # install.packages("remotes") remotes::install_github("biostats-r/biostats.tutorials") ``` ## 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 - Dr Josh Lynn - Dr Emily G. Simmonds - Dr Jonathan Soule - Dr Richard J. Telford This is [BioCeed](https://bioceed.w.uib.no/) product.