Data analysis for the project MCTdownUnder

Author

Affiliation

Shane L Hogle

University of Turku

Keywords

Microbiology, Ecology, Evolution, Antimicrobial resistance (AMR)

1 Manuscript:

1.1 Published record

TBD

1.2 Preprint

TBD

2 Introduction

The goal of this project is to examine how …

3 Experiment overview

This is how we did our experiment…

4 Analysis overview

This is how we did our data analysis…

5 Availability

Data and code in this GitHub repository (https://github.com/slhogle/MCTdownUnder) are provided under GNU AGPL3. The rendered project site is available at https://slhogle.github.io/MCTdownUnder/, which has been produced using Quarto notebooks. The content on the rendered site is released under the CC BY 4.0. This repository hosts all code and data for this project, including the code necessary to fully recreate the rendered webpage.

An archived release of the code is available from Zenodo: https://zenodo.org/records/EVENTUAL_ZENODO_RECORD

6 Reproducibility

The project uses renv to create a reproducible environment to execute the code in this project. See here for a brief overview on collaboration and reproduction of the entire project. To get up and running from an established repository, you could do:

install.packages("renv")
renv::restore()

To initiate renv for a new project:

install.packages("renv")
# initialize
renv::init()
# install some new packages
renv::install("tidyverse")
# record those packages in the lockfile
renv::snapshot()