1 Introduction

This webbook contains all the code used for the comparative study on the generation of metagenomic data from faeces of various species using three extraction methods. The raw code used for rendering this webbook is available in the following Github repository:

https://github.com/earthhologenome/EHI_technical_considerations

1.1 Prepare the R environment

1.1.1 Environment

To reproduce all the analyses locally, clone this repository in your computer using:

RStudio > New Project > Version Control > Git

And indicating the following git repository:

https://github.com/earthhologenome/EHI_technical_considerations.git

Once the R project has been created, follow the instructions and code chunks shown in this webbook.

1.1.2 Libraries

The following R packages are required for the data analysis.

# Base
library(R.utils)
library(knitr)
library(tidyverse)
library(devtools)
library(tinytable)
library(rairtable)
library(phyloseq)
library(ggtree)
library(ape)
library(ggnewscale)
library(ggtreeExtra)
library(nlme)
library(broom)
library(broom.mixed)
library(ggdist)
library(sjPlot)
library(multcomp)
library(car)
library(cluster)
library(vegan)
library(ggrepel)

  1. University of Copenhagen, ↩︎