Chapter 1 Introduction

This webbook contains all the code used for the study on the effect of probiotics on Salmonella infection in broiler chicken.

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/3d-omics/AMAC005_salmonella_trial.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(broom)
library(broom.mixed)

# For tree handling
library(ape)
library(phyloseq)
library(phytools)

# For plotting
library(ggplot2)
library(ggrepel)
library(ggpubr)
library(ggnewscale)
library(gridExtra)
library(ggtreeExtra)
library(ggtree)
library(ggh4x)

# For statistics
library(spaa)
library(vegan)
library(Rtsne)
library(geiger)
library(hilldiv2)
library(distillR)
library(ANCOMBC)
library(lme4)
library(Hmsc)

  1. University of Copenhagen, ↩︎