1 Introduction

This webbook contains all the dadta and code used for the comparative study on the generation of genomic and metagenomic data from faeces of various vertebrate species using three extraction methods.

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_extraction_test.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(rairtable)
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(MuMIn)
library(sjPlot)
library(ggeffects)

1.1.3 Color codes

vertebrate_colors <- c(`Calotriton asper`="#157a73",
                    `Lissotriton helveticus`="#47bfb6",
                    `Salamandra atra`="#92d4d1",
                    `Chalcides striatus`="#4a7015",
                    `Natrix astreptophora`="#7ea845",
                    `Podarcis muralis`="#b9d98d",
                    `Plecotus auritus`="#5e1717",
                    `Sciurus carolinensis`="#aa3333",
                    `Trichosurus vulpecula`="#bf7777",
                    `Geospizopsis unicolor`="#9e6b24",
                    `Perisoreus infaustus`="#dba55a",
                    `Zonotrichia capensis`="#dbbd93",
                    `Extraction control`="#7a7a7a",
                    `Library control`="#4a4a4a")

  1. University of Copenhagen, ↩︎