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Last update: 2025-05-15

Chapter 1 Introduction

This webbook contains all the code used for data analysis in study of the individual-level respirometry tests of Calotriton asper from different elevations and acclimation in distinct temperatures. metagenomic data of Podarcis muralis and Podarcis liolepis lizards from different environments during an experimental setup.

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/alberdilab/calotriton_respirometry.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(readxl)
library(readr)
library(hms)
library(dplyr)

# For respirometry data
library(respR)

# For plotting
library(ggplot2)
library(ggpmisc)
library(ggpubr)

# For statistics
library(nlme)
library(lme4)
library(rstatix)