Chapter 1 Introduction
Welcome to the official documentation for the R package IsoriX.
This bookdown (a particular form of R documentation) explains how to use IsoriX and provide information about the underlying methods.
The content will keep evolving so to remain up to date with the current version of IsoriX, as well as to become progressively more complete and accurate.
In early versions of IsoriX, the documentation was included as vignettes attached to the package, but we have decided to move the content here.
That way, we can include more content, display better pictures and update the documentation independently from the package.
1.1 What is IsoriX?
IsoriX is an R package that can be used for building isoscapes and inferring the geographic origin of organisms based on their isotopic signature (Courtiol et al. 2019).
This package employs a new statistical framework based on mixed models (GLMMs) for doing all of this.
As most other packages dedicated to specific applications, IsoriX is essentially a simple interface to several other packages more general in scope.
Specifically, it uses the package spaMM for fitting and predicting isoscapes, and for performing the assignment.
The spatial data generated by IsoriX are organised into rasters via the package terra (since IsoriX version 0.9.1, and before via raster).
IsoriX also heavily relies on the package rasterVis for plotting the maps using the powerful lattice visualization system.
Knowing these packages is not necessary to handle IsoriX, but it certainly helps for advanced applications.
1.2 Who are we?
The current IsoriX core team includes:
- Alexandre Courtiol
- François Rousset
- Stephanie Kramer-Schadt
Alex does the programming for IsoriX.
François does the programming for spaMM so as to make IsoriX working always better.
Alex and François are also the ones that have cooked up together the statistical framework behind IsoriX.
Stephanie is the person who initiated this project and who has co-supervised many students whose projects relied on IsoriX.
Alex and Stephanie are both based in the Leibniz Institute for Zoo and Wildlife Research in Berlin (Germany).
François is based at the Institut des Sciences de l’Evolution in Montpellier (France).
The extended IsoriX team also includes students that helped us with the coding and proofreading (Colin Vullioud, Leonie Walter),
users and participants of the Leibniz-IZW summer schools on stable isotopes who made feedbacks,
as well as all the authors listed in the main IsoriX publication (Courtiol et al. 2019):
## Courtiol A, Rousset F, Rohwäder M, Soto DX, Lehnert L, Voigt CC, Hobson
## KA, Wassenaar LI, Kramer-Schadt S (2019). "Isoscape computation and
## inference of spatial origins with mixed models using the R package
## IsoriX." In Hobson KA, Wassenaar LI (eds.), _Tracking Animal Migration
## with Stable Isotopes_, second edition. Academic Press, London.1.3 Who are you?
We don’t know all IsoriX users, but we would love to!
For us it is important to know who uses IsoriX in order to best allocate our efforts and make IsoriX better for those who use it.
So if you are thinking of using IsoriX, please subscribe to our Google group (a mailing list) and feel free to write us a little message about your project.
In this documentation, we will try to please from the very newbie to the experienced users. We will however assume that you already know R a little bit. If it is not the case, you should read an Introduction to R or any other introduction to R before continuing. We will also assume that you all know a little bit about stable isotopes and isoscapes. For the stats bits, we will also assume that you know generalized linear models and hopefully a little bit about mixed models, too.
1.4 We need your help!
No member of the IsoriX core team has IsoriX, nor even stable isotope, as its main research topic.
We developed it so as to help our colleagues and others, but we cannot dedicate a huge amount of time to it.
So, we would greatly appreciate any help to improve IsoriX and/or its documentation.
There are plenty of things you could do to help us, irrespective of your knowledge and skills.
Please check chapter 8 for details, or contact us using our mailing list.