Welcome to IsoriX

This is the development repository of IsoriX, an R package aiming at building isoscapes using mixed models and inferring the geographic origin of organisms based on their isotopic ratios.

Where to learn about IsoriX?

You can start by reading our bookdown!

Then, it may not be a bad idea to also have a look at our papers: here and there.

Another great source of help is our mailing list. First register for free (using your Google account) and then feel free to send us questions.

For specific help on IsoriX functions and objects, you should also check the documentation embedded in the package after having installed and attached (= loaded) it:

help(package = "IsoriX")

How to download and install IsoriX?

You can download and install the stable version of IsoriX directly from within R by typing:

install.packages("IsoriX", dependencies = TRUE)

Note: if you get into troubles due to gmp, magick, maps, maptools, rgeos, rgdal, rgl or testthat, retry using simply:

install.packages("IsoriX")

These packages offer additional functionalities but some of them are particularly difficult to install on some systems.

If you want the development version of IsoriX, you can download and install it by typing:

remotes::install_github("courtiol/IsoriX/IsoriX")

Mind that you need the R package remotes to be installed for that to work. Mind also that the development version, being under development, can sometimes be broken. So before downloading it make sure that the current build status is . The current built status is provided at the top of this readme document.

Installation behind a proxy?

Also, if you access the network via a proxy, you may experience troubles with install_github. In such case try something like:

library(httr)
with_config(use_proxy("192.123.4.5:6789"), remotes::install_github("courtiol/IsoriX/IsoriX"))

Off course, unless you are in the same institute than some of us, replace the numbers ("192.123.4.5:6789") with those corresponding to your proxy settings!

How can you contribute?

There are plenty way you can contribute! If you are fluent in R programming, you can improve the code and develop new functions. If you are not so fluent, you can still edit the documentation files to make them more complete and clearer, write new vignettes, report bugs or make feature requests (see our bookdown for details).

Main packages behind IsoriX

IsoriX heavily depends on two R packages: spaMM & rasterVis.