This complete tutorial introduces all the possibilities of the
virtualspecies package. It was written with the objective
to be helpful for both beginners and experienced R users. You can read
this tutorial in full or jump to the particular section you are looking
for. In each section, you will find simple examples introducing each
function, followed by detailed examples for almost every possible
parametrisation in virtualspecies.
After a small introduction on the spatial data used as input for the
virtualspecies package (section 1.), you will be introduced
to the basics of generating virtual species distributions: the two
possible approaches to create species-environment relationships
(sections 2. and 3.), followed by the conversion of environmental
suitability to presence-absence (section 4.). After that, you will see
how to generate random virtual species (section 5.), and most
importantly, how to explore, extract, and use the outputs of
virtualspecies (section 6.). Then, you will see how to
sample occurrence points (section 7.). Finally, you will learn about how
to general dispersal limitations to your virtual species in section
8.
I will make extensive use of climate data as an example here, but remember that you can use other types of data, as long as it is in the format described in section 1.
virtualspecies has been updated to version 1.6 in
September 2023. The major change in this update is that now this package
relies upon the R package terra rather than
raster; in addition, internally it uses functions from the
package sf rather than sp. This update was
required since multiple spatial packages are going to be retired from R,
and future developments and improvements of spatial packages will rely
on terra and sf.
This update may cause some breaking changes. I maintained
the changes as minimal as possible so that previous code (version <=
1.5) will still be compatible with the new code (version >= 1.6).
However, objects generated in versions <= 1.5 will likely not be
compatible with the package version 1.6. They can still be converted
manually to become compatible, using functions from the package
terra such as rast(). If you find yourself in
trouble, email me about that. In addition, the methods in functions
limitDistribution() and sampleOccurrences()
have changed slightly because they now use the package
rnaturaleath (formerly they used
rworldmap).
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Do not hesitate if you have a question, find a bug, or would like to add a feature in virtualspecies: mail me!