An R package for Post Vortex Simulation Analysis.
Using this package, data of population viability analysis (PVA) generated with the software Vortex (Lacy & Pollak 2013) can be collated, plotted and analysed using basic (e.g. pairwise comparisons of scenarios) or more advanced statistics (e.g. fitting regression models).
The stable version of
vortexR can be installed with:
install.packages("vortexR", dependencies = TRUE)
The latest development versions of
vortexR and its supplementary data package
vortexRdata can be installed with:
# install.packages("devtools") devtools::install_github("carlopacioni/vortexRdata") devtools::install_github("carlopacioni/vortexR")
Fresh Windows installations of R will require Rtools for Windows.
If installation with
you can run
rJava require a Java Development Kit (JDK)
installed and registered correctly with R.
Make sure to install a 64-bit JDK if you are using a 64-bit version of R.
A typical installation path for Java-based packages like
glmulti in a
GNU/Linux-based operating system (here: Ubuntu 16.04 LTS) along the lines of
- On the terminal, install Java:
sudo apt-get install openjdk-8-jdkand verify with
- Set default Java installation:
sudo update-alternatives --config java
- Set default Java compiler:
sudo update-alternatives --config javac
- Set the environment variable
JAVA_HOMEto your preferred Java installation: (here we use /usr/lib/jvm/java-8-openjdk-amd64/jre) by appending the line
sudo echo "JAVA_PATH=\"/usr/lib/jvm/java-8-openjdk-amd64/jre\"" >> /etc/environment
source /etc/environmentto instantly export the new environment variable
- Verify that
echo $JAVA_HOMEprints the
- Register Java with R:
sudo R CMD javareconf
- In R, install
Independently of vortexR, a
sudo R CMD javareconf (and possibly the installation
rJava and Java-using packages like
glmulti) will be required after each
update of R and / or your Java installation.
A typical installation under Windows could follow:
- Download and install Java
- Find "Environment Variables", add variable
JAVA_HOME(Windows 10 tutorial, Windows 7 tutorial), verify on Command Prompt (Win + r, "cmd", Enter):
- Make sure that the environment variable 'JAVA_HOME' is set properly and points to a 64-bit version jof Java(JDK or SE Runtime). For 64-bit Revolution R you need to make sure that you have a 64-bit version of Java installed.
- Make sure that the Java 'CLASSPATH' variable is set properly.
For the 64-bit version of the JDK, this could be e.g.
- Check your system PATH settings. On Windows, goto
Control Panel ---> System --> Advanced Settings ---> Environment Variables. Your path should include the directories:
C:\Program Files\Java\jre6\bin\serverand the R installation directory, e.g.
- Make sure that the environment variables
RHOMEare BOTH set and point to the R installation directory, e.g.
- In R, install
If you have still problem installing and loading
glmulti package and/or
rJava, you may not have Java installed or are not using the same Java version as R.
Make sure that if you are using a 64-bit version of R, you also have installed
a 64 bit version of Java (most automatic installation via web browser will
install a 32-bit version).
Your mileage may vary depending on your operating system and your versions of Java and R. Stack Overflow's R community is a great source for troubleshooting.
??vortexR to see a broad description of the package.
help(package = "vortexR") to see the documentations available.
Read the vignette for a more comprehensive description of the package.
Be aware, if you did not use
build_vignette=TRUE this documentation may
not be available from within R. In these cases, download the PDF of these documents.
On some platforms,
??vortexR may not work even if you used
If you use
vortexR, please use the citation generated from
We are happy to receive feedback and contributions through bug reports and pull requests.
We aim to follow the style suggestions by
formatR::tidy_dir("R", width.cutoff = 79),
devtools::check(check_version = T, force_suggests = T, cran = T).
In a new environment, e.g. after an upgrade of R, running the tests could
require to install vortexR's dependencies with
install.packages("vortexR", dependencies = T).
Note on R 3.4.0: update lintr to solve bug roxygen #627.
Building the documentation
The static HTML behind the GitHub pages is built with
The documentation should be re-built before each submission.