vortexR

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).

Install

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 build_vignette=TRUE fails, you can run install_github("carlopacioni/vortexR").

Java-based packages

The packages glmulti and 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 DigitalOcean’s tutorial:

On the terminal, install Java: sudo apt-get install openjdk-8-jdk and verify with java -version
Set default Java installation: sudo update-alternatives --config java
Set default Java compiler: sudo update-alternatives --config javac
Set the environment variable JAVA_HOME to your preferred Java installation: (here we use /usr/lib/jvm/java-8-openjdk-amd64/jre) by appending the line JAVA_PATH=/path/to/your/Java/binary to /etc/environment: sudo echo "JAVA_PATH=\"/usr/lib/jvm/java-8-openjdk-amd64/jre\"" >> /etc/environment
Run source /etc/environment to instantly export the new environment variable JAVA_HOME
Verify that echo $JAVA_HOME prints the /path/to/your/Java/binary
Register Java with R: sudo R CMD javareconf
In R, install rJava with install.packages("rJava")
Install glmulti with install.packages("glmulti")

Independently of vortexR, a sudo R CMD javareconf (and possibly the installation of 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): echo %JAVA_HOME%
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. C:\Program Files\Java\jdk1.7.0_02\jre\lib\ext
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\server and the R installation directory, e.g. C:\Revolution\R-Enterprise-7.3\R-3.1.1\bin\x64.
Make sure that the environment variables RPATH and RHOME are BOTH set and point to the R installation directory, e.g. C:\Revolution\R-Enterprise-7.3\R-3.1.1\bin\x64
In R, install rJava and glmulti

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.

Learn

Use ??vortexR to see a broad description of the package. Use 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 build_vignette=TRUE.

Use

If you use vortexR, please use the citation generated from citation('vortexR').

Contribute

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), lintr::lint_package(), and 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 pkgdown.

devtools::install_github("hadley/pkgdown")
pkgdown::build_site()

The documentation should be re-built before each submission.