Software required for "Boot Camp" in wildlife study design and data analysis
If you are using a computer which belongs to your organisation and you have to get your IT colleagues to install the software for the workshop please ask them to go to either http://bcss.org.my/software/ or http://bcssmalaysia.org.my/software/ (they should be identical).Participants are asked to bring a laptop computer to the workshop.
Windows (7, 8 or 10), Mac (El Capitan or later), or Ubuntu (Trusty or Xenial or Bionic) all work. Other Linux distros should also work, but we have not tried. Our code has been most thoroughly tested on Windows machines.
They will need the following applications installed:
On recent versions of Windows, the path to the
userís Documents directory is typically
After installing R, you can check this by running
If "\\\\" or "//" or non-Western characters or unicode hex values (eg, <U+611B>) appear in the output, some R functions will fail.
Please ensure that the set up is typical with all-ascii characters in the path; if necessary, please set up a new user account for use during the workshop. Alternatively, use the workaround described here.
Old versions which run on 10.6 Ė 10.10 are still available for download, but they are not compatible with other packages we need to run.
You will need the XQuartz utility; install this if necessary.
Ubuntu and other Linux distros: R 3.3.0 and above are no longer supported for Ubuntu 12.04 (Precise); only LTS versions are supported; see this blog post for information on installing R 3.5 on Bionic.
The versions of R and
JAGS on the official repositories are not up to date, and may not
even be cross-compatible. If you use Ubuntu, go
for a method to install R and JAGS and the
This is free, open-source software. It works across all platforms.
If you have a version prior to 3.5.0, please update. Version 3.6.0 was released on 23 April 2019.
If you have version 3.5.x and can't upgrade, that's ok, but you may not be able to get the latest versions of add-in packages. If you have 3.4.x, please upgrade to 3.5.3: 3.5.x uses a different C++ compiler and new packages may not work on earlier versions of R.
Uninstall the old version before installing the new version. (On Windows, you can have multiple versions installed, but the user will run into compatibility issues if they start an old version by mistake.)
Mac users may get a slew of warnings when they open R, eg,
Firewalls: For parallel processing, R uses sockets to communicate between processes running on different cores; this usually causes a firewall window to pop up the first time it is used. You need to "Allow access" for R to private networks.
This is also free, open-source software which works across all platforms. If you have a version prior to 4.2.0, please uninstall and install the new version (currently 4.3.0).
All operating systems: look for the latest version download link just below the menu bar here. If that is not the version you want, use the links further down the page. Completely uninstall the old version of JAGS first.
Windows: Version 4.3.0 resolves compatibility issues with different R versions that were a problem with 4.2.0.
Mac: Downloads for Mac OS X (Mavericks or later) are here.
JAGS does not appear in the Applications lists on Macs or Ubuntu. To check that it is installed properly and to see the version, open the Terminal and type "jags".
After installing R and JAGS, install the
Installation of R packages (aka add-ins aka plug-ins) does not require
administrator privileges. They are stored in the user's area (Windows default:
The procedure is the same for all platforms.
and press Enter/Return. A box may pop up asking about personal libraries: click Yes. You will need to select a mirror web site near you, or choose 0-cloud, which is a world-wide network.
If you get a message asking "Do you want to install from sources...", just click No or type "n" and press enter.
Check everything works! Open R and load
You should get a message saying "Linked to JAGS 4.x.x". If you get an error
message, the most likely cause is a mismatch between the versions of JAGS and
Other R packages: Open R and copy/paste the following line into the Console:
If you get a message asking "Do you want to install from sources...", just click No or type "n" and press enter. (This arises when source code for a new version is uploaded to CRAN but the binaries have not yet been updated.)
Many other packages on which the above four depend will also be downloaded and installed, 18MB in all.
If you have problems installing R packages, don't worry: we can fix this at the beginning of the workshop.
If you have suggestions, comments or questions about installing the software needed for the workshop please email firstname.lastname@example.org.
Page updated 2 May 2019 by Mike Meredith