Software and materials for the workshop on Bayesian analysis with
JAGS and R in Kuala Lumpur, from 4 to 10 March 2018.
Extra files for Monday
Click on image to see larger version.
Before the workshop
- Check your laptop specs! Your computer should have 4 or 8
'logical' cores. To check the number of cores available, open R
and do: parallel::detectCores().
We will be generating some very large objects, so you will need
at least 4 Gb of installed RAM, preferably 8 or 16 Gb.
We will be doing a lot of heavy-duty number
crunching, so if your laptop tends to overheat, you may need a
- Check your operating system: You can use Windows 7, 8 or 10,
provided it uses a 64-bit processor. You can use a Mac with OS X
10.11 (El Capitan) or later; if you have a Mac, you will need the XQuartz utility installed.
- Check that you have recent versions of necessary software:
R 3.4.1 or later and JAGS 4.2.0 or later. The version of R appears at the top of
the console window when you open R; also check that you are
running the 64-bit version of R. Doing library(rjags) will produce a message with the version of JAGS in use.
- Download and preview the workshop materials (see
- Look through the R Skills Review again - both your answers
and the suggested answers - and make sure you have these skills
at your finger-tips.
You will need the following software installed on your laptop:
R, JAGS and
- You should have R 3.4.1 or later; 3.4.x is faster than previous
versions but R 3.4.0 had a bug; if you
have an old version please install the newest.
- You will also need JAGS
4.2.0 or later. Look for the download link just below the menu bar
- Install the
rjags package and check that it loads
correctly: When you do
library(rjags) you should get a message telling you that
rjags has linked to
JAGS 4.2.0 or 4.3.0.
Other R packages
- You should have the following CRAN packages installed:
install.packages(c("jagsUI", "AHMbook", "secr", "wiqid", "shiny", "githubinstall", "loo", "rgdal"))
- Also install the
makeJAGSmask package from Github with
- If you have problems installing R packages, don't worry: we
can fix this at the beginning of the workshop.
A spreadsheet program
- You should have either
LibreOffice Calc (which is free software) or Microsoft Excel.
A PDF reader
- You need a PDF Reader which allows you to annotate PDFs, such as
The outline schedule for the workshop is
here (PDF, 23KB).
Click here to
download the materials for days 1 to 3 (ZIP, 323KB)
Materials for days 4 to 6 will be distributed on USB drives at the
extract the files and put them in a folder on your hard disk, eg, in My Documents.
Don't put it on the Desktop as some programs can't easily access the
The instructor team
Ngumbang Juat, BCSS staff and gibbon researcher.
Chee Pheng, senior
researcher with WCS Malaysia.
Mike Meredith, BCSS and WCS, background in park and