Software and materials for the workshop on Bayesian analysis with
JAGS and R at King Mongkut's University of Technology Thonburi (KMUTT),
Thailand, from 3 to 14 July 2017.
Scripts for Wednesday 5 July (ZIP, 3KB)
Script we did Wednesday
afternoon (ZIP, 3KB)
Scripts we did Saturday afternoon
Blue ridge salamanders @ Wikipedia
Willow tits, the
Swiss Breeding Bird Survey
Grand skinks in New Zealand
Khana Tiger Reserve
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
10.9 (Mavericks) or later; if you have a Mac, you will need the XQuartz utility installed.
- Check that you have the current versions of necessary software:
R 3.4.0 and JAGS 4.2.0. 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
- Prepare ONE PowerPoint SLIDE to introduce yourself and send
We'll put those together and show them during the introductions
at the beginning of the workshop. The aspect ratio should be
4:3; go to Page Setup and select Slides sized for: On-screen
- 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 3.4.0 or later; 3.4.0 is faster than previous
versions; if you
have an old version please install the newest. Update:
R 3.4.1 was released on 30 June; if not on your local mirror, get it
- You will also need JAGS
4.2.0. If necessary, use the new Windows installer, "JAGS-4.2.0-Rtools33.exe"
as the "JAGS-4.2.0.exe" installer is not compatible with R
3.3.0 or later. This is not an issue with Mac or Linux.
- 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
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, 123KB).
Click here to
download the materials for days 1 to 3 (ZIP, 288KB)
Click here to
download the materials for days 4 to 6 (ZIP, 49KB)
Materials for days 7 to 10 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
Many of the Bayesian analyses need long runs, sometimes several
hours, to get good estimates. We have "precooked" these, but the
files with the results are huge (totaling several GB) so will be
distributed on USB drives at the workshop.
The instructor team
Ngumbang Juat, BCSS staff and gibbon researcher.
Lukmann Haqeem bin Alen ("Bob"), WWF Malaysia, orangutan
field researcher in Sarawak.
Dusit Ngoprasert, KMUTT lecturer, interested in large mammals
Mike Meredith, BCSS and WCS, background in park and