Software and materials for the workshop on "Bayesian analysis with
JAGS and R" in Bhutan, from 11 to 23 September 2018.
Extra scripts for orangutan
New version of wiqid package
Before the workshop
- Check your laptop specs!
- Your computer should have a 64-bit processor and 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.
- Check your operating system: You can use Windows 7, 8 or 10
or a Mac with OS X
10.11 (El Capitan) or later. If you have a Mac, you will need the XQuartz utility installed.
- If you have problems with your operating
system, see here for
- We will be doing a lot of heavy-duty number
crunching, so if your laptop tends to overheat, you may need a
- Check that you have recent versions of necessary software (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
- 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 3.5.0 or later; 3.5.x is faster than previous
versions; 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", "loo", "rgdal", "devtools"))
- Also install the
saveJAGS packages from Github with
- If you have problems installing R packages, don't worry: we
can fix this at the beginning of the workshop.
A text editor which shows line numbers
- Error messages from JAGS specify the line number in the model
file, and you won't want to count lines from the top. Notepad
doesn't do this, but
RStudio do, and
emacs has an option to show line numbers.
A spreadsheet program
- You should have either
LibreOffice Calc (which is free software) or Microsoft Excel.
Other spreadsheet programs will likely work, provided they can
open and save
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, 27KB).
Click here to download the
materials for days 1 to 3 (ZIP, 310KB)
Materials for days 4 to 10 include some very large files, so they 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.
Lukmann Haqeem, senior
researcher with WWF Malaysia.
Mike Meredith, BCSS and WCS, background in park and