Software and materials for the Boot Camp in Nepal, 26 Sept - 8 Oct 2018
Crabs comparison script
Where's Waldo data
Gecko capture file
Before the workshop
Before the workshop, please do the following:
- Complete the Knowledge Survey and email back to
or print it out and hand it in when you
arrive at the Boot Camp venue.
- Prepare ONE PowerPoint SLIDE to introduce yourself and your
work, 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
- Check the operating system on your LAPTOP: you should have
Windows 7, 8 or 10; Mac 10.11 (El Capitan) or later; or Ubuntu
Trusty or Xenial. Our software will not work on Windows XP or
'big cat' versions on Mac. If you have a Mac, you will need the XQuartz utility installed.
- Download and install the necessary software (see
below) on your laptop, in particular the R and JAGS
programs. If you need help from the IT department to install
software, ask them to go to http://bcss.org.my/software/
for more details. If you already have these installed, check
that you have recent versions.
- Download and preview the workshop materials (see
below). Look at the PDFs and the internet links. We don't
expect you to have read everything - and we won't actually use
everything - but you should know what's
in the folders.
You will need the following software installed on your laptop:
R, JAGS and
- If you use a Mac, see
here. If you use Ubuntu, go
here. What follows
applies to Windows users.
- Download and install
statistical software. You should have version 3.5.0 or later; if you
have an old version please install the newest.
- If you use Nepali fonts (or other non-Western fonts), open R and
type (or copy-paste):
You should see something like this appear:
tempdir() ; Sys.getenv("R_USER")
If the output includes non-Western characters or strange symbols or
something like <U+611B>, some of the functions we need will not work. Please contact us at the beginning of the
workshop for a workaround.
- Download and install
JAGS: look for the download link
just below the menu bar
You should have version 4.2.0 or later, current version is 4.3.0.
- After installing R and JAGS, install
rjags by opening R and typing
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
Check that it works by typing:
You should get a message telling you that
rjags has linked to
JAGS 4.2.0 or JAGS 4.3.0.
- Note on Firewalls: For parallel processing, R uses 'sockets' to
communicate between processes running on different cores. This is the same
protocol used for internet access and usually causes a firewall window to
pop up the first time it is used. You need to "Allow access" for R to
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.
install.packages(c("wiqid", "shiny", "secr", "beeswarm", "jagsUI"))
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
Calc (which is free software) with the Java Runtime Environment
(JRE) needed to run Solver (there are 32-bit and 64-bit JREs,
make sure you have the right one for your LibreOffice
- Microsoft Excel 2010 or later with the Solver add-in
(see here for details). If you have an earlier version of Excel, upgrade
or install LibreOffice.
Don't use Kingsoft WPS software, as their Solver
doesn't work properly.
A PDF reader
- You need a PDF Reader which allows you to annotate PDFs, such as
The provisional schedule for the workshop is
Click here to download
materials for Days 1 to 9 (ZIP, 8.9MB)
Materials for Day 10 will be distributed towards the end of the
extract the files and put them in a folder on your hard disk, eg, in
Documents. Don't put them on the Desktop as some programs can't easily access the
Please "think before you print"! Paper copies of
the files beginning "PRN_..." will be distributed at the workshop.
The instructor team
Ngumbang Juat, BCSS staff and gibbon researcher.
Tan Win Sim, WCS Malaysia
Jeevan Rai, Friends of Nature, Nepal
Mike Meredith, BCSS and WCS, background in park and