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Workshop materials

"Boot Camp" in wildlife study design and data analysis

 

Software and materials for the Boot Camp at Swinburne University, Kuching, 4-15 December 2017

Group photos

 

Download here: Photo1, Photo2, Photo3

 

Additional materials

Data for Socks in Box activity is here.

Where's Waldo data is here.

Gecko capture file is here.

Before the workshop

Before the workshop, please do the following:

  1. Download the Knowledge Survey and fill it in; email back to stats.bcss@gmail.com, or print it out and hand it in when you arrive at the Boot Camp venue.
     
  2. Prepare ONE PowerPoint SLIDE to introduce yourself and send to <stats.bcss@gmail.com>. 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 Show (4:3).
     
  3. 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.
     
  4. 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.
     
  5. 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.

Software:

You will need the following software installed on your laptop:

R, JAGS and rjags

  • If you use a Mac, see here. If you use Ubuntu, go here. What follows applies to Windows users.
     
  • Download and install R statistical software. You should have version 3.4.1 or later; if you have an old version please install the newest (currently 3.4.3).
     
  • Download and install JAGS version 4.2.0 or later. Version 4.3.0 is now available: look for the download link just below the menu bar here.
     
  • After installing R and JAGS, install rjags by opening R and typing
    install.packages("rjags")
    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.

    Check that it works by typing:
    library(rjags)
    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 private networks.

Other R packages

  • Open R and copy/paste the following line into the Console:
    install.packages(c("wiqid", "shiny", "secr", "beeswarm", "jagsUI"))
    If you get a message asking "Do you want to install from sources...", just type "n" and press enter.
     

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) 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 installation); or
  • 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 Adobe Reader.
     

Materials:

The provisional schedule for the workshop is here.

Click here to download materials for Days 1 to 3 (ZIP, 1.6MB)

Click here to download materials for Days 4 to 6 (ZIP, 3.3MB)

Click here to download materials for Days 7 to 9 (ZIP, 4.6MB)

Materials for Day 10 will be distributed towards the end of the workshop.

After downloading, extract the files and put them in a folder on your hard disk, eg, in Documents. Don't put it on the Desktop as some programs can't easily access the desktop.

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.

Sri Rao, TRCRC staff.

Mike Meredith, BCSS and WCS, background in park and wildlife management.

 

Page updated 13 December 2017 by Mike Meredith