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Workshop materials

"Boot Camp" in wildlife study design and data analysis

 

Software and materials for the Boot Camp at Mandalay, 2 - 14 July 2019

Before the workshop

Before the workshop, please do the following:

  1. Complete the Knowledge Survey and email back to <ngumbangjuat@hotmail.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 your work, and send to <ngumbangjuat@hotmail.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 or Mac 10.11 (El Capitan) or later. Linux distros such as Ubuntu Xenial or Bionic should also work. 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. If you already have these installed, check that you have recent versions.
     
  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

You should have R version 3.5.1 or later; if you have an older version please install the newest. (Version 3.6.0 was released on 23 April.) You should have JAGS version 4.2.0 or later, current version is 4.3.0. Uninstall old versions before installing new.
 

Windows Mac
  • You must have Windows 7, 8 or 10.
     
  • Go to this page. and download the latest version of R, currently R-3.6.0-win.exe.
     
  • Download and install JAGS: look for the download link just below the menu bar here, or go here and download the latest version, currently JAGS-4.3.0.exe.
     

 

  • You must have Mac 10.11 (El Capitan) or later with the XQuartz utility.
     
  • Go to this web page. and go to "Latest release" section. The first link is usually the one you want, currently R-3.6.0.pkg. Download and run this.
     
  • When you first open R, you may get warning messages such as
    During startup - Warning messages:
    1: Setting LC_CTYPE failed, using "C"
    2: Setting LC_COLLATE failed, using "C" ...etc

    In that case run this line in R:
    system("defaults write org.R-project.R force.LANG en_US.UTF-8")
    then close R. When you open R again there should be no warnings.
     
  • Download and install JAGS from this page. Read the installation information and download the latest .dmg file, currently JAGS-4.3.0.dmg.
     
  • JAGS does not appear in the Applications listed in Finder. To check that it's installed, go to Finder > Applications > Utilities > Terminal and type "jags". You should get a message with the version of JAGS.
  • 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 4.3.0.

  • 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 click "No" or 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) or Microsoft Excel 2010 or later; other programs are likely ok but the instructors may not be familiar with them.
 

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.

The workshop materials are currently being revised and will be posted here one week before it begins.

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

Click here to download materials for Days 4 to 6 (ZIP, 3.1MB)

Click here to download materials for Days 7 to 9 (ZIP, 5.1MB)

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 them 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.

Dusit Ngoprasert ("Soy"), KMUTT Thailand

Colin Strine, Suranaree University, Thailand

 

Page updated 23 June 2019 by Mike Meredith