MATRIX POPULATION MODELS FOR WILDLIFE CONSERVATION AND MANAGEMENT

4 - 9 March, 2019
University of Florida, Gainesville

1. Software

   You will need to bring your own laptop computer with the following programs/packages pre-installed (available for free download):

   • R (https://cran.r-project.org/bin/windows/base/)
   • R Studio (https://www.rstudio.com/products/rstudio/download/)
   • MARK (http://www.phidot.org/software/mark/). MARK runs on Windows opereating system. Mac users: MARK runs on Windows operating systems. Detailed installation instructions can be found at: http://www.phidot.org/software/mark/downloads/.
   • R packages (these packages can be installed from RStudio interface):
     • RMark (https://cran.r-project.org/web/packages/RMark/index.html). You will need MARK for RMark to work.
       Some helpful tips for Mac users: http://www.phidot.org/forum/viewtopic.php?f=21&t=3233.
     • popbio (https://cran.r-project.org/web/packages/popbio/index.html)
2. Getting ready

   We will be happy to work with you regardless of your backgrounds or skill levels. However, your learning experience would be substantially enhanced with:

   • Some familiarity with R and RStudio. There are many free online resources
     • https://www.google.com/search?client=firefox-b-1-d&q=introduction+to+R
     • https://www.google.com/search?client=firefox-b-1-d&q=Introduction+to+R+studio
   • Basic understanding of matrix algebra. There are many online resources that would help with both ( https://stattrek.com/tutorials/matrix-algebra-tutorial.aspx);
   • Familiarity with capture-mark-recapture methods (http://www.phidot.org/software/mark/docs/book/) and models of population dynamics.

   Serious population modelers will find the following textbooks to be very useful:

   • Caswell, H. 2001. Matrix population models: Construction, analysis, and interpretation. Sunderland, MA: Sinauer Associates.
   • Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology. Sunderland: Sinauer.
   • Williams, B. K., J. D. Nichols, and M. J. Conroy. 2002. Analysis and management of animal populations. Academic Press.
   • Ellner, S. P. Child, D. Z. and M. Rees. 2016. Data-driven modeling of structured populations. Springer, Swizerland.
3. Course-related material

   All course-related material (lecture notes, exercises, computer codes) will be provided in the class (hard copy or download). Some papers that provide nice overview of topics covered in this course are:

   • Lebreton 2006 popdy_models_CRBiologie.pdf
   • Lebreton and Nichols 2009AER.pdf
   • Nichols_et_al_1992_ProjectionMatrix_1992.pdf
   • Schaub_and_Abadi 2011 integrated pop models J Ornithol.pdf
4. Working with your data or project

   An important feature of the workshop is that you will be able to develop models for your biological questions and data. We hope that this workshop will help some (or all) of you develop models that will help you address specific ecological questions or solve conservation problems. You should think about the following points in order to mentally prepare for topics that will be extensively covered in the workshop:

   • Prioritize a subset of your questions/objectives - it may not be possible to address all of them!
   • Life history/life cycle of your study organism (individual development and progression over the life course).
   • Population structure (age, size, life-history stages, spatial structure etc.).
   • Estimates or guesstimates of key vital demographic parameters: we will start there! We will review methods for estimating demographic parameters but we will not have time to analyze data during the workshop to estimate survival, fecundity or other demographic parameters.
   • The main features that you may be necessary to address your questions in a model include (but are not limited to): environmental variation, demographic stochasticity, resource constraints and density-dependence.
5. More on class projects and data

   All participants are expected (graduate students are required) to work on a project related to some aspect of population modeling (matrix population models, integrated population models, integral projection models, or direct estimation and modeling of λ). We suggest working in groups of ≤3. You are encouraged to bring your data (and questions) so you get help and advice from your instructors. Here are some possible options:

   • Bring your own data or pair-up with someone who has appropriate data. Type of data you need would depend on the modeling framework to be used and questions/objectives to be addressed. However, data must be adequate to address interesting and relevant questions.
   • Many published studies make data publicly available (journals such as Journal of Animal Ecology and Ecological Monographs require data to be publicly available). These data can be used for the in-class project, with proper acknowledgement of the original data source. For example, see: http://www.oikosjournal.org/appendix/oik-00035), Reimer et al. (2019; https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/eap.1855?af=R).
   • Many important questions in population ecology can be addressed using simulation studies. You can ask questions that can be addressed using simulated data. Example: Coggins et al. (2007; Fish and Fisheries 8: 196-210).
   • Ideas that make use of published data frequently make excellent projects. Examples, Koon et al. (2006; Ecological Modelling 197: 418-430); Stahl & Oli (2006; Ecological Modeling 198:183-194; van de Kerk et al; http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070354)
   • Population projection matrices for many animal and plant species are publicly available for download at http://www.compadre-db.org/. See Salguero-Gomez et al. (2016) for details. These data can be used for class projects (or more broadly, demographic analyses).

• Jean-dominique LEBRETON (Jean-dominique.LEBRETON@cefe.cnrs.fr)
• Jim Hines (jhines@usgs.gov);
• Madan Oli (olim@ufl.edu)

links

• Files for participants
• zipfile containing all files