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--- 2014:courses:kraenkel:single_species [2014/02/03 13:20] – prado
+++ 2014:courses:kraenkel:single_species [2024/01/09 18:45] (current) – external edit 127.0.0.1
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 ====== Single species - additional resources ======
+===== Handouts =====
   * {{:2014:courses:kraenkel:lecture_1_14.pdf|Class presentation}}
+===== Sites =====
+  * NIMBioS: National Institute for Mathematical and Biological Synthesis [[http://www.nimbios.org/]]
 ===== Read More =====
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   * Rules of thumb for judging ecological theories, by Ginzburg & Jensen: [[http://www.sciencedirect.com/science/article/pii/S0169534703003495]]
   * The ecological literature, an idea-free distribution, by S. Scheimer: [[http://onlinelibrary.wiley.com/doi/10.1111/ele.12196/full]]. A great editorial on the current state of theory in ecology.
-  * Kraenkel's career in Mathematical Biology Profiles from the SMB Newsletter: [[http://www.smb.org/publications/newsletter/bios.shtml]]
+  * My career in Mathematical Biology Profiles from the SMB Newsletter: [[http://www.smb.org/publications/newsletter/bios.shtml]]
   * Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better , Joel Cohen: [[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020439]]
+  * Modeling Population Dynamics, lecture notes by Andre de Ross: [[http://staff.science.uva.nl/~aroos/downloads/pdf_readers/syllabus.pdf]]
+  * Single-species models for many-species food webs: [[http://www.nature.com/nature/journal/v417/n6888/full/417541a.html]]
+==== History and epistemology ====
+  * Population dynamics from first principles. Chapter 2 from [[http://press.princeton.edu/titles/7436.html|Complex Population Dynamics]]. Peter Turchin, Princeton Univ Press,  2003.
+  * [[http://www.press.uchicago.edu/ucp/books/book/chicago/M/bo3630803.html|Modelling Nature]], Sharon Kingsland, Chicago Univ Press.
 ==== Second-order ODEs====
-Differential equations used to described population dynamics are in general of first order. In the book [[http://books.google.com.br/books?id=9pZfyyRP0ccC&printsec=frontcover&hl=pt-BR&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false|Ecological Orbits]] [[http://life.bio.sunysb.edu/ee/ginzburglab|Lev Ginzburg]] and [[http://www.colyvan.com/|Mark Colyvan]] make a strong point that second-order equations bring out important insights on population dynamics. In a nutshell, they stress that acceleration should be modelled instead of velocities to fully understand how populations grow and decline.
+Differential equations used to described population dynamics are in general of first order. In the book [[http://books.google.com.br/books?id=9pZfyyRP0ccC&printsec=frontcover&hl=pt-BR&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false|Ecological Orbits]] [[http://life.bio.sunysb.edu/ee/ginzburglab|Lev Ginzburg]] and [[http://www.colyvan.com/|Mark Colyvan]] make a strong point that second-order equations bring out important insights on population dynamics. In a nutshell, they stress that acceleration should be modelled instead of velocities to fully understand how populations growth and decline.
 ==== Counting individuals ====
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 ==What is an individual?==
-As odd as it may sound, this is a difficult question for a huge proportion of living beings, like:
+As odd as it may sound, this is a difficult question for a huge proportion of organisms. Therefore defining birth and death is far from trivial. The two best known cases, not mutually exclusive are:
-  * Modular species, like corals and plants:
-  * Clonal species, like bacteria and protozoa: [[http://books.google.com.br/books/about/Sex_and_Death_in_Protozoa.html?id=0lCengzqXfsC&redir_esc=y| Sex and Death in Protozoa: the History of an Obsession]], by  [[http://biology.mcgill.ca/faculty/bell/|Graham Bell]].
-===== Sites =====
+  * Modular organisms, like corals and plants: [[http://www.gbv.de/dms/bs/toc/013555383.pdf|Population Biology and Evolution of clonal organisms]]
+  * Clonal organisms, like bacteria and protozoa: [[http://books.google.com.br/books/about/Sex_and_Death_in_Protozoa.html?id=0lCengzqXfsC&redir_esc=y| Sex and Death in Protozoa: the History of an Obsession]], by  [[http://biology.mcgill.ca/faculty/bell/|Graham Bell]].
-  * NIMBioS: National Institute for Mathematical and Biological Synthesis [[http://www.nimbios.org/]]
+==What is the size a population?==
+In general we do not know the exact size of populations in field or even in lab conditions. The same is true for other demographic parameters, like survival or fecundity. So we have to rely on //estimates// of population parameters. This is a very active topic in ecological statistics. See Chapter I of the book [[https://www.elsevier.com/books/occupancy-estimation-and-modeling/mackenzie/978-0-12-088766-8|Occupancy Estimation and Modeling]] for an nice overview.