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Resources for Theoretical Ecology

Programming ~ Math reference ~ LaTeX ~ Organizations ~ Summer programs ~ Modeling philosophy ~ Just for fun



Programming

Numerical Recipes in C: good for algorithms
Resources for both Matlab and R:
Matlab intro and useful commands, R useful commands (created for courses in theoretical population biology)
An introduction to Matlab or R for dynamical models in biology (from Ellner & Guckenheimer, full supplemental lab materials available here)
Matlab/R translation
Software carpentry: learning R, Matlab, and Python, plus best practices and version control
Fast Matlab programming (note: the concept of "vectorization" applies to R as well):
MATLAB array manipulation tips and tricks
Matlab vectorisation tricks
Writing Fast MATLAB Code
Vectorization Tips (scroll down to "Drea's Desk: Vectorization Tips")
Matlab Tips and Tricks
Matlab mini-course
Programming in R:
Rseek - searchable database for R
Primer in Ecology with R and related code
R in a Nutshell

Math reference

Encyclopedia of Mathematics
Wolfram MathWorld: good for explanations of mathematical concepts
algCalc.pdf: review of basic algebra & calculus (developed for ESP121)

LaTeX

LaTeX commands
BibTeX entries
Web of Science to BibTeX conversion
BibTeX style files for Ecology, American Naturalist, Ecology Letters, Journal of Ecology, and Oikos (under "Data and Other Files" - note the useful R help files too) -- and go here for a more recent American Naturalist file
BibTeX and LaTeX style files for a number of ecology and evolution journals (including Ecology, Ecology Letters, Evolution, Genetics, JTB, PLoS, PNAS, Nature, and Science - note the long list of helpful LaTeX links as well)
Still can't find a BibTeX style file for the journal you're submitting to?  The makebst macro in custom-bib is an excellent resource for creating a .bst file, typically for use with natbib.sty.  The files I've created with this are:
gcb.bst for Global Change Biology
jxb.bst for the Journal of Experimental Biology
consbiol.bst for Conservation Biology -- this also needs \bibpunct{(}{)}{;}{a}{}{} in the preamble.
All are posted as zip files, so decompress before using.  Also, be sure to include \usepackage{natbib} in the preamble.
Learning LaTeX by example (see the .tex file first)
Helpful LaTeX links
Writing in LaTeX but submitting to a journal that doesn't accept .tex or .pdf format? There are a number of LaTeX/Word and LaTeX/rich text converters; I typically use latex2rtf

Organizations

The Theoretical Ecology Section of ESA plus the Theory Section wiki for job postings and teaching resources
Evolutionary Demography Society

Summer programs

Mathematical and Theoretical Biology Institute (ASU)
Enhancing Linkages Between Mathematics and Ecology (KBS)
NIMBioS Graduate Student Fellows
IIASA Young Scientists
Mathematical Biosciences Institute (OSU)
IAS School of Mathematics Women and Mathematics Program
Complex Networks (Lake Como School of Advance Studies)
Pacific Institute for the Mathematical Sciences: Dynamics of Biological Systems

Philosophy of modeling in biology

May (2004): Uses and abuses of mathematics in biology
"Here mathematics is seen in its quintessence: no more, but no less, than a way of thinking clearly."
Caswell (1988): Theory and models in ecology: A different perspective
"Models are to theoretical problems as experiments are to empirical problems."
Levins (1966): The strategy of model building in population biology
"The validation of a model is not that it is 'true' but that it generates good testable hypotheses relevant to important problems."
Starfield (1997): A pragmatic approach to modeling for wildlife management
"A wildlife manager can no more make a defensible decision without a formal model than somebody in the business world can make a deal without 'running the numbers.'"
Fretwell (1990): Say that in algebra!
"Nearly everyone I talked about my ideas understood very quickly just what I was trying to say.  All I had to do was show them the models."
Aber (1997): Why don't we believe the models?, Dale & van Winkle comment, Aber reply, Dale & van Winkle reply
Cohen (2004): Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better
Chapter on "Building dynamical models" from Ellner & Guckenheimer textbook

Just for fun

PhD Comics
The Mathematics Genealogy Project
Marine ecology genealogy
Programming in Matlab?  Running into problems?  Ask it "why".


Note also the theory-specific writing resources on the Communications page of this website:
How to write a theoretical ecology paper that people will cite
Advice on writing modeling papers for mixed theoretical/empirical audiences

Know of any links that should be included in these lists but aren't?  See something out-of-date?  Please let me know!
Last updated September 2016