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I've been stumped for quite a while trying to decide what the criteria really are for when one should use AIC vs BIC. Burnham and Anderson talk about it quite a bit, but they are such staunch AIC...
Back to chapter 11 notes
p. 363: unfortunate font choice: is very ugly
p. 363: I forgot to mention the product and quotient rules! Product rule:
(1)
Quotient rule:
(2)
p. 366: add recent...
Books on ecological modeling/statistics/R, hopefully with comments and ratings (???) from a broad spectrum of readers/users at varying levels of expertise …
[TWS] These comments were provided by...
Back to notes on chapter 3
p. 104: other references of interest for Jensen's Inequality: Schmitt et al. 1999, Welsh et al. 1987
p. 107: unfortunately y-axis scales don't match in Figure 4.1
p....
Back to chapter 4 notes
p. 149: see errata for a problem with Figure 5.1b
p. 159: technically, "accept" in the table should be "fail to reject"
p. 161: should refer to 5.5b instead of "right...
Back to notes from chapter 5
p. 173 I really shouldn't use O (uppercase "oh") or l (lowercase "ell") for any variable names — it's too easy to confuse them with 0 and 1. (Add to the list c, q,...
Notes on specific chapters
Chapter 1 (Introduction and Background)
Chapter 2 (Exploratory Data Analysis and Graphics)
Chapter 3 (Deterministic Functions for Ecological Modeling)
Chapter 4...
My contact information:
Ben Bolker, bolker@ufl.edu
Department of Zoology, University of Florida
620B Bartram Hall
PO Box 118525
Gainesville, FL 32611-8525
I don't teach freelance courses on ecological models and data (although maybe I should!), but a few do exist. Here's a list of the ones I know...
There seems to be a general opinion among statistical graphics nerds (examples here, here, and here) that the traditional way of plotting grouped continuous data (e.g. growth rates across...
If this wiki works as I hope, it will come to contain a variety of useful information relating to the book:
answers to frequently asked questions
errata (not too many I hope)
clarifications or...
Note (16 Sep 2009): The second printing is now underway and I am hopeful that all the errors listed in the "first printing errata" section below have been corrected …
Errata in the second...
rm(list=ls())
X = read.csv("errata-dates.txt",
colClasses=c("character","numeric","factor","factor"))
X$date <- as.Date(X$date,format="%d-%m-%Y")
X = X[order(X$date),]
n <-...
4 August 2008
I missed Aaron Ellison and Brian Dennis's talk today at ESA about "what literate ecologists should know about statistics" (I opted for Gordon Fox's talk about diversity gradients...
This section shows somewhat longer worked examples.
simulating/analyzing overdispersed, spatially correlated count data (e.g. negative binomial/Poisson-lognormal)
simulating/analyzing seed...
Q:Can negative log-likelihoods (or AICs) be negative?
A: no, not technically, but there are two cases where we can get negative values for the "negative log-likelihood" function we use (which in...
Does this page come into being with a "discussion" section?
how about this one?
does this automatically get a "discuss" button when newly created?
Materials for Geneseo UMB course, 1-5 June
Monday
epi lecture 1 (basics): epi1.xml epi1.pdf
epi lecture 2 (thinking about data): epi2.xml epi2.pdf
lab 1: lab1.xml lab1.pdf
data/script files:...
If you are allowed to edit pages in this Site, simply click on edit button at the bottom of the page. This will open an editor with a toolbar pallette with options.
To create a link to a new page,...
5 August 2008
Brian Dennis commented to me at ESA today that he doesn't agree with my categorization of AIC etc.-based methods (what I call "model selection") as not being frequentist. I see what...
For now, I am leaving this site completely open — anyone can edit it.
Materials for Mendoza course, 29 June - 10 July
Monday
morning
outline (pdf, html)
overview (pdf, html, R, Rnw)
incantation for making Tinn-R copy and paste blocks correctly:
.trPaths <-...
Agustina Novillo
CONICET
Richness altitudinal gradients in small mammals: I have 4 transects from 32°lat to 35° lat. At each transect I have 5 altitudinal sample points, where I measure small...
Bibliography
1. Mazerolle, Marc J. 2006. Improving data analysis in herpetology: using Akaike's Information Criterion (AIC) to assess the strength of biological hypotheses. Amphibia-Reptilia 27...
Marc Mazerolle, whom I criticized on p. 216 of the book for saying that Akaike weights were probabilities (rather than being "similar to" probabilities or other such waffle-words), sent me a nice...
p. 7: I would now add Hanna Kokko's new book, "Modelling For Field Biologists: and Other Interesting People" (CUP 2007, ISBN 0521538564) to my list of useful modeling/theory books
pp. 11-12: Aaron...
Back to notes on chapter 9
p. 318: the original paper used quantile regression to analyze these data: the quantreg package in R does quantile regression.
p. 319 caution: it's generally (much)...
Back to chapter 10 notes
p. 344: need R refs for errors in variables, RMA (reduced major axis) regression, etc.
p. 347: R has a simex package
p. 353: conf region is funny — transformed...
Back to notes on chapter 1
p. 40: there is now a third graphics system in R, called ggplot (for "Grammar of Graphics"). This package, by Hadley Wickham, implements L. Wilkinson's grammar of...
Back to notes on chapter 2
p. 78: I don't think I ever defined the product rule:
(1)
It should definitely go in the Appendix.
p. 79: would be nice to redo all figures with TeX labels, math...
Back to notes on chapter 6
p. 232: other simulated annealing codes exist. For example, Canham and Uriarte cite Goffe, W. L., G. D. Ferrier, and J. Rogers. 1994. Global optimization of statistical...
Back to notes on chapter 7
p. 266 I have changed the behavior of profile (called by confint) so that it now returns the better-fitting parameter values as a vector — this simplifies putting them...
Back to notes on chapter 8
rough notes, need to be polished
p. 299: cf. linear vs exponential survival models (goby data), Beverton-Holt vs. survival analysis
p. 300: note * vs : for denoting...
Here are some quick (and hopefully, interesting) thoughts on two separate kinds of pronoun trouble that have come up in my graduate teaching recently, (1) the ever-controversial "singular they"...
Seed dispersal/inverse modeling example
Intro
Goal: to simulate some seed dispersal data and try to fit it via inverse modeling. The set-up here is a little bit different from the typical case...
Welcome page
Frequently asked questions
Notes on specific chapters
Errata
Software (R) issues
Miscellaneous thoughts
Related books
What is a Wiki Site?
How to edit pages?
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Members:
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This section will be for general comments about using R for ecological modeling, and some points about the software (emdbook and bbmle2) I've written to support the book.
Mark Connolly points out...
Define a spatially correlated negative binomial model. For the moment, leave the spatial correlation model
relatively unspecified as ; will probably end up being something relatively simple like...
<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.btitle=Ecological Models and Data in...
The following figure:
Is produced by this code:
## closed-form solution for theta-logistic
tlogfun = function(t,theta=1.1,n0=0.1,r=1,K=1) {...
transcribe Martin Schlather's comments into the chapter notes sections
deal with questions about fir fecundity WinBUGS runs, estimation of Bayes factor
redo goby analysis with a "fuzzed" version...
contact
Aaron Ellison wrote:
On the footnote to p. 174, you talk about simulating 1000 samples (binomial p = .75, n =10, size = 4) and comparing the ml estimate to the observed value (-7.57). You find...
Re-do Vonesh functional response analysis pp. 310-311. The only real disadvantage of inverse GLM (i.e., GLM with a link function is a slightly less direct parameter interpretation: intercept =...
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A Wiki ([ˈwiː.kiː] <wee-kee> or [ˈwɪ.kiː] <wick-ey>) is a type of website that allows users to add, remove, or otherwise edit...
1 August 2008
I really enjoyed reading Breiman 2001 (Statistical Science 3:199-215), in which he says (approximately) that statisticians are too concerned with "true models" and that they should...
