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What's the best way to implement the logistic model in R?
I’m teaching my population dynamics class using R for the first time. I want the students to use a simple logistic population model to make predictions about how population size will respond to different management actions. So, I need to figure out the best way to implement a discrete time, logistic growth model in R.
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Accounting for exposure days
Every year I suggest a student use Terry Shaffer’s log exposure models for nest survival (Shaffer 2004). And every year I spend hours trying to figure out why the code in the help section of
?family
doesn’t work. So this year I’m writing it down.
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Statistics training
This tweet sparked a host of comments about the need for R prep courses, as well as some great gifs! This is my R prep course, with a few other computational skills thrown in for good measure.
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What about that 1970's ice age?
A good friend posted this link to FB. I read the post, did some background reading, and debated whether to write this post or not. I’ve been writing it in my head anyway, so time to get it out!
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Slow Science
I’ve heard a number of calls for faculty to slow down, think, and write. This is the latest, by Allison Adams from Emory University. I’m trying, but it’s hard.
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Diversity matters. Everywhere.
Yesterday a colleague posted a link to an article in The Federalist calling out liberals for not listening. I think the author has a point.
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Testing disqus comments
At a reader’s request I’m attempting to add disqus comments to my blog posts. Ignore this post!
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Statistical training in ecology
This article made the rounds of twitter recently. I agree. There is a mismatch between statistical practice and training. Almost the first thing I did was flip to the appended data and see how they categorized UNL. I was relieved to see that we have a course “beyond linear models”; mine!
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Should I use sumtozero contrasts?
A sumtozero contrast codes a categorical variable as deviations from a grand mean. Social scientists use them extensively. Should ecologists?
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Can you sum the sensitivities?
TL;DR No.
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R vs. ArcGIS
This question arose from these exercises.
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Lists of models in a data.frame
So a couple weeks ago I had a stab at putting a list of fitted models into a data.frame. I didn’t succeed. So, here’s another try.
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How do predators change population growth, part II?
Last week I starting thinking about how predation might affect a species that otherwise experiences logistic growth due to intraspecific competition. I looked at predators with both Type I and Type II functional responses to their prey. What about predators with Type III responses?
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How do predators change population growth?
The logistic model of population growth includes the effects of predation. Predators are one of the factors contributing to death rates, and so if a species has any predators at all, predation is part of the logistic model. This isn’t widely appreciated. What I want to do here is ask what kinds of predation are consistent with the basic logistic model.
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Happy houR!
It’s happy houR. I’m in a happy place, and I’m going to spend an hour trying to learn something new. Earlier today I watched a video of Hadley Wickham explaining his approach to handling many models. Now I want to see if this combination of
purrr
andbroom
can make my approach to multimodel inference easier.
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Scaling and Centering
Centering and rescaling covariates is a common task prior to building almost any sort of statistical model. Although function
scale()
will scale scale and center numeric matrices, it always returns amatrix
. Most model fitting functions take data.frames. And althoughscale()
will take a data.frame as an input, it fails with an error if there is even one column that is a categorical variable. That’s always bugged me, and I’ve been musing about a solution for awhile. I’ve also wanted to try making an R package using the fancy automation tools available in RStudio and packagedevtools
. Today those musings and desires collided, and I give you scaler!
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The sex ratio of chickens
I got the following email the other day
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The trouble with tibbles
Hadley Wickham’s
dplyr
package makes complex data manipulations easy to describe. However, dplyr functions all return “tibbles” rather than data.frames. Class tbl inherits from data.frame, so you can use tbls everywhere you use data.frames. Except when you can’t.
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Welcome to Jekyll & GitHub!
So this is going to be the new home of all the material from AMinPractice.
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