[R-sig-eco] what's the best R implementation of a Logistic population model?

[Jeremy Chacon]

Hi Drew,

Since there is a closed-form solution to the logistic model, it's easy, you
can just code the solution into a function:

logistic <- function(times, r, K, Y0){
  numer = K * Y0 * exp(r * times)
  denom = K + Y0 * (exp(r * times) - 1)
  return(numer / denom)
}

times = seq(from = 0, to = 100, by = 1)
r = 0.4
K = 1000
Y0 = 1

plot(times, logistic(times, r, K, Y0), type = "l")

If, however, you want them to do numerical simulation, then the deSolve
package (which you've been reading about) is the way to go:

install.packages('deSolve')
library(deSolve)

logistic_de <- function(times, y, parms){
  dN = y * parms[1] * (1 - y / parms[2])
  return(list(dN))
}

y0 = 1
parms = c(0.4, 1000)
times = seq(from = 0, to = 100, by = 1)

out = ode(y = y0, times = times, func = logistic_de, parms = parms)
plot(out)

Note that there are better (i.e. easier to read) ways to code the function
for the logistic for deSolve numerical solving, but this is the easiest.


Jeremy



On Thu, Feb 23, 2017 at 1:35 PM, Drew Tyre <atyre2 at unl.edu> wrote:

> Hi all,
>
> I'm teaching a population dynamics course for upper level undergraduates.
> I am using R for the first time (first time using it in this class, not my
> first time!). So I needed to make a small function to simulate a logistic
> population model, and it occurred to me that other's may have already
> solved this problem in a better way. I'm looking for pointers to other
> implementations, and/or feedback on how I've set it up. A bit of
> description of my goals and the function are at
>
> http://atyre2.github.io/2017/02/22/whats-the-best-logistic-model.html
>
> I have looked at Karline Soetaert and Peter Herman's book A practical
> guide to ecological modelling, as well as Henry Steven's book A primer of
> Ecology with R, and discuss their approaches at the above blog post.
>
> Thank you for your time and attention!
> --
> Drew Tyre
>
> School of Natural Resources
> University of Nebraska-Lincoln
> 416 Hardin Hall, East Campus
> 3310 Holdrege Street
> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
> fax: +1 402 472 2946
> email: atyre2 at unl.edu
> http://snr.unl.edu/tyre
> http://atyre2.github.io
> ORCID: orcid.org/0000-0001-9736-641X
>
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>



-- 

*___________________________________________________________________________Jeremy
M. Chacon, Ph.D.*

*Post-Doctoral Associate, Harcombe Lab*
*University of Minnesota*
*Ecology, Evolution and Behavior*

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