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

[Thomas Petzoldt]

Hi,

here a few slides about growth modelling from a recent course, that are 
still online:

http://www.simecol.de/modecol/

and especially:

http://www.simecol.de/modecol/slides-odemodels.html

Besides this, the two books of Karline Soetaert and the book of Hank 
Stevens are definitely an excellent choice for this topic.

Thomas

See also:
https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models


Am 23.02.2017 um 21:56 schrieb 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
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
>
>


-- 
Dr. Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany

E-Mail: thomas.petzoldt at tu-dresden.de
http://tu-dresden.de/Members/thomas.petzoldt

-- limnology and ecological modelling --