[R] Population growthrate with Euler-Lotka
David Stevens
david.stevens at usu.edu
Mon Jun 30 13:11:36 CEST 2014
Mark - good on you for jumping into R with both feet.
In addition to Simon's advice, the error message you are getting means
that the two endpoints (r.range in your case) do not give function
values that are of the opposite sign and so either the function has no
roots on the interval or has and even number of roots on the interval
(2,4,6,...). Neither situation is good for your case because uniroot
finds the single root (where the y-value = 0) on the interval. Once the
reading issues are settled, try narrowing or expanding the r.range. A
good way to find a proper r.range is to plot the function vs. r and
locate the range of r where the function crosses zero. Then use the
region of r around that point as your r.range. You also learn a lot
about that function by studying that plot.
Regards
David
On 6/30/2014 1:39 AM, Mark Christjani wrote:
> Hi everybody,
>
> I`m Mark and I do my PhD in biology. I try using R to calculate a population
> growth rate of animals grown on different types of food. Our workgroup has a
> R-skript to do so, but sadly nobody, who knows how this works. I`ve never
> used R before, but got some stuff figured out myself. The skript goes:
>
> setwd("c:/Mark")
> table <- read.table("r-TCO-Scene-Kontrolle.csv")
> table
> x <- c(table$x)
> L <- c(table$lx)
> m <- c(table$mx)
> r.range<- c(0, 5)
> eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> res$root
>
> I understood that the first 3 lines are simply to load my data and show it
> in the workspace console. The next 4 lines define variables of my .csv table
> for R. Thus far, everything works fine. Now comes the Euler-Lotka equation,
> but somehow, this does not seem to work out as supposed. I tried to find a
> solution on the internet, but I think this formula is somewhat special so I
> could not find a suitible solution for my special problem. The console says:
>
>
> > setwd("c:/Mark")
> >
> > table <- read.table("r-TCO-Scene-Kontrolle.csv")
> >
> > table
> V1
> 1 x;lx;mx
> 2 1;1;0
> 3 2;1;0
> 4 3;1;0
> 5 4;1;0
> 6 5;1;0
> 7 6;1;0
> 8 7;1;0
> 9 8;1;0
> 10 9;1;0
> 11 10;1;0
> 12 11;0.2;3.5
> >
> > x <- c(table$x)
> > L <- c(table$lx)
> > m <- c(table$mx)
> > r.range<- c(0, 5)
> >
> > eulerlotka <- function(r) sum(L * m * exp(-r * x)) - 1
> > res <- uniroot(f = eulerlotka, interval = r.range, tol = 1e-8)
> Error in uniroot(f = eulerlotka, interval = r.range, tol = 1e-08) :
> f() values at end points not of opposite sign
> >
> > res$root
>
> Does anybody have an idea how to get this running?
>
> Thanks in advance
>
> Kind regards
> Mark
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
David K Stevens, P.E., Ph.D.
Professor and Head, Environmental Engineering
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT 84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stevens at usu.edu
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