[R] help with population matrix

[Roy Mendelssohn - NOAA Federal]

See if this helps at all:

http://cran.r-project.org/web/packages/popbio/popbio.pdf

-Roy M.
On Feb 18, 2013, at 8:49 AM, John Kane <jrkrideau at inbox.com> wrote:

> Currently your code does not seem to make any sense
> ===comments in line====
> 
> John Kane
> Kingston ON Canada
> 
> 
>> -----Original Message-----
>> From: sf62 at st-andrews.ac.uk
>> Sent: Mon, 18 Feb 2013 16:09:49 +0000
>> To: r-help at r-project.org
>> Subject: [R] help with population matrix
>> 
>> Hi guys, I am a biologist and an R newbie, and I'm learning how to create
>> a
>> simple population model.
>> 
>> So, I have a population matrix ("pop")of 30 age classes of female (1:4
>> are
>> non-breeders, 5:30 are breeders) which will be modelled for 100 years.
>> 
>>> pop <- matrix(0,30,100)
>> 
>> I then populate this matrix with 3 young adult females.
>> 
>>> pop[5, 1] <- 3
> 
> What is this expected to do?
>> 
>> I then want to run this for 100 years, with stochasticity, to see how
>> this
>> population does over time.
>> 
>>> for (y in 1:100)  {
>>>    pop[1,t+1] <- rbinom(1,colSums(pop[5:30, t]), b/2)
>> 
>> (I haven't filled these in but you don't need them, they all have
>> different
>> survival probabilities to the sexually-mature adults.)
>> 
>>>   pop[5, t+1] <- rbinom(1, pop[4, t], s2)
>>>   pop[6, t+1] <- rbinom(1, pop[5, t], s2)
>> .....
>>>   pop[30, t+1] <- rbinom(1, pop[29, t], s2)
>> }
>> 
> What is t , s2 b etc?
> 
> 
> 
>> So my question is: is there any way of populating this matrix without
>> having to explicitly write 30 lines of code? Because lines 5 - 30 are all
>> going to be the same, and yet even after 5 hours (literally) of web
>> searching and R manual reading I can't find a way to index the rows,
>> which
>> seems to be what's needed here.
>> 
>> Any insight is welcome here, including a different way of modelling this
>> population.
>> Many thanks, Sam.
> 
> This may be one of the cases where it really is better to have some detailed explanation of what you want rather than how to code it.
> 
> ____________________________________________________________
> FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.