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Does anyone know of example r-code/packages for carrying out analysis? Preferably this would have examples from real experimental data of two or more competing species... Thanks Chris Buddenhagen [[alternative HTML version deleted]]

Hello, I am an R newbie, trying to use lsoda to solve standard Lotka-Volterra competition equations. My question is: how do I pass a parameter that varies with time, like say, phix <- 0.7 + runif(tmax) in the example below. # defining function lotvol <- function(t,n,p){ x <- n[1]; y <- n[2] rx <- p["rx"]; ry <- p["ry"...

Hello, I have a syntactic problem with ode. How do I specify vectors of equations in ordinary differential equation systems. (i.e. in my case I want to simulate an a priory undefined number of species that have different parameters but the same behaviour) I demonstrate this using the Lotka Volterra example. The code below does not work and I have not a good idea how to specify this right. ## ======================================================================= ## Example1: Predator-Prey Lotka-Volterra model (with logistic prey) ## ================================================...

...a needs at each point in time (see???), other than the previous time step's values of y and the parms. Any help? Also, any rule of thumb advice regarding rtol and atol would be appreciated. p <- c(r1=.01, r2=.01, a12=0.5, a21=0.6, k1=1,k2=1) t <- 1:20 lvcomp2 <- function(y, t, p) { # Lotka - Volterra model of two competing populations dN1.dt <- p["r1"] * y[1] * (1-(y[1] + p["a12"]*y[2])/p["k1"]) dN2.dt <- p["r2"] * y[2] * (1-(y[2] + p["a21"]*y[1])/p["k2"]) list(c(dN1.dt,dN2.dt),c(???)) } outlv <- lsoda(c(.1,.1),t, l...

...ackage also provides a library of molecular, ecological and epidemiological example models (as demos) that can easily be customized and extended. Currently the following models are included, Decaying-Dimerization Reaction Set, Linear Molecular Chain System, single-species logistic growth model, Lotka predator-prey model, Rosenzweig-MacArthur predator-prey model, and Kermack-McKendrick SIR model. The release consists of several bug fixes, improved documentation, and a revised more 'R-like' management of model parameters. A vignette providing a tutorial of basic SSA theory, usage of t...

...ackage also provides a library of molecular, ecological and epidemiological example models (as demos) that can easily be customized and extended. Currently the following models are included, Decaying-Dimerization Reaction Set, Linear Molecular Chain System, single-species logistic growth model, Lotka predator-prey model, Rosenzweig-MacArthur predator-prey model, and Kermack-McKendrick SIR model. The release consists of several bug fixes, improved documentation, and a revised more 'R-like' management of model parameters. A vignette providing a tutorial of basic SSA theory, usage of t...

Hello, I am working on a paper of ecological modelling in R. I have made a Lotka Volterra model for tree animal species. I was trying to get the model in R but there are some errors. Since i am not so experienced with R i can't find the bugs in my script. I hope if there is someone who can help me handle this problem. Greetz Roel This is the script i wrote: library(ode...

Hello there, Suppose you want to solve the following system of ODE's (a simple Lotka-Volterra predator prey model) dP/dt = beta*P*V - mu*P dV/dt = r*V - beta*P*V where P and V are the numbers of predators and prey. Now, this is easy to do, but suppose you have a system of equations like this, dP1/dt = beta1*P1*V1 - mu1*P1 dP2/dt = beta2*P2*V2 - mu2*P2 dV1/dt = r1*V1 - beta1*P1...

dear all. Would someone be kind and willing to explain the code below for a person who has never used R? ( that is if one has enough time and inclination) It implements gillepsie's stochastic algorithm for Lotka Volterra model. What would help me tremendously is to see the breakdown of the line by line code into plain english. thanks for any insights or other comments. sean library(stepfun) lv <- function(N=1000,cvec=c(1,0.005,0.6),x=c(50,100)) { m<-length(cvec) n<-lengt...

I'm fairly new to R, and I'm trying to write out a population model that satisfies the following; the system consists of s species, i= 1, 2,...,s network of interactions between species is specified by a (s x s) real matrix, C[i,j] x[i] being the relative population of the "ith" species (0 =< x[i] =< 1, sum(x[i]=1) the evolution rule being considered is as follows;