search for: rk4

All- I am interested in estimating a parameter that is the starting value for an ODE model. That is, in the typical combined fitting procedure using nls and lsoda (alternatively rk4), I first defined the ODE model: minmod <- function(t, y, parms) { G <- y[1] X <- y[2] with(as.list(parms),{ I_t <- approx(time, I.input, t)$y dG <- -1*(p1 + X)*G +p1*G_b dX <- -1*p2*X + p3*(I_t-I_b) list(c(dG, dX)) }) } Then I estimated the parameters of t...

Hi, I'm new to R and have a problem with a little test program (see below). Why doesn't <<- in function rk4 assign the new value to y so that it is seen in rktest. I thought that <<- does exactly this. But it seems that I didn't get it right. I would be very appreciative for an explanation of that behaviour of <<-. I know how to write the whole thing so that it works (return the updated...

...on dy/dx = xy-1 with y(0) = sqrt(pi/2). This can be used in computing the tail of the normal distribution. (The actual solution is y(x) = exp(x^2/2) * Integral_x_inf {exp(-t^2/2) dt} = Integral_0_inf {exp (-xt - t^2/2) dt}. For large x, y ~ 1/x, starting around x~2.) I'm testing both lsoda and rk4 from the package odesolve. rk4 is accurate using step length 10^-2 and probably would be with even larger steps. lsoda is pretty accurate out to about x=4, then starts acting strangely. For step length 10^-3, y suddenly starts to increase after 4, when it should be strictly decreasing. For step le...

I'm trying to use odesolve for integrating various series of coupled 1st order differential equations (derived from a system of enzymatic catalysis and copied below, apologies for the excessively long set of parameters). The thing that confuses me is that, whilst I can run the function rk4: out <- rk4(y=y,times=times,func=func, parms=parms) and the results look not unreasonable: out<-as.data.frame(out) par(mfrow=c(4,1)) for (i in 2:(dim(out)[2]))plot(out[,1],out[,i], pch=".", xlab="time", ylab=names(out)[i]) If I try doing the same thing with lsoda: out...

Dear Colleagues, Our group is also working on implementing the use of R for pharmacokinetic compartmental analysis. Perhaps I have missed something, but > fit <- nls(noisy ~ lsoda(xstart, time, one.compartment.model, c(K1=0.5, k2=0.5)), + data=C1.lsoda, + start=list(K1=0.3, k2=0.7), + trace=T + ) Error in eval(as.name(varName), data) : Object

Dear All, I am trying to use ode solver "rk4" to solve an ODE system, however, it keeps saying: Error in eval(expr, envir, enclos) : object "dIN" not found. The sample codes are enclosed as follows, please help me. Thank you very much! rm(list=ls()) library(odesolve) # The ODE system ode <- function(t,x,p){...

Dear All, I am trying to use ode solver "rk4" to solve an ODE system, however, it keeps saying: Error in eval(expr, envir, enclos) : object "dIN" not found. The sample codes are enclosed as follows, please help me. Thank you very much! rm(list=ls()) library(odesolve) # The ODE system ode <- function(t,x,p){...

Dear All, I was using rk4 and lsoda to solve a ODE system. However, both of them gave bad accurate solutions, especially compared with Matlab solver ODE45. For example, ODE45 gave solutions that can go to a stable level (about 1.6) when time goes to infinity, however, the solutions from lsoda are decreasing to very very sma...

Hello, I want to know if there are some functions or packages to solve differential and integral equation using R. Thanks. Shao chunxuan. [[alternative HTML version deleted]]

Dear list The deSolve package allows you to specify the model code in C or Fortran. Thanks to the excellent vignette this works fine. However I have not yet managed to use forcing functions in C code. In pure R code this works very well with approxfun() specified outside the model: ############################################### #Model lvml <- function(t, x, parms) {

Hello! I would like to know if R can solve Differential Equations... I don't think so because, in my point, I see R like a Statistical System, not a Math System. Am I wrong? Thank you very much. M??rcio de Medeiros Ribeiro Graduando em Ci??ncia da Computa????o Departamento de Tecnologia da Informa????o - TCI Universidade Federal de Alagoas - UFAL Macei?? - Alagoas - Brasil Projeto CoCADa

...? ? ??? ? ? # Rate of change? ? ? dA <- inA+BtoA-AtoB-Aout? ? ? dB <- inB+AtoB-BtoA-Bout? ? ??? ? ??? ? ? return (list (c(dA, dB)))? ? })? }??? #Step 4: Define some starting values for the pools??? state <- c(A=5, B=3)??? ?return (ode(y=state, times=t,func=derivs, parms=parms, method="rk4"))} # Starting values of fluxes/parameterspars <- c(kinA=5, kAtoB=0.3, kAout=0.1, kinB=2, kBtoA=0.3, kBout=0.3) #Model results Mod(time, pars)data <- data.frame(Mod(time, pars))plot(Mod(time, pars)) The result does not look right. I could not figure out where I made a mistake in compilin...

Dear R Gang, I'm interested in using R and the nls package for fitting kinetic models. I'm having some difficulty getting a model specified for nls though. The math for the model that I want to fit is dg(t)/dt = K1 f(t) - k2 g(t) where g(t) and f(t) are measured data at a sequence of times t. K1 and k2 are the parameters of the model. If I solve this, the solution is g(t) = K1

Installing odesolve in Raqua 1.8.0 or 1.8.1 under MacOSX gives the following message: Warning message: Installation of package odesolve had non-zero exit status in: install.packages(ui.pkgs, CRAN = getOption(where), lib = .libPaths()[1]) Moreover, in the source of odesolve is no makefile. Does anyone know how to get a proper installation? Maartje

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Hi R-Helpers, Sorry to bother you, but I have a simple task that I can't figure out how to do. For example, I have some names in two columns NamesWide<-data.frame(Name1=c("Tom","Dick"),Name2=c("Larry","Curly")) and I simply want to get a single column

Hi R Helpers, I have been looking for an example of how to execute different dplyr mutate statements on the same dataframe in a single step. I show how to do what I want to do by going from df0 to df1 to df2 to df3 by applying a mutate statement to each dataframe in sequence, but I would like to know if there is a way to execute this in a single step; so simply go from df0 to df1 while executing