search for: odes

Hi there R-helpers: I'm having problems with the function ode() found in the package deSolve. It seems that when my state variables are too numerous (>33000 elements), the function throws the following error: Error in vode(y, times, func, parms, ...) : cannot allocate memory block of size 137438953456.0 Gb In addition: Warning message: In vode(y, times, func, parms, ...) : NAs

...by = 1), beta = sample(c(100, 200, 400, 600), 10, replace = TRUE), gamma = sample(c(25, 26, 27, 28), 10, replace = TRUE)) To study the disease dynamics, I also am developing a compartmental model based on a system of ordinary differential equations (ODEs). Here is an example to represent the system of ODEs: solve_sir_model <- function (times, parameters) { sir_model <- function (times, states, parameters) { with(as.list(c(states, parameters)), { dSdt <- -beta*S*I dIdt <- beta*S*I-gamma*I dRdt <- gamma*I...

Hi, I have a data-matrix: > PID sato hrs fim health 214 3 4.376430 6.582958 5 193 6 4.361825 3.138525 6 8441 6 4.205771 3.835886 7 7525 6 4.284489 3.245139 6 6806 7 4.168926 2.821833 7 5682 7 1.788707 1.212653 7 5225 6 1.651463 1.436980 7 4845 6 1.692710 1.267359 4 4552 5 1.686448 1.220539 6

Hello. I'm solving ODEs in R. I need "as many methods as possible", so I downloaded the Fortran functions from http://www.netlib.org/ode/. Then I created DLLs and dyn.loaded them to R. Problem is that I don't know how to use them. I've been trying for many days and can't solve it. So I would be very...

I have a problem integrating the 'standard map' ( http://en.wikipedia.org/wiki/Standard_map http://en.wikipedia.org/wiki/Standard_map ) with deSolve: By using the modulo-operator '%%' with 2*pi in the ODEs (standardmap1), the resulting values of P and Theta, should not be greater than 2pi. Because this was not the case, i was thinking that the function 'ode' has some internal problems with the '%%' or integrating periodical ODEs, so I wrote a modulo-function by myself (modulo and stan...

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){ with(as.list(c(x,p)),{ if(IN==0){ dIN <- 1 switch <- c } else { switch <- 0 }...

Hi all, I try to assess the parameters (K1,K2) of a model that describes the adsorption of a molecule onto on adsorbent. equation: dq/dt = K1*C*(qm-q)-K2*q I know the value of 'qm' and I experimentally measure the variables 'q', 'C', and the time 't'. t C q 1 0 144.05047 0.0000000 2 565 99.71492 0.1105625 3 988 74.99426

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){ with(as.list(c(x,p)),{ if(IN==0){ dIN <- 1 switch <- c } else { switch <- 0 }...

I'm just getting to grips with using ode function and have used the examples and vignettes to produce a small model of a one-pool, michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate into pool A is constant (fluxoa) however the rate of flux out of pool A is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A )) ). This function works fine and

Dear all, Has anybody tried numerical solving of ODE's and/or transport equations in R? (Don't ask how we ended up in using R for this job, in the first place!) More precisely, does anybody know any technical issue that could make the work insecure in the sense of propagation of errors? Is there any track of evidence that R is, in this kind of task, less reliable than e.g. MatLab?

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 small (about 1e-130) numbers. Does R have more accurate ODE solvers as

Hi all, I study epidemiology of soilborne disease. I have this ode model dS/dt = - (rp(t) X + rs(t) I) * S with X=1 ; rp(t) = ap exp( - bp*t) ; rs(t) = as exp (-0.5 ( ln (t/ds) / bs)? ) The data I have are not directly the infected individuals (which is a hidden state) but the Diseases ones (individuals who show aerial symptoms). I have studied with experiments the relationship between the

I am trying to to write a wrapper function for the ode solver (under the package desolve) to enable it to take multivariate arrays. I know how to do it for 1 dimension arrays but my code breaks down when I try to do it for 2 dimensional arrays. Here is my code diffwrap<-function(t,y,mu)vdpol(t=t,A[1:3,1:4]<-y[1:12],B[1:12]<-y[13:24],mu=mu) vdpol<-function(t,A,B,mu) { list(c(mu,

Hello All, I'm struggling to solve this ODE using R, vdpol <- function (h, v, t) ( list(c ( -0.1*v/(pi*(2*10*h-h^2)), (v = (-0.1*v/(pi*(2*10*h-h^2))^2) + 2*9.81*h)) )) library(deSolve) yini <- (c(h = 20, v=0)) nonstiff <- ode(y = yini, func = vdpol, times= seq(0, 30, by =

Hello, I am trying to get the output from the numerical simulation of a system of ordinary differential equations for a range of values for three parameters. I am using the ode() function (deSolve package) to run the numerical simulation and apply() to run the simulation function for each set of parameter values. I am having trouble getting the apply() function to work. Here is an

...Unsuffered Consequences > > > > > > ________________________________ > > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > ur?eny pouze jeho adres?t?m. > > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? > jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze > sv?ho syst?mu. > > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?soben...

Hello, I am solving a set of ODEs using deSolve and have run into a problem I would appreciate some advice on. One of the parameters (m) in the ODEs changes between two states when one of the variables (D) crosses a threshold (D_T) for the first time in either direction. Additionally, when the variable crosses the threshold (either...

...t; > >>> ________________________________ > >>> Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou > >> ur?eny pouze jeho adres?t?m. > >>> Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? > >> jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze > >> sv?ho syst?mu. > >>> Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento > email > >> jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > >>> Odes?latel e-mailu...

...th lognorm function but maybe somebody already solved such task. Best regards Petr ________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p...

...some kind of "Linux R for Windows dummies" available? Best regards Petr ________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p...