similar to: A Hodgkin Huxley Model

Hi All I have been struggling with this model for some time now and I just can't get it to work correctly. The messages I get when running the code is: DLSODA- Warning..Internal T (=R1) and H (=R2) are such that in the machine, T + H = T on the next step (H = step size). Solver will continue anyway. In above message, R = [1] 0 0 DINTDY- T (=R1) illegal In above message, R = [1]

Hi All Having been pointed the use of events and roots in deSolve, I was able to implement the Izchikevich model of spiking neurons. However, I'm not too sure of defining the event. The deSolve documentation says: An event is triggered when the ball hits the ground (height = 0) Then velocity (y2) is reversed and reduced by 10 percent. The root function, y[1] = 0, triggers the event: >

Hi All I am getting the above mentioned error when I run the code below. I don't know why because I have implemented the function and I'm calling the function with a parameter. I'm obviously missing the plot ... Can someone perhaps point out the error of my ways? Error: > out<-ode(y=init, times=times, func=G1999, parms=parms, method="lsoda") Error in m_Na(v) : attempt

Dear R-users, I'm running an MLE procedure where some ODEs are solved for each iteration in the maximization process. I use mle2 for the Maximum likelihood and deSolve for the ODEs. The problem is that somewhere along the way the ODE solver crashes and I get the following error message: DLSODA- Warning..Internal T (=R1) and H (=R2) are such that in the machine, T + H = T on the next

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

Hi All I have Googled the message Error in J[time] : invalid subscript type 'closure', but can't quite make sense from the results that I get. What does it mean? I'm trying to access an element in an array. Here is a short bit of code that produces the error: s_fun <- function(parms,time) { with(as.list(c(parms)),{ print(J[time]) }) } times = seq(from=0, to=100, by =

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 by increasing or decreasing), there is a time delay (delay)

hey can anybody help me? i have to simulate the richardson Arms race model on R.. for my simulation class...

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

Hello, I am developing an agent-based model to simulate the spread of infectious diseases in heterogeneous landscapes composed of habitat polygons (or clumps of connected cells). To simplify the model, I consider a habitat grid (or raster) containing the polygon ID of each cell. In addition, I have epidemiological parameters associated with each polygon ID. At each time step, the parameter values

> On Apr 18, 2018, at 1:04 AM, Hannah Meredith <hrmeredith12 at gmail.com> wrote: > > 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.

Dear list - Does anyone have any ideas / comments about why I am receiving the following warning when I run lsoda: 1: lsoda-- at t (=r1), too much accuracy requested in: lsoda(start, times, model, parms) 2: for precision of machine.. see tolsf (=r2) in: lsoda(start, times, model, parms) I have tried changing both rtol and atol but without success. I saw the thread in the

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

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,

This is applicable to either using optim or the differential equation solver or any similar solver Suppose I want to use the differential equation solver and this is my code d<-y[2] vdpol<-function(t,y) { list(c(1, d, 3, 4 ) } stiff<-ode(y=rep(0,4),times=c(0,1),func=dvdpol,parms=1) The thing is I want d to be composed of one of state variables in the

Dear All, I like to simulate a physiologically based pharmacokinetics model using R but am having a problem with the daspk routine. The same problem has been implemented in Berkeley madonna and Winbugs so that I know that it is working. However, with daspk it is not, and the numbers are everywhere! Please see the following and let me know if I am missing something... Thanks a lot in advance,

---------- Forwarded message --------- De: Jose Betancourt Bethencourt <betanster en gmail.com> Date: sáb, 26 oct 2024 a las 16:14 Subject: OPTIMIZACIÓN To: <r-help-es-request en r-project.org> Estimados Corri este código y funciona todo bien , menos la ultima parte de optimización apreciaria su ayuda José # Cargar bibliotecas necesarias library(deSolve) library(optimx) #

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

To whomever may be of help, I am a student in a graduate modeling class at the University of North Carolina at Wilmington. I am trying to get a STELLA model converted into R. I am in the process of trying to 're-write' the script into R, but I seem to be missing pieces (i.e. parm values) that are keeping me from being able to replicate this model into R. Does anyone have an idea of a

Hi, I've solved a simple differential equation describing the degradation of amino acid carbon (THAA-C) using deSolve. Code is a follows: # Input of model parameters, a and b describes form of curve, i is apparent initial age of Org. C. parameters <- c(a = a, b = b, i=i) # Initial value of the model, G state = c(G = G) #specifies the function degradation as a function of