Displaying 20 results from an estimated 200 matches similar to: "ODE"
2012 Jul 03
1
Wrapper function for multivariate arrays for ode
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,
2016 Apr 26
0
vectors of equations in ode / desolve
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.
##
2013 Apr 10
0
Problem with ode
Hi,
I am trying to run a 1D nutrient-phytoplankton-zooplankton model in R
using the package 'deSolve'. The code is shown below:
DEPTH = seq(2.5, 147.5, 5)
NPZ = function(t, state, params){
with(as.list(params), {
P <- state[1:NB]
Z <- state[(NB + 1): (2*NB)]
N <- state[(2*NB + 1): (3*NB)]
F.I = function(z, hr){
I0 = function(hr){
2012 Jul 18
1
Defining a variable outside of optim or differential equation solver.
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
2013 Apr 21
1
lsoda question from deSolve package
Dear List,
Wonder if you have some thoughts on the following question using lsoda in desolve:
I have the following data and function:
require(deSolve)
times <- c(0:24)
tin <- 0.5
D <- 400
V <- 26.3
k <-0.056
k12 <- 0.197118
k21 <- 0.022665
yini <- c(dy1 = 0,dy2 = 0)
events <- data.frame(var = "dy1",time = c(10,15),value = c(200,100),method =
2011 Oct 02
0
deSolve - Function daspk on DAE system - Error
I'm getting this error on the attached code and breaking my head but can't
figure it out. Any help is much appreciated. Thanks, Vince
CODE:
library(deSolve)
Res_DAE=function(t, y, dy, pars) {
with(as.list(c(y, dy, pars)), {
res1 = -dS -dES-k2*ES
res2 = -dP + k2*ES
eq1 = Eo-E -ES
eq2 = So-S -ES -P
return(list(c(res1, res2, eq1, eq2)))
})
}
pars <- c(Eo=0.02,
2011 Oct 03
0
deSolve - Function daspk on DAE system - Error (Vince)
Vince,
When that happens, one possible reason is that your DAE is of index > 1,
which cannot be solved by daspk.
The solver radau, also from deSolve can handle DAEs up to index 3, but
you need to rewrite the problem in the form M*y' = f(x,y), where M is a
mass matrix.
If you do that for your problem, and solve it with radau, then radau
complains that the "matrix is repeatedly
2010 Dec 11
2
Predator Prey Models
Dear R-users,
I am currently modifying a previously developed predator prey model and
was curious if there was a way to add in a disturbance to the model (let's
say at time t=100). The disturbance can be the introduction of 40 prey
(N=40) and 10 predators (Pred = 10). I would like to see my model go from a
state of equilibrium (up to t = 99), show this disturbance (at t = 100) and
then
2010 Dec 23
0
epidemiology ode likelihood, hierarchical model
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
2010 Sep 16
1
More accurate ODE solver?
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
2011 Mar 15
1
precompiled ode with spline input
I tried to use lsode with precompiled C code instead of an R function
defining the derivatives. No problem so far.
However, now I need to implement an ODE that contains spline functions,
i.e. the derivatives at given time points depend on the value of a
spline function at this time point. What is an efficient way to
implement this in precompiled C code?
--
Daniel Kaschek <daniel.kaschek at
2013 May 02
2
ODE solver
I am trying to use the package ode and periodically it will come up with
this error message
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.
And then the program just take very long to run. Is there anyway to get the
program to terminate when this warning is issued instead of continuing to
run ?
2003 May 29
0
ODE solvers in R (was:The Wrong Choice: Locked in by license restrict...
Dear Colleague:
I am glad to hear from you. I was going to contact you and ask if you have
notes on the steps involved on how you implemented LSODA. I will gladly take the
project on. In addition to dassl, I want to implement ODESSA also. In other
words, my project is a "suite" of ode solvers for R. The application of these
solvers will be to the study of the distribution of
2012 Apr 27
0
How to find eigenfunctions and eigenvalues of a fourth order ODE
Dear all,
I am having trouble with the following problem. Suppose we have the fourth
order ODE with boundary conditions:
http://r.789695.n4.nabble.com/file/n4591748/problem.jpg problem.jpg
where q(t) is a known function.
Note here the lambda parameter is changing, so essentially we have a series
of ODEs. lambda is called an eigenvalue, the solution y is called an
eigenfunction associated with
2013 Jan 27
0
Package for multi-dimensional terminal value ODE solver
Hi,
I did some googling. I found multiple ODE solver packages. But I am
wondering if there is any terminal value ODE solver (linear case) for
multi-dimension case or not? I have not come across any. Any guidance would
be appreciated.
Robert
[[alternative HTML version deleted]]
2009 May 13
2
ode first step
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
2011 Jan 25
1
deSolve: Problem solving ODE including modulo-operator
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
2011 Aug 16
1
deSolve, extracting variable values from inside ode function
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
2011 Oct 22
1
estimation of ode from data
Hello,
I'm used to working with R in estimation of distributions and statistical models. I'd like to estimate a simple model of an output y(t) based on a concentration as independent variable, using a timed series of experimental data; I've seen this I think somewhere in R? I'd appreciate to hear if anybody has used this with success.
regards,
S
2012 Apr 25
1
Using apply() with a function involving ode()
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