Displaying 20 results from an estimated 900 matches similar to: "Fitting data with optim or nls--different time scales"
2005 Jul 27
4
odesolve/lsoda differences on Windows and Mac
Hi -
I am getting different results when I run the numerical integrator
function lsoda (odesolve package) on a Mac and a PC. I am trying to
simulating a system of 10 ODE's with two exogenous pulsed inputs to the
system, and have had reasonably good success with many model parameter
sets. Under some parameter sets, however, the simulations fail on the
Mac (see error message below). The
2005 Oct 25
2
solving ODE's in matrix form with lsoda()
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*V1
2001 May 11
1
lsoda
I am running R 1.2.3 with ESS5.1.18 with Windows 98.
I am trying to use lsoda in the odesolve apckage and am having problems.
Question:
The return value of the function of the system of ode's has to be a list
that includes first, the ode's and second, "a vector
(possibly with a `names' attribute) of global values that are
required at each point in `times'."
I
2008 Nov 21
1
lsoda warning "too much accuracy requested"
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
2008 Aug 29
1
nls() fails on a simple exponential fit, when lm() gets it right?
Dear R-help,
Here's a simple example of nonlinear curve fitting where nls seems to get
the answer wrong on a very simple exponential fit (my R version 2.7.2).
Look at this code below for a very basic curve fit using nls to fit to (a)
a logarithmic and (b) an exponential curve. I did the fits using
self-start functions and I compared the results with a more simple fit
using a straight lm()
2023 May 09
1
RandomForest tuning the parameters
Hi Sacha,
On second thought, perhaps this is more the direction that you want ...
X2 = cbind(X_train,y_train)
colnames(X2)[3] = "y"
regr2<-randomForest(y~x1+x2, data=X2,maxnodes=10, ntree=10)
regr
regr2
#Make prediction
predictions= predict(regr, X_test)
predictions2= predict(regr2, X_test)
HTH,
Eric
On Tue, May 9, 2023 at 6:40?AM Eric Berger <ericjberger at gmail.com>
2008 Apr 09
3
LSODA not accurate when RK4 is; what's going on?
I'm solving the differential equation 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
2005 Dec 05
1
how to save output all together
Dear R users:
I have a problem about catch the value from function.
I have following two functions (part):
sbolus1 <- function()
{
.......
for( i in 1:Subject) {
kel<-par1
Vd<-par2
PKindex<-sbolus1.out(PKtime,kel,Vd,defun,par1,par2,Dose,i)
}
savefile(PKindex)
}
sbolus1.out<-function(PKtime,kel,Vd,defun,par1,par2,Dose,i)
{
time<-PKtime$time
2004 Jan 22
4
Fitting compartmental model with nls and lsoda?
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
2003 Nov 05
3
using LSODA in R
R help list subscribers,
I am a new user of R. I am attempting to use R to explore a set of
equations specifying the dynamics of a three trophic level food chain. I
have put together this code for the function that is to be evaluted by
LSODA. My equations Rprime, Cprime, and Pprime are meant to describe the
actual equation of the derivative. When I run LSODA, I do not get the
output that
2004 Oct 06
1
Foreign code problem
Hello,
I wanted to test the odesolve package and tried to use compiled C-code.
But when I do:
erg <- lsoda(y, times, "mond", parms, rtol, atol, tcrit=NULL, jacfunc=NULL,
verbose=FALSE, dllname="mond", hmin=0, hmax=Inf)
I get the error message:
Error in lsoda(y, times, "mond", parms, rtol, atol, tcrit = NULL,
jacfunc =
2005 Nov 06
1
Problem defining a system of odes as a C library with lsoda
I have been trying to make use of the odesolve library on my
university's Linux grid - currently R version 2.0.1 is installed and
the system runs 64-bit Scientific Linux based on Redhat. I cannot seem
to get lsoda working when I define the model as a shared C library. For
example, the following snippet uses the mymod.c example bundled with
the package:
### START
rm(list=ls())
2004 Sep 06
1
A naive lsoda question....
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"]
Kx <-
2004 Jun 10
2
odesolve: lsoda vs rk4
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:
2005 Jul 19
2
Michaelis-menten equation
Dear R users:
I encountered difficulties in michaelis-menten equation. I found
that when I use right model definiens, I got wrong Km vlaue,
and I got right Km value when i use wrong model definiens.
The value of Vd and Vmax are correct in these two models.
#-----right model definiens--------
PKindex<-data.frame(time=c(0,1,2,4,6,8,10,12,16,20,24),
2002 Feb 01
1
typo and user-proofing in odesolve() (PR#1295)
A couple of minor points about the odesolve package
(which I am otherwise enjoying very much):
1. "scalar" is misspelled as "scaler" in the definitions of
the rtol and atol parameters
2. it is possible to crash R by doing something dumb, e.g
failing to read the documentation carefully enough and (a)
returning only a vector of derivatives and not a list of
(derivatives,
2012 Nov 26
1
Help on function please
Dear All,
I could use a bit of help here, this function is hard to figure out (for me at least) I have the following so far:
PKindex<-data.frame(Subject=c(1),time=c(1,2,3,4,6,10,12),conc=c(32,28,25,22,18,14,11))
Dose<-200
Tinf <-0.5
defun<- function(time, y, parms) {
dCpdt <- -parms["kel"] * y[1]
list(dCpdt)
}
modfun <- function(time,kel, Vd) {
out <-
2009 Dec 06
2
Error in eval(expr, envir, enclos) : object 'N' not found
I'm running an LSODA to generate some graphs, but I need to stop at a certain
point and use those values to generate another LSODA output. This is
working fine, but when I try to run the second LSODA, I get the "Error in
eval(expr, envir, enclos) : object 'N' not found". Any ideas what can be
causing this? I have no object 'N' anywhere in the script. I made an
2006 Apr 25
1
Windows MinGW compiler clarification, consequences
The information at
http://cran.r-project.org/doc/manuals/R-admin.html#The-MinGW-compilers
and
http://www.murdoch-sutherland.com/Rtools/
is slightly inconsistent about the compiler used to build Windows
binary packages available through cran.
The 'candidate' package of the recommended MinGW-5.0.0.exe installs
g++/g77 3.4.4 (as does the updated installer MinGW-5.0.2.exe). "An
2013 Feb 18
1
attempt to apply non-function
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