By the way, if someone could forward the original question to me (I'm
subscribed to but not currently receiving R-help, as I found I was
spending too much time reading it!) I might think of something more
useful. (alternatively, when was it posted; I can find it on gmane,
too).
Woody
R. Woodrow
Hi, all.
lsoda can certainly not handle complex parameters. You can try (as Hank
suggested) limiting hmax. You can also crank up relative and absolute
precision by specifying smaller values of rtol and atol. I've seen
similar problems in which the state variable becomes negative, with very
Without more detail - a reproducible example - it is hard to give you
concrete advice.
I wonder if the functions NLL23 and NLL21 depend on numerical solutions
of a system of ODEs, since you invoke the odesolve package? If so, try
switching to the Nelder-Mead optimizer, enforcing the parameter
lsoda does not solve delay differential equations, which is what you
need to be able to do. A quick search on netlib (netlib.org) turned up
one match for delay differential equations: ode/ddverk.f, which might
help (though not in R).
R. Woodrow Setzer, Ph. D.
National Center for Computational
Joerg van den Hoff [EMAIL PROTECTED] wrote on 08/16/2006
08:22:03 AM:
Earl F. Glynn wrote:
[deleted]
efg
[deleted]
(I think this is recognized by d. bates, but simply way down his 'to
do'
list :-().
joerg
No doubt Doug Bates would gladly accept patches ... .
Prof. Ripley:
Thanks for diagnosing Wuming Gong's problem.
I'm not sure I would have recognized the solution so quickly. I have
uploaded to CRAN a new version of odesolve with Makevars fixed.
R. Woodrow Setzer, Ph. D.
National Center for Computational Toxicology
US Environmental Protection
Hi Ariel,
The problem is that I specified the wrong dependency in the DEPENDS
field of the DESCRIPTION file of the package: I specified R version of
at least 2.2.1, but that should have been 2.3.1. You have two choices
-- upgrade your R to 2.3.1, or install odesolve 0.5.13. I will send an
Dear Karline Soetaert,
I've just returned from a week of travel, so have not had a great deal
of time to look at your request. From a brief rereading of the original
lsoda documentation, it looks as if all I need to do is set a flag to a
different value (jt to 4), and leave it up to the user to
Hank,
I don't understand why you think memory is the problem, here. I'd try
writing my model in C or Fortran (there is an example in the odesolve
package). That speeds things up a lot, and is what I do with slow
systems.
R. Woodrow Setzer, Jr.
National Center for Computational Toxicology
US
I've been talking offline with Hank Stephens about this; note that in
the example he quotes, he set hmin = 0.1, and the quoted error message
says that the stepsize had reached hmin with no convergence. I believe
that he intended to set hmax (because of the pulsed input). Then, Peter
Dalgaard's
I will have added most of the solvers from the ode package odepack by
Alan Hindmarsh, LLNL, to odesolve this year. These are all solvers in
the lsode family.
I would also like to add solver(s) for DAEs, like daskr (Brown,
Hindmarsh, Petzold), but that may take a bit longer.
If other folks are
Back on January 16, a message on R-help from Ravi Varadhan described a
problem with gnls using weights=varPower(). The problem was that the
fit failed with error
Error in eval(expr, envir, enclos) : Object . not found
I can reliably get this error in version 2.0.1-patched 2004-12-09 on
Windows
lsoda doesn't pass along the names attribute of the state vector, y. If
you want to use the names of the state vector in your code, you need to
reassign it inside your ode function. I should either fix this in the
code for lsoda, or at least document it! For example, I can run the
following
Dear Hank,
Last question first: really, only you can say for sure if 4e-281 and
5e-11 are small enough; it depends on the units you measure your state
variables in. However, this strategy cannot get the state variables to
exactly 0. Obviously, you could get closer to 0.0 faster by setting
I have plans to add dassl to odesolve. However, I won't have time in
the immediate future. If someone wanted to take this on, I'd be happy
to give advice and continue to manage the package ... .
R. Woodrow Setzer, Jr.Phone: (919) 541-0128
Experimental Toxicology
I'm having trouble figuring out how to create a function using body-
(). The help file for body() says that the argument should be a list of
R expressions. However if I try that I get an error:
tmpfun - function(a, b=2){}
body(tmpfun) - list(expression(z - a + b),expression(z^2))
Error in
I did not know about stepsize being an issue. I had thought that
problems with convergence in this case were due to bad approximations of
the finite difference gradient. I guessed that around the optimum,
numerical errors would come to dominate the gradient calculations,
causing convergence to
When I run Rcmd check on a package on my Windows 2000 machine, I get a
series of error messages like the following:
* checking generic/method consistency ...c:\DOCUME~1\R5018~1.WOO\LOCALS~1\Temp/R
utils138414013: cannot open c:DOCUME~1R5018~1.WOOLOCALS~1Temp/Rin138408157: no s
uch file
It looks
TMPDIR seems to be OK:
echo %TMPDIR%
C:/DOCUME~1/R5018~1.WOO/LOCALS~1/Temp
I'll poke around in the Perl code to see what I can find.
R. Woodrow Setzer, Jr.Phone: (919) 541-0128
Experimental Toxicology Division Fax: (919) 541-4284
Pharmacokinetics Branch
I do not understand why, but changing the definition of TMPDIR to C:/tmp
solved the problem.
R. Woodrow Setzer, Jr.Phone: (919) 541-0128
Experimental Toxicology Division Fax: (919) 541-4284
Pharmacokinetics Branch
NHEERL B143-05; US EPA; RTP, NC 27711
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