MCSim source code is now under CVS access on GNU Savannah

All the source code of MCSim is now accessible online via CVS on GNU Savannah.
You can fetch the latest code (almost!) as well as past versions.
You can also envision contributing to the project ;^)...
Just go to http://cvs.savannah.gnu.org/viewvc/mcsim/?root=mcsim
(for help go to https://savannah.gnu.org/cvs/?group=mcsim)
From now on maintenance an diffusion of the software will be made via Savannah.

F. Bois

MCSim version 5.2.beta available

The version 5.2.beta of MCSim is now available at http://fredomatic.free.fr
This is a technical upgrade before porting to the GNU official development 
platform.

Installation problems for libmcsim.so

From anonymous MCSim User:
Question: Installation Problem for libmcsim.so
Date: Tue, 20 Nov 2007

Hi,

I tried to install MCSim on my Red Hat Enterprise Linux WS vs.4 
(64-bit Intel EM64T) 
and kept getting the following error message:

make[1]: Entering directory `Programs/mcsim/sim'
Linking libmcsim.so...
/usr/bin/ld: /tmp/cckVUj.o: relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
/tmp/cckVUj.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [libmcsim.so] Error 1

I edited a line in sim/Makefile by adding -fPIC to the LFLAGS line:

LFLAGS = -lgsl -lgslcblas -lm -fPIC

It did solve my problem, but when I ran further with the example 
(mcsim.perc) and got another error message: 

$ ./mcsim.perc
./mcsim.perc: error while loading shared libraries: libgsl.so.0: cannot 
open shared object file: No such file or directory

What should I do?

mcsim using MinGW on Windows XP

I am about to embark on compiling and setting up mcsim to use mingw on
Windows XP.  I did this a long time ago with a much earlier version of
mcsim, but I gather others have already done this with the current
version-- would you be willing to share what I need to do?
Thanks!

R. Woodrow Setzer, Ph. D.
National Center for Computational Toxicology
US Environmental Protection Agency
Mail Drop B205-01/US EPA/RTP, NC 27711
Ph: (919) 541-0128    Fax: (919) 541-1194

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mailing list moderation

Greetings,

It appears that this mailing list, help-mcsim <at> gnu.org, (among many others),
has no known owner/moderator, and accepts mail from non-subscribers.
The result is passing through of lots of spam.

So we need to do something.  I'm writing to get input on the best thing
to do.  Please reply to me if you have any thoughts on the following:

(1) If this list is obsolete and should be deleted.  We'd keep the
    archives, just make the address inactive, so any future mail to it
    would bounce.

(2) If the list is *not* obsolete, and should remain as a live address.
    In many cases there is so much junk in the archives that it is hard
    to tell, hence my query.  In other cases, I could guess, but I felt
    it would be best to just inquire about everything.

In case (2), if you can volunteer to help moderate the list (and/or
others!), that would be most appreciated.  But even if not, I'd still
like to know if the list is still live; I'm recruiting volunteer
moderators to help with the job.

Any other information or suggestions is welcome too.  For example, if
someone is already administering the list but just isn't listed in the
mailman interface.

Thanks much,
Karl

MCSim question

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From: help-mcsim <at> gnu.org
To: bug-bash <at> gnu.org
Date: Sun, 15 May 2005 06:48:27 UTC
Subject: Deutsche Buerger trauen sich nicht ...
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Auslaenderbanden terrorisieren Wahlkampf - deutsche Buerger trauen sich nicht ihre Meinung zu sagen!

Weiter auf:
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Auslaender ueberfallen nationale Aktivisten:
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Arrays in MCSim

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MCMC with user-defined LnLike

Hi

Thanks for the documentation.  I did not have the proper translation tools.

In an earlier message, I asked:
- Can a user-defined likelihood function be easily implemented in
MCSim?
You wrote:
it depends what you want to
  do with it. Assume you want the likelihood for one data point. You
should be able to represent your data
  as an input function, taking the observed value at a prescribed
observation time. Then the likelihood
  should be representable as a standard function of the parameters,
state and output variables and that data.
  Now if you want to compute the total likelihood for a dataset you
have to find a way to (say) form the product
  of individual datapoints likelihood. To do that you can setup an
output variable to act as an accumulator:
  this_point-like = f(params, this_data)
  total_like = total_like * this_point-like
  Just make sure that it behave correctly. That should be easy for
discrete-time sims. For integration it's more difficult
  because Calc-Deriv (the "model") may be called several times within
an integration step and the product would be formed
  too often (to avoid that I tend to use control input function of the
Spikes form).
  An alternative is to code the product in the "yourcode.c" file. The
TransformPred function is called after a Monte Carlo
  simulation and can be used for that. If you are not using MC
simulations you may need to add calls to TransformPred
  elsewhere in the program.

Thanks for these helpful tips.  The accumulator was part of the question.

I am also wondering if this likelihood function can be used in MCMC simulations?  I have looked briefly at a
paper describing this model, and I think it is essentially the MVK 2-stage clonal growth cancer model.  The
likelihood contribution is different for survivors, fatal tumors, and incidental tumors.  I believe
that the contributions work out as follows:
 S(t)=exp(-H(t)) for the survivors,
 h(t)S(t) for the fatal tumors, and
 S(t)F(t) for the incidental tumors, 
 where S(t) is the survival function, H(t) is the cumulative hazard function, h(t) is the instantaneous
hazard, and F(t) is the cumulative probability of a malignant transformation.  Each type of contribution
is based on H(t), a function of the number of 2nd stage mutations.

Is there an easy way to set this model up in MCSim to do MCMC analysis of the data?  My first guess was to modify
the LnLikeData, or add a user distribution to LnDensity and put the function in 'yourcode.c' or wherever
the other likelihoods are calculated.  The thing about adding a distribution to LnDensity is that I did not
know if 'mod' would let me get away with an unknown distribution name.  Can I add it to a list of keywords someplace?

You may be aware of more appropriate distributions that I have not thought of for these data, so any
suggestions are welcome.

Thanks again,
Eric

 
C. Eric Hack

Toxicology Excellence for Risk Assessment (TERA)
2300 Montana Avenue
Suite 409
Cincinnati, OH 45211
(513) 542 7475 x 19

Rép. : Help-mcsim Digest, Vol 15, Issue 10

Hi !

Let see: 

- The latest version of the doc, with pdf etc. is attached. Your Unix
system should be able to
  automatically create the pdf ps etc from the texinfo file (that's
precribed in the makefile, but
  it may not work if you do not have the translation tools).

- The difference between v5beta and v5beta2 were minor and cosmetic.
See the MCSim-changelog 
  in the doc section for important changes. 

- Can a user-defined likelihood function be easily implemented in
MCSim? : it depends what you want to
  do with it. Assume you want the likelihood for one data point. You
should be able to represent your data
  as an input function, taking the observed value at a prescribed
observation time. Then the likelihood
  should be representable as a standard function of the parameters,
state and output variables and that data.
  Now if you want to compute the total likelihood for a dataset you
have to find a way to (say) form the product
  of individual datapoints likelihood. To do that you can setup an
output variable to act as an accumulator:
  this_point-like = f(params, this_data)
  total_like = total_like * this_point-like
  Just make sure that it behave correctly. That should be easy for
discrete-time sims. For integration it's more difficult
  because Calc-Deriv (the "model") may be called several times within
an integration step and the product would be formed
  too often (to avoid that I tend to use control input function of the
Spikes form).
  An alternative is to code the product in the "yourcode.c" file. The
TransformPred function is called after a Monte Carlo
  simulation and can be used for that. If you are not using MC
simulations you may need to add calls to TransformPred
  elsewhere in the program.

- I should be able to use vector indexing, right? : yes.

- Some If-then-else blocks can be implemented using the ( ? : )
construct. An alternative
  is the create a baseline model.c file and then change it manually
(it's written in C).
 Just make sure you keep a copy so that mod doesn't overwrite it at the
next compilation.

I hope this helps.

Best regards.

Frederic

==========================
Frederic Y. Bois,
Unite de Toxicologie Experimentale, responsable
INERIS
Parc ALATA, BP 2
5, rue Taffanel
60550 Verneuil en Halatte
FRANCE
tel: + 33 (0)3 44 55 65 96
fax: + 33 (0)3 44 55 66 05
email: frederic.bois <at> ineris.fr
web: http://www.ineris.fr, http://toxi.ineris.fr

>>> help-mcsim-request <at> gnu.org Mercredi 21 Juillet 2004 18:05:10 >>>

Message: 1
Date: Thu, 15 Jul 2004 07:54:38 -0500
From: "Eric Hack" <kcahcire <at> msn.com>
Subject: MCSim beta version documentation
To: help-mcsim <at> gnu.org 
Message-ID: <BAY4-F18KUUVbbpKlkj0001219f <at> hotmail.com>
Content-Type: text/plain; format=flowed

Dear group,

First, does anyone have the latest version of the beta version
documentation 
that has been translated from texinfo to html?  How about PDF,
postscript, 
or other formats?

Secondly, I think I downloaded version 5 beta, but I see that the
latest is 
version 5 beta 2.  Is this an updated beta?  If so, what is new?

Thanks,
Eric

Message: 2
Date: Tue, 20 Jul 2004 14:37:42 -0400
From: "Eric Hack" <hack <at> tera.org>
Subject: translating a model into MCSim
To: <frederic.bois <at> Ineris.fr>
Cc: help-mcsim <at> gnu.org 
Message-ID:
	<ABEC59A68A73FA4F9C93E89B308F14CE299237 <at> TERAS0002.tera.org>
Content-Type: text/plain; charset="us-ascii"

Dear Frederic,

I want to translate a model to MCSim and have a couple of questions.
The model is a discrete-time model and the data are time (duration) of
exposure, outcome (tumor or no), and frequency at many time points and
exposure levels.  The model incorporates an ad hoc likelihood function
which was being used to obtain MLEs for the parameters.

Can a user-defined likelihood function be easily implemented in MCSim?

There are also several logical constructs that I think may be
difficult
to translate to MCSim.  The code includes many if-then-else blocks, do
loops, goto statements, and scheduled code blocks (to run at specific
value of independent variable).  I think all of the do loops and goto
statements facilitate array operations, so I should be able to use
vector indexing, right?  Can the if-then-else blocks be coded in the
model definition file, or should I code these into the model.c file
after the translation by mod?

Thank you,

Eric

 
C. Eric Hack

Toxicology Excellence for Risk Assessment (TERA)
2300 Montana Avenue
Suite 409
Cincinnati, OH 45211
(513) 542 7475 x 19

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