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

[Frédéric BOIS]

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: address@hidden
web: http://www.ineris.fr, http://toxi.ineris.fr


>>> address@hidden Mercredi 21 Juillet 2004 18:05:10 >>>

Message: 1
Date: Thu, 15 Jul 2004 07:54:38 -0500
From: "Eric Hack" <address@hidden>
Subject: MCSim beta version documentation
To: address@hidden 
Message-ID: <address@hidden>
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" <address@hidden>
Subject: translating a model into MCSim
To: <address@hidden>
Cc: address@hidden 
Message-ID:
        <address@hidden>
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

doc.tar.gz
Description: GNU Zip compressed data