R help - Aug 2011 - use of modMCMC

Dear all,

I used modFit of the package FME to fit a set of ODE to a ste of eperiemntal
data.

The summary of this fit give me the following error
> summary(Fit)
Residual standard error: 984.1 on 452 degrees of freedom
Error in cov2cor(x$cov.unscaled) : 'V' is not a square numeric matrix
In addition: Warning message:
In summary.modFit(Fit) : Cannot estimate covariance; system is singular

This is due becasue the Hessian matrix has all the entries equal to 0.

In these cases, on the help page of modFit, it is suggested to use modMCMC
to generate new sets of parameters. modMCMC performs a Markov Chain Monte
Carlo simulation.

I do not understand very well how modMCMC can be used in a context of
parameter estimation. Could someone help me in understanding the use of this
function and its utility for parameter fiting?

Thank you very much in advance,
Paola.
-- 
*Paola Lecca, PhD*
*The Microsoft Research - University of Trento*
*Centre for Computational and Systems Biology*
*Piazza Manci 17 38123 Povo/Trento, Italy*
*Phome: +39 0461282843*
*Fax: +39 0461282814*

	[[alternative HTML version deleted]]

Dear all,



I used modFit of the package FME to fit a set of ODE to a ste of
experimental data.

The summary of this fit give me the following error
> summary(Fit)
Residual standard error: 984.1 on 452 degrees of freedom
Error in cov2cor(x$cov.unscaled) : 'V' is not a square numeric matrix
In addition: Warning message:
In summary.modFit(Fit) : Cannot estimate covariance; system is singular


This is due becasue the Hessian matrix has all the entries equal to 0 in my
system.

In these cases, on the help page of modFit, it is suggested to use modMCMC
to generate new sets of parameters. modMCMC performs a Markov Chain Monte
Carlo simulation.

I do not understand very well how modMCMC can be used in a context of
parameter estimation. Could someone help me in understanding the use of this
function and its utility for parameter fitting?



Thank you very much in advance,

Paola.
-- 
*Paola Lecca, PhD*
*The Microsoft Research - University of Trento*
*Centre for Computational and Systems Biology*
*Piazza Manci 17 38123 Povo/Trento, Italy*
*Phome: +39 0461282843*
*Fax: +39 0461282814*

	[[alternative HTML version deleted]]