Re: [R] Stochastic SEIR model
On Thu, Nov 16, 2006 at 02:55:07PM +0100, Massimo Fenati wrote: Dear colleagues, Im a new R-help user. Ive read the advertisements about the good manners and I hope to propose a good question. Im using R to build an epidemiological SEIR model based on ODEs. The odesolve package is very useful to solve deterministic ODE systems but Id like to perform a stochastic simulation based on Markov chain Montecarlo methods. I dont know which packages could be used to do it (I tried with sde but without results). Have you some suggestions about useful methods and/or function in R for reaching my aim. Hi Max, I don't know what SEIR is. R has some MCMC packages (RSiteSearch(MCMC) will help you there), but it is easy to write a Metropolis/Gibbs sampler yourself, making use of the structure of your problem. The sde package is for approximating likelihoods of continuous time stochastic differential equations (which is a difficult problem by itself). It is hard to give more advice without knowing what you are trying to achieve -- it is good that you have read the posting guide, but please give more details if you want more specific answers. HTH, Tamas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stochastic SEIR model
Dear Max, Check out the BUGS software available (free) at http://www.mrc-bsu.cam.ac.uk/bugs/. It is easy to use and there are several packages in R which comport with the varying BUGS programs (R2WinBUGS, bRugs, rbugs, etc.). Best wishes, Amy Paternostro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stochastic SEIR model
Thanks for your fast advises.
A simple examples of SEIR model is shown below:
#expample of very simple SEIR model#
library(odesolve)
times-seq(0,1200,1)
parms-c(
b=0.35, #BETA OR COEFFICIENT OF TRANSMISSION
pl=1/7, #LATENCY
g=1/21, #RECOVERY
a=0.05/7#LETHALITY IN ADULT
)
xstart-c(S=100,E=0,I=1,R=0,nn=101)
model-function(t,x,parms){
S -x[1]
E -x[2]
I -x[3]
R -x[4]
nn -x[5]
with(as.list(parms),{
dS--S*b*I/nn
dE-S*b*I/nn-E*pl
dI-E*pl-I*(a+g)
dR-I*g
dnn-dS+dE+dI+dR
list(c(dS,dE,dI,dR,dnn))
})
}
out-as.data.frame(lsoda(xstart,times,model,parms))
plot(times,out$S,type=l)
lines(times,out$E,col=green)
lines(times,out$I,col=red)
lines(times,out$R,col=blue)
#
I'd like to vary one or more parameters (with several
distribution) for obtaining probabilistic results from the
model projections.
Now I'll try also with winBUGS, but I've never worked with
it. I hope..
Thank you very much.
Max
On Thu, 16 Nov 2006 09:26:12 -0500
Tamas K Papp [EMAIL PROTECTED] wrote:
On Thu, Nov 16, 2006 at 02:55:07PM +0100, Massimo Fenati
wrote:
Dear colleagues,
Im a new R-help user. Ive read the advertisements
about
the good manners and I hope to propose a good question.
Im using R to build an epidemiological SEIR model based
on ODEs. The odesolve package is very useful to solve
deterministic ODE systems but Id like to perform a
stochastic simulation based on Markov chain Montecarlo
methods. I dont know which packages could be used to do
it (I tried with sde but without results).
Have you some suggestions about useful methods and/or
function in R for reaching my aim.
Hi Max,
I don't know what SEIR is. R has some MCMC packages
(RSiteSearch(MCMC) will help you there), but it is
easy to write a
Metropolis/Gibbs sampler yourself, making use of the
structure of your
problem.
The sde package is for approximating likelihoods of
continuous time
stochastic differential equations (which is a difficult
problem by
itself).
It is hard to give more advice without knowing what you
are trying to
achieve -- it is good that you have read the posting
guide, but please
give more details if you want more specific answers.
HTH,
Tamas
MASSIMO FENATI
-
Istituto Nazionale per la Fauna Selvatica
Via Cà Fornacetta, 9
40064 - Ozzano dell'Emilia (BO)- Italy
tel: +39 0516512245
cel: +39 3392114911
fax: +39 051796628
e-mail: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stochastic SEIR model
Dear Massimo
This site have some code that may help you to get started.
http://www.statistik.lmu.de/~hoehle/software/
Also if you want to take an agent-based approach, you may want to take a
look at the simecol package
Regards,
Francisco
Massimo Fenati wrote:
Thanks for your fast advises.
A simple examples of SEIR model is shown below:
#expample of very simple SEIR model#
library(odesolve)
times-seq(0,1200,1)
parms-c(
b=0.35, #BETA OR COEFFICIENT OF TRANSMISSION
pl=1/7, #LATENCY
g=1/21, #RECOVERY
a=0.05/7#LETHALITY IN ADULT
)
xstart-c(S=100,E=0,I=1,R=0,nn=101)
model-function(t,x,parms){
S -x[1]
E -x[2]
I -x[3]
R -x[4]
nn-x[5]
with(as.list(parms),{
dS--S*b*I/nn
dE-S*b*I/nn-E*pl
dI-E*pl-I*(a+g)
dR-I*g
dnn-dS+dE+dI+dR
list(c(dS,dE,dI,dR,dnn))
})
}
out-as.data.frame(lsoda(xstart,times,model,parms))
plot(times,out$S,type=l)
lines(times,out$E,col=green)
lines(times,out$I,col=red)
lines(times,out$R,col=blue)
#
I'd like to vary one or more parameters (with several
distribution) for obtaining probabilistic results from the
model projections.
Now I'll try also with winBUGS, but I've never worked with
it. I hope..
Thank you very much.
Max
On Thu, 16 Nov 2006 09:26:12 -0500
Tamas K Papp [EMAIL PROTECTED] wrote:
On Thu, Nov 16, 2006 at 02:55:07PM +0100, Massimo Fenati
wrote:
Dear colleagues,
I’m a new R-help user. I’ve read the advertisements
about
the good manners and I hope to propose a good question.
I’m using R to build an epidemiological SEIR model based
on ODEs. The odesolve package is very useful to solve
deterministic ODE systems but I’d like to perform a
stochastic simulation based on Markov chain Montecarlo
methods. I don’t know which packages could be used to do
it (I tried with sde but without results).
Have you some suggestions about useful methods and/or
function in R for reaching my aim.
Hi Max,
I don't know what SEIR is. R has some MCMC packages
(RSiteSearch(MCMC) will help you there), but it is
easy to write a
Metropolis/Gibbs sampler yourself, making use of the
structure of your
problem.
The sde package is for approximating likelihoods of
continuous time
stochastic differential equations (which is a difficult
problem by
itself).
It is hard to give more advice without knowing what you
are trying to
achieve -- it is good that you have read the posting
guide, but please
give more details if you want more specific answers.
HTH,
Tamas
MASSIMO FENATI
-
Istituto Nazionale per la Fauna Selvatica
Via Cà Fornacetta, 9
40064 - Ozzano dell'Emilia (BO)- Italy
tel: +39 0516512245
cel: +39 3392114911
fax: +39 051796628
e-mail: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Dr. Francisco J. Zagmutt
College of Veterinary Medicine and Biomedical Sciences
Colorado State University
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stochastic SEIR model
see also: http://www.zoo.ufl.edu/bolker/eid/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
