R help - Sep 2011 - Using capture.output within a function

Dear R-users

I'm running a maximum likelihood procedure using the spg package. I'd
like
to save some output produced in each iteration to a file, but if I put the
capture.output() within the function I get the following message; Error in
spg(par = startval, fn = loglik, gr = NULL, method = 3, lower = lo,  :
  Failure in initial function evaluation!Error in -fn(par, ...) : invalid
argument to unary operator

I have considered putting the capture.output() after the function, but there
are some issues with R stalling on me so I'd like that the output is saved
for each iteration and not only at completion.

Any suggestions on how to get this done would be much appreciated.

Kristian Lind

*Below an example of what I'm trying to do...*


loglik <- function(w){

    state <- c(    b_1 = 0,
                b_2 = 0,
                a = 0)
    #declaring ODEs
    Kristian <-function(t, state, w){
    with(as.list(c(state, w)),
        {
        db_1 = -((w[1]+w[8])*b_1+(w[2]+w[6]*w[8]
+w[7]*w[9])*b_2+0.5*(b_1)^2+w[6]*b_1*b_2+0.5*
((w[6])^2+(w[7])^2)*(b_2)^2)
        db_2 = -w[3]*b_2+1
        da = w[1]*w[4]*b_1+(w[2]*w[4]+w[3]*w[5])*b_2
        list(c(db_1, db_2, da))
        })
    }

    # time making a sequence from t to T evaluated at each delta seq(t, T,
by = delta)
    times <- seq(0, 10, by = 0.5)

    outmat <- ode(y = state, times = times, func = Kristian, parms = w)
    print(w)
    print(outmat)
.
.
.
f<-rep(NA, 1)
f[1] <- 1/(T-1)*sum(log(pJ$p)-log(pJ$J))
f
capture.output(outmat, file = "spgoutput.txt", append = TRUE)
}
fit <- spg(fn =loglik, ...)

	[[alternative HTML version deleted]]

On 11-09-02 5:24 AM, Kristian Lind wrote:
> Dear R-users
>
> I'm running a maximum likelihood procedure using the spg package.
I'd like
> to save some output produced in each iteration to a file, but if I put the
> capture.output() within the function I get the following message; Error in
> spg(par = startval, fn = loglik, gr = NULL, method = 3, lower = lo,  :
>    Failure in initial function evaluation!Error in -fn(par, ...) : invalid
> argument to unary operator
It looks as though you put capture.output() last in your function, so 
the result of the function is the result of the capture.output call, not 
the function value.

Duncan Murdoch
>
> I have considered putting the capture.output() after the function, but
there
> are some issues with R stalling on me so I'd like that the output is
saved
> for each iteration and not only at completion.
>
> Any suggestions on how to get this done would be much appreciated.
>
> Kristian Lind
>
> *Below an example of what I'm trying to do...*
>
>
> loglik<- function(w){
>
>      state<- c(    b_1 = 0,
>                  b_2 = 0,
>                  a = 0)
>      #declaring ODEs
>      Kristian<-function(t, state, w){
>      with(as.list(c(state, w)),
>          {
>          db_1 = -((w[1]+w[8])*b_1+(w[2]+w[6]*w[8]
> +w[7]*w[9])*b_2+0.5*(b_1)^2+w[6]*b_1*b_2+0.5*
> ((w[6])^2+(w[7])^2)*(b_2)^2)
>          db_2 = -w[3]*b_2+1
>          da = w[1]*w[4]*b_1+(w[2]*w[4]+w[3]*w[5])*b_2
>          list(c(db_1, db_2, da))
>          })
>      }
>
>      # time making a sequence from t to T evaluated at each delta seq(t, T,
> by = delta)
>      times<- seq(0, 10, by = 0.5)
>
>      outmat<- ode(y = state, times = times, func = Kristian, parms = w)
>      print(w)
>      print(outmat)
> .
> .
> .
> f<-rep(NA, 1)
> f[1]<- 1/(T-1)*sum(log(pJ$p)-log(pJ$J))
> f
> capture.output(outmat, file = "spgoutput.txt", append = TRUE)
> }
> fit<- spg(fn =loglik, ...)
>
> 	[[alternative HTML version deleted]]
>
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