[R] Problems in programming a simple likelihood

Ravi Varadhan rvaradhan at jhmi.edu
Thu Apr 19 20:01:57 CEST 2007 

Hi Deepankar,

Dimitris' code works just fine.  Your problem is that the output of optim
does not have a corresponding "summary" method.  Instead you should simply
type the name of the object returned by "optim" to look at the results.

> out <- optim(mu.start, mlogl, method = "CG", y = women$J, X = cbind(1,
women$M, women$S))
> out
$par
[1] -3.0612277 -1.4567141  0.3659251

$value
[1] 13.32251

$counts
function gradient 
     357      101 

$convergence
[1] 1

$message
NULL

Hope this helps,
Ravi.

----------------------------------------------------------------------------
-------

Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvaradhan at jhmi.edu

Webpage:  http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html

 

----------------------------------------------------------------------------
--------

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Deepankar Basu
Sent: Thursday, April 19, 2007 12:42 PM
To: Dimitris Rizopoulos
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Problems in programming a simple likelihood

Dimitris,

Thanks a lot for your suggestion and also for suggestions that others
have provided. I am learning fast and with the help of the R community
will be able to get this going pretty soon. Of course, right now I am
just trying to learn the language; so I am trying to program a standard
probit model for which I know the answers. I could easily get the
estimates with "glm". But I want to program the probit model to make
sure I understand the subtleties of R. 

I tried running the alternate script that you provided, but it is still
not working. Am I making some mistake?

Here is what I get when I run your script (which shows that the maximum
number of iterations was reached without convergence):

> source("probit1.R")
> summary(out)
            Length Class  Mode
par         3      -none- numeric
value       1      -none- numeric
counts      2      -none- numeric
convergence 1      -none- numeric
message     0      -none- NULL

Here is the script (exactly what you had suggested):

mlogl <- function (mu, y, X) {
    zeta <- as.vector(X %*% mu)
    y.logic <- as.logical(y)
    lgLik <- numeric(length(y))
    lgLik[y.logic] <- pnorm(zeta[y.logic], log.p = TRUE)
    lgLik[!y.logic] <- pnorm(zeta[!y.logic], lower.tail = FALSE, log.p =
TRUE)
    -sum(lgLik)
}

women <-
read.table("http://wps.aw.com/wps/media/objects/2228/2281678/Data_Sets/ASCII
/Women13.txt", 
header=TRUE)

mu.start <- c(-3, -1.5, 0.5)
out <- optim(mu.start, mlogl, method = "BFGS", y = women$J, X = cbind(1,
women$M, women$S))
out

glm.fit(x = cbind(1, women$M, women$S), y = women$J, family =
binomial(link = "probit"))$coefficients


Thanks.
Deepankar


On Thu, 2007-04-19 at 09:26 +0200, Dimitris Rizopoulos wrote:
> try the following:
> 
> mlogl <- function (mu, y, X) {
>     zeta <- as.vector(X %*% mu)
>     y.logic <- as.logical(y)
>     lgLik <- numeric(length(y))
>     lgLik[y.logic] <- pnorm(zeta[y.logic], log.p = TRUE)
>     lgLik[!y.logic] <- pnorm(zeta[!y.logic], lower.tail = FALSE, log.p 
> = TRUE)
>     -sum(lgLik)
> }
> 
> women <- 
>
read.table("http://wps.aw.com/wps/media/objects/2228/2281678/Data_Sets/ASCII
/Women13.txt", 
> header=TRUE)
> 
> mu.start <- c(0, -1.5, 0.01)
> out <- optim(mu.start, mlogl, method = "BFGS", y = women$J, X = 
> cbind(1, women$M, women$S))
> out
> 
> glm.fit(x = cbind(1, women$M, women$S), y = women$J, family = 
> binomial(link = "probit"))$coefficients
> 
> 
> I hope it helps.
> 
> Best,
> Dimitris
> 
> ----
> Dimitris Rizopoulos
> Ph.D. Student
> Biostatistical Centre
> School of Public Health
> Catholic University of Leuven
> 
> Address: Kapucijnenvoer 35, Leuven, Belgium
> Tel: +32/(0)16/336899
> Fax: +32/(0)16/337015
> Web: http://med.kuleuven.be/biostat/
>      http://www.student.kuleuven.be/~m0390867/dimitris.htm
> 
> 
> ----- Original Message ----- 
> From: "Deepankar Basu" <basu.15 at osu.edu>
> To: <r-help at stat.math.ethz.ch>
> Sent: Thursday, April 19, 2007 12:38 AM
> Subject: [R] Problems in programming a simple likelihood
> 
> 
> > As part of carrying out a complicated maximum likelihood estimation, 
> > I
> > am trying to learn to program likelihoods in R. I started with a 
> > simple
> > probit model but am unable to get the code to work. Any help or
> > suggestions are most welcome. I give my code below:
> >
> > ************************************
> > mlogl <- function(mu, y, X) {
> > n <- nrow(X)
> > zeta <- X%*%mu
> > llik <- 0
> > for (i in 1:n) {
> >  if (y[i]==1)
> >   llik <- llik + log(pnorm(zeta[i,], mean=0, sd=1))
> >  else
> >   llik <- llik + log(1-pnorm(zeta[i,], mean=0, sd=1))
> >    }
> > return(-llik)
> > }
> >
> > women <- read.table("~/R/Examples/Women13.txt", header=TRUE)  # DATA
> >
> > # THE DATA SET CAN BE ACCESSED HERE
> > # women <-
> >
read.table("http://wps.aw.com/wps/media/objects/2228/2281678/Data_Sets/ASCII
/Women13.txt", 
> > header=TRUE)
> > # I HAVE CHANGED THE NAMES OF THE VARIABLES
> > # J is changed to "work"
> > # M is changed to "mar"
> > # S is changed to "school"
> >
> > attach(women)
> >
> > # THE VARIABLES OF USE ARE
> > #   work: binary dependent variable
> > #   mar: whether married or not
> > #   school: years of schooling
> >
> > mu.start <- c(3, -1.5, 10)
> > data <- cbind(1, mar, school)
> > out <- nlm(mlogl, mu.start, y=work, X=data)
> > cat("Results", "\n")
> > out$estimate
> >
> > detach(women)
> >
> > *************************************
> >
> > When I try to run the code, this is what I get:
> >
> >> source("probit.R")
> > Results
> > Warning messages:
> > 1: NA/Inf replaced by maximum positive value
> > 2: NA/Inf replaced by maximum positive value
> > 3: NA/Inf replaced by maximum positive value
> > 4: NA/Inf replaced by maximum positive value
> >
> > Thanks in advance.
> > Deepankar
> >
> > ______________________________________________
> > R-help at 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.
> > 
> 
> 
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>

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