Re: [R] how to avoid NaN in optim()

2010-10-01 Thread Ravi Varadhan
i Varadhan Cc: arindam fadikar; r-help@r-project.org Subject: Re: [R] how to avoid NaN in optim() Here is how you do it: library(BB) Amat <- matrix(c(1,0,0,1,-1,-1), 3, 2, byrow=TRUE) b <- c(0, 0, -1) p0 <- c(0.5, 0.4) spg(p0, lik ( 176,182 , 60 ,17) , project="projectLinear&quo

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Berend Hasselman
arindam fadikar wrote: > > > loglik <- function(par) > { > p=par[1] > q=par[2] > r <- 1 - p - q > if (c(p,q,r) > rep(0,3) && c(p,q,r) < rep(1,3) ) > { > -(2 * nO * log (r) + nA * log (p^2 + 2 * p * r) > + nB * log (q^2 + 2 * q * r) >

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Joshua Wiley
_ >> >> Ravi Varadhan, Ph.D. >> Assistant Professor, >> Division of Geriatric Medicine and Gerontology >> School of Medicine >> Johns Hopkins University >> >> Ph. (410) 502-2619 >> email: rvarad...@jhmi.

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Ravi Varadhan
er 30, 2010 3:04 pm Subject: Re: [R] how to avoid NaN in optim() To: Ravi Varadhan Cc: arindam fadikar , r-help@r-project.org > You also need the constrain that par[1] + par[2] < 1 in order to avoid > NaNs. > > You can do this using the `projectLinear' argument in `spg'

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread arindam fadikar
ogy > School of Medicine > Johns Hopkins University > > Ph. (410) 502-2619 > email: rvarad...@jhmi.edu > > > ----- Original Message - > From: arindam fadikar > Date: Thursday, September 30, 2010 2:17 pm > Subject: [R] how to avoid NaN in optim() > To:

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Ravi Varadhan
, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Ravi Varadhan Date: Thursday, September 30, 2010 2:54 pm Subject: Re: [R] how to avoid NaN in optim() To: arindam fadikar

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Ravi Varadhan
Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: arindam fadikar Date: Thursday, September 30, 2010 2:17 pm Subject: [R] how to avoi

Re: [R] how to avoid NaN in optim()

2010-09-30 Thread Ravi Varadhan
___ Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: arindam fadikar Date: Thursday, September 30, 2010 2:17 pm Subject: [R] how to

[R] how to avoid NaN in optim()

2010-09-30 Thread arindam fadikar
hi , lik <- function(nO, nA, nB, nAB){ loglik <- function(par) { p=par[1] q=par[2] r <- 1 - p - q if (c(p,q,r) > rep(0,3) && c(p,q,r) < rep(1,3) ) { -(2 * nO * log (r) + nA * log (p^2 + 2 * p * r) + nB * log (q^2 + 2 * q * r) +