Re: [R] how to avoid NaN in optim()
You do not have to worry about re-defining your function to handle the
constraints on parameters. You can let the optimizer worry about it.
lik - function(nO, nA, nB, nAB){
loglik - function(par)
{
p=par[1]
q=par[2]
r - 1 - p - q
-(2 * nO * log (r) + nA * log (p^2 + 2 * p * r)
+ nB * log (q^2 + 2 * q * r)
+ nAB * (log(2) +log(p) +log(q)))
}
}
library(BB)
# constraints: x[1] 0; x[2] 0; x[1] + x[2] 1
Amat - matrix(c(1,0,0,1,-1,-1), 3, 2, byrow=TRUE)
b - c(0, 0, -1)
c1 - runif(1)
p0 - c(c1, max(0.01, 0.99-c1))
spg(p0, lik ( 176,182,60,17) , project=projectLinear,
projectArgs=list(A=Amat, b=b, meq=0))
Hope this helps,
Ravi.
-Original Message-
From: Ravi Varadhan [mailto:rvarad...@jhmi.edu]
Sent: Thursday, September 30, 2010 3:09 PM
To: Ravi 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,
projectArgs=list(A=Amat, b=b, meq=0))
Hope this helps,
Ravi.
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: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 3:04 pm
Subject: Re: [R] how to avoid NaN in optim()
To: Ravi Varadhan rvarad...@jhmi.edu
Cc: arindam fadikar arindam.fadi...@gmail.com, 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'.
library(BB)
?spg
Ravi.
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: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 2:54 pm
Subject: Re: [R] how to avoid NaN in optim()
To: arindam fadikar arindam.fadi...@gmail.com
Cc: r-help@r-project.org
Change the `else NA' to `else Inf' in your loglik function and
then
run the following:
library(BB)
p0 - runif(2)
spg(p0, lik (176,182 , 60 ,17) , lower=0, upper=1)
This will give you correct results.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range
(0,0,0)
to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
[R] how to avoid NaN in optim()
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0) to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org 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] how to avoid NaN in optim()
Change the `else NA' to `else Inf' in your loglik function and then run the
following:
library(BB)
p0 - runif(2)
spg(p0, lik (176,182 , 60 ,17) , lower=0, upper=1)
This will give you correct results.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0) to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org 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] how to avoid NaN in optim()
I forgot to mention:
You actually got correct results with using optim and `CG'. The warning
messages were just telling you that there were some log(negative number)
operations during the iterative process.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0) to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org 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] how to avoid NaN in optim()
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'.
library(BB)
?spg
Ravi.
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: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 2:54 pm
Subject: Re: [R] how to avoid NaN in optim()
To: arindam fadikar arindam.fadi...@gmail.com
Cc: r-help@r-project.org
Change the `else NA' to `else Inf' in your loglik function and then
run the following:
library(BB)
p0 - runif(2)
spg(p0, lik (176,182 , 60 ,17) , lower=0, upper=1)
This will give you correct results.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0)
to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org 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] how to avoid NaN in optim()
thanks Ravi yes , we were getiing the correct results but we thought
there should be a way to avoid those NaN values ... and now we are done
the if condition was written wrongly there ... instead of that if we do
p 0 q 0 r 0 p 1 q 1 r 1
its perfectly fine .. but is there a smart way to write this condition ?
On Fri, Oct 1, 2010 at 12:30 AM, Ravi Varadhan rvarad...@jhmi.edu wrote:
I forgot to mention:
You actually got correct results with using optim and `CG'. The warning
messages were just telling you that there were some log(negative number)
operations during the iterative process.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0) to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org 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] 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,
projectArgs=list(A=Amat, b=b, meq=0))
Hope this helps,
Ravi.
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: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 3:04 pm
Subject: Re: [R] how to avoid NaN in optim()
To: Ravi Varadhan rvarad...@jhmi.edu
Cc: arindam fadikar arindam.fadi...@gmail.com, 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'.
library(BB)
?spg
Ravi.
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: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 2:54 pm
Subject: Re: [R] how to avoid NaN in optim()
To: arindam fadikar arindam.fadi...@gmail.com
Cc: r-help@r-project.org
Change the `else NA' to `else Inf' in your loglik function and
then
run the following:
library(BB)
p0 - runif(2)
spg(p0, lik (176,182 , 60 ,17) , lower=0, upper=1)
This will give you correct results.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range
(0,0,0)
to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org 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] how to avoid NaN in optim()
On Thu, Sep 30, 2010 at 12:04 PM, arindam fadikar
arindam.fadi...@gmail.com wrote:
thanks Ravi yes , we were getiing the correct results but we thought
there should be a way to avoid those NaN values ... and now we are done
the if condition was written wrongly there ... instead of that if we do
p 0 q 0 r 0 p 1 q 1 r 1
its perfectly fine .. but is there a smart way to write this condition ?
combine p, q, and r. Here imagine x = c(p, q, r)
x - c(.5, .5, .5)
all(x 0 x 1)
x2 - c(.5, .5, 1.01)
all(x2 0 x2 1)
In this case you will not want to use because x has more than one
element. all() basically just checks that everything is TRUE.
Josh
On Fri, Oct 1, 2010 at 12:30 AM, Ravi Varadhan rvarad...@jhmi.edu wrote:
I forgot to mention:
You actually got correct results with using optim and `CG'. The warning
messages were just telling you that there were some log(negative number)
operations during the iterative process.
Ravi.
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 arindam.fadi...@gmail.com
Date: Thursday, September 30, 2010 2:17 pm
Subject: [R] how to avoid NaN in optim()
To: r-help@r-project.org
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
i want to maximize this likelihood function over the range (0,0,0) to
(1,1,1). so i tried
optim ( c(0.3,0.3), lik ( 176,182 , 60 ,17) , method = CG)
and obtained the following :
optim(c(0.3,0.3), fn, method=CG)
$par
[1] 0.26444187 0.09316946
$value
[1] 492.5353
$counts
function gradient
130 19
$convergence
[1] 0
$message
NULL
Warning messages:
1: In log(q^2 + 2 * q * r) : NaNs produced
2: In log(q) : NaNs produced
3: In log(q^2 + 2 * q * r) : NaNs produced
4: In log(q) : NaNs produced
please help ...
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
r-h...@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
--
Arindam Fadikar
M.Stat
Indian Statistical Institute.
New Delhi, India
[[alternative HTML version deleted]]
__
R-help@r-project.org 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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
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Re: [R] how to avoid NaN in optim()
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)
+ nAB * (log(2) +log(p) +log(q)))
}
else
NA
}
loglik
}
.
Extending the tests in the if in loglik to
if (c(p,q,r) rep(0,3) c(p,q,r) rep(1,3) (p^2 + 2*p*r)0
(q^2 + 2*q*r)0)
would also help.
/Berend
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