Re: [R] simplification of code using stamp?

2006-10-26 Thread Rainer M Krug 
hadley wickham wrote:
 I get the following, which is not what I am looking for.

   test[1:10,]
 expertxx seeds runvalue
 1  BW x001025   1 rsqs, slope, d.slope, intercept, d.intercept
 2  BW x001025   2 rsqs, slope, d.slope, intercept, d.intercept
 3  BW x001025   3 rsqs, slope, d.slope, intercept, d.intercept
 4  BW x001025   4 rsqs, slope, d.slope, intercept, d.intercept
 5  BW x001025   5 rsqs, slope, d.slope, intercept, d.intercept
 6  BW x001028   1 rsqs, slope, d.slope, intercept, d.intercept
 7  BW x001028   2 rsqs, slope, d.slope, intercept, d.intercept
 8  BW x001028   3 rsqs, slope, d.slope, intercept, d.intercept
 9  BW x001028   4 rsqs, slope, d.slope, intercept, d.intercept
 10 BW x001028   5 rsqs, slope, d.slope, intercept, d.intercept
 
 That's because stamp doesn't produce great output at the moment (have
 a look at the str(test) to see that you have a data frame containing a
 list of vectors)
 
 The following code should put it a more reasonable form:
 
 tidy - function(x) {
  bind - function(i) data.frame(x[i, -ncol(x),drop=FALSE], t(a$value[[i]]))
  l - lapply(1:nrow(x), bind)
  do.call(rbind.fill, l)
 }
 
 tidy(test)
Thanks Hadley - I'll look at the code.


 
 (but unless you provide a reproducible example I can't be sure that it
 works with your data)
 
 Regards,
 
 Hadley


-- 
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa

Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:   +27 - (0)83 9479 042

email:  [EMAIL PROTECTED]
[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.

[R] simplification of code using stamp?

2006-10-25 Thread Rainer M Krug 
Hi

I have the following code which I would like to simplify. Id does linear 
regressions and returns the r-squares, and the coefficients.
It runs slow, as it is doing the regressions for each - is it possible 
to get the values in a dataframe which looks as follow:

expert | xx | seeds | r.squared | slope | intercept

Thanks in advance,

Rainer


library(reshape)
rsqs - as.data.frame(
   stamp(
 tc.long,
 expert * xx * seeds ~ .,
 function(df) try( summary( lm(distance ~ 
generation, data=df))$r.squared, silent=TRUE )
 )
   )

slope - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance ~ 
generation, data=df))$coefficients[2], silent=TRUE )
  )
)

d.slope - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( lm(distance ~ 
generation, data=df))$coefficients[4], silent=TRUE )
)
  )

intercept - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance 
~ generation, data=df))$coefficients[1], silent=TRUE )
  )
)

d.intercept - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( 
lm(distance ~ generation, data=df))$coefficients[3], silent=TRUE )
)
  )

-- 
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa

Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:   +27 - (0)83 9479 042

email:  [EMAIL PROTECTED]
[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] simplification of code using stamp?

2006-10-25 Thread ONKELINX, Thierry 
I think your script is slow because it has to recalculate the same model
five times. I've tried to avoid this by rewriting your function(df).

function(df){
fit - summary(lm(distance ~ generation, data=df))
result - c(fit$$r.squared, $coefficients[2], $coefficients[4],
$coefficients[1], $coefficients[3])
names(result) - c(rsqs, slope, d.slope, intercept,
d.intercept),
}

Cheers,

Thierry



ir. Thierry Onkelinx

Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
and Forest

Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance

Gaverstraat 4

9500 Geraardsbergen

Belgium

tel. + 32 54/436 185

[EMAIL PROTECTED]

www.inbo.be 

 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt

A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney

-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens Rainer M Krug
Verzonden: woensdag 25 oktober 2006 11:22
Aan: r-help@stat.math.ethz.ch
Onderwerp: [R] simplification of code using stamp?

Hi

I have the following code which I would like to simplify. Id does linear

regressions and returns the r-squares, and the coefficients.
It runs slow, as it is doing the regressions for each - is it possible 
to get the values in a dataframe which looks as follow:

expert | xx | seeds | r.squared | slope | intercept

Thanks in advance,

Rainer


library(reshape)
rsqs - as.data.frame(
   stamp(
 tc.long,
 expert * xx * seeds ~ .,
 function(df) try( summary( lm(distance ~ 
generation, data=df))$r.squared, silent=TRUE )
 )
   )

slope - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance ~ 
generation, data=df))$coefficients[2], silent=TRUE )
  )
)

d.slope - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( lm(distance ~

generation, data=df))$coefficients[4], silent=TRUE )
)
  )

intercept - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance

~ generation, data=df))$coefficients[1], silent=TRUE )
  )
)

d.intercept - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( 
lm(distance ~ generation, data=df))$coefficients[3], silent=TRUE )
)
  )

-- 
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa

Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:   +27 - (0)83 9479 042

email:  [EMAIL PROTECTED]
[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.

__
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] simplification of code using stamp?

2006-10-25 Thread ONKELINX, Thierry 
Resending the function because of a typo in the result vector.

function(df){
fit - summary(lm(distance ~ generation, data=df))
result - c(fit$r.squared, fit$coefficients[2],
fit$coefficients[4],
fit$coefficients[1], fit$coefficients[3])
names(result) - c(rsqs, slope, d.slope, intercept,
d.intercept),
}

Cheers,

Thierry

-

ir. Thierry Onkelinx

Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
and Forest

Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance

Gaverstraat 4

9500 Geraardsbergen

Belgium

tel. + 32 54/436 185

[EMAIL PROTECTED]

www.inbo.be 

 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt

A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney


-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens ONKELINX, Thierry
Verzonden: woensdag 25 oktober 2006 11:36
Aan: [EMAIL PROTECTED]; r-help@stat.math.ethz.ch
Onderwerp: Re: [R] simplification of code using stamp?

I think your script is slow because it has to recalculate the same model
five times. I've tried to avoid this by rewriting your function(df).

function(df){
fit - summary(lm(distance ~ generation, data=df))
result - c(fit$$r.squared, $coefficients[2], $coefficients[4],
$coefficients[1], $coefficients[3])
names(result) - c(rsqs, slope, d.slope, intercept,
d.intercept),
}

Cheers,

Thierry



ir. Thierry Onkelinx

Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
and Forest

Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance

Gaverstraat 4

9500 Geraardsbergen

Belgium

tel. + 32 54/436 185

[EMAIL PROTECTED]

www.inbo.be 

 

Do not put your faith in what statistics say until you have carefully
considered what they do not say.  ~William W. Watt

A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney

-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens Rainer M Krug
Verzonden: woensdag 25 oktober 2006 11:22
Aan: r-help@stat.math.ethz.ch
Onderwerp: [R] simplification of code using stamp?

Hi

I have the following code which I would like to simplify. Id does linear

regressions and returns the r-squares, and the coefficients.
It runs slow, as it is doing the regressions for each - is it possible 
to get the values in a dataframe which looks as follow:

expert | xx | seeds | r.squared | slope | intercept

Thanks in advance,

Rainer


library(reshape)
rsqs - as.data.frame(
   stamp(
 tc.long,
 expert * xx * seeds ~ .,
 function(df) try( summary( lm(distance ~ 
generation, data=df))$r.squared, silent=TRUE )
 )
   )

slope - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance ~ 
generation, data=df))$coefficients[2], silent=TRUE )
  )
)

d.slope - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( lm(distance ~

generation, data=df))$coefficients[4], silent=TRUE )
)
  )

intercept - as.data.frame(
stamp(
  tc.long,
  expert * xx * seeds ~ .,
  function(df) try( summary( lm(distance

~ generation, data=df))$coefficients[1], silent=TRUE )
  )
)

d.intercept - as.data.frame(
  stamp(
tc.long,
expert * xx * seeds ~ .,
function(df) try( summary( 
lm(distance ~ generation, data=df))$coefficients[3], silent=TRUE )
)
  )

-- 
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa

Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:   +27 - (0)83 9479 042

email:  [EMAIL PROTECTED]
[EMAIL PROTECTED

Re: [R] simplification of code using stamp?

2006-10-25 Thread Rainer M Krug 
ONKELINX, Thierry wrote:
 Resending the function because of a typo in the result vector.
 
 function(df){
   fit - summary(lm(distance ~ generation, data=df))
   result - c(fit$r.squared, fit$coefficients[2],
 fit$coefficients[4],
 fit$coefficients[1], fit$coefficients[3])
   names(result) - c(rsqs, slope, d.slope, intercept,
 d.intercept),
 }

You are right - the problem is that it isd calculating the regressions 
five time. I implemented your code, and when I print the resulting 
data.frame from

test - as.data.frame(
   stamp(
 tc.long,
 expert * xx * seeds * run ~ .,
 function(df)
 {
   try(
   {
 fit - summary( lm(distance ~ 
generation, data=df) )
 result - c(fit$r.squared, 
fit$coefficients[2], fit$coefficients[4], fit$coefficients[1], 
fit$coefficients[3])
 names(result) - c(rsqs, slope, 
d.slope, intercept, d.intercept)
   },
   silent=TRUE
   )
 }
 )
   )

I get the following, which is not what I am looking for.

  test[1:10,]
expertxx seeds runvalue
1  BW x001025   1 rsqs, slope, d.slope, intercept, d.intercept
2  BW x001025   2 rsqs, slope, d.slope, intercept, d.intercept
3  BW x001025   3 rsqs, slope, d.slope, intercept, d.intercept
4  BW x001025   4 rsqs, slope, d.slope, intercept, d.intercept
5  BW x001025   5 rsqs, slope, d.slope, intercept, d.intercept
6  BW x001028   1 rsqs, slope, d.slope, intercept, d.intercept
7  BW x001028   2 rsqs, slope, d.slope, intercept, d.intercept
8  BW x001028   3 rsqs, slope, d.slope, intercept, d.intercept
9  BW x001028   4 rsqs, slope, d.slope, intercept, d.intercept
10 BW x001028   5 rsqs, slope, d.slope, intercept, d.intercept
 

 
 Cheers,
 
 Thierry
 
 -
 
 ir. Thierry Onkelinx
 
 Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
 and Forest
 
 Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
 methodology and quality assurance
 
 Gaverstraat 4
 
 9500 Geraardsbergen
 
 Belgium
 
 tel. + 32 54/436 185
 
 [EMAIL PROTECTED]
 
 www.inbo.be 
 
  
 
 Do not put your faith in what statistics say until you have carefully
 considered what they do not say.  ~William W. Watt
 
 A statistical analysis, properly conducted, is a delicate dissection of
 uncertainties, a surgery of suppositions. ~M.J.Moroney
 
 
-- 
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)

Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa

Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell:   +27 - (0)83 9479 042

email:  [EMAIL PROTECTED]
[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] simplification of code using stamp?

2006-10-25 Thread hadley wickham 
 I get the following, which is not what I am looking for.

   test[1:10,]
 expertxx seeds runvalue
 1  BW x001025   1 rsqs, slope, d.slope, intercept, d.intercept
 2  BW x001025   2 rsqs, slope, d.slope, intercept, d.intercept
 3  BW x001025   3 rsqs, slope, d.slope, intercept, d.intercept
 4  BW x001025   4 rsqs, slope, d.slope, intercept, d.intercept
 5  BW x001025   5 rsqs, slope, d.slope, intercept, d.intercept
 6  BW x001028   1 rsqs, slope, d.slope, intercept, d.intercept
 7  BW x001028   2 rsqs, slope, d.slope, intercept, d.intercept
 8  BW x001028   3 rsqs, slope, d.slope, intercept, d.intercept
 9  BW x001028   4 rsqs, slope, d.slope, intercept, d.intercept
 10 BW x001028   5 rsqs, slope, d.slope, intercept, d.intercept

That's because stamp doesn't produce great output at the moment (have
a look at the str(test) to see that you have a data frame containing a
list of vectors)

The following code should put it a more reasonable form:

tidy - function(x) {
  bind - function(i) data.frame(x[i, -ncol(x),drop=FALSE], t(a$value[[i]]))
  l - lapply(1:nrow(x), bind)
  do.call(rbind.fill, l)
}

tidy(test)

(but unless you provide a reproducible example I can't be sure that it
works with your data)

Regards,

Hadley

__
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.