Hi, I am trying to use the following model formula in gls() in the nlme package: R ~ Turb + offset(ssb) Unfortunately, gls() seems to ignore the offset argument and give results that are identical to R ~ Turb This is not the case when I use lm() - however, I would like to include a corAR1() term as well, which is why I am using gls(). Is this known and intended behaviour? If so, is there a recommended workaround/alternative? Best wishes, Mark
Offset() in gls() in nlme
5 messages · ONKELINX, Thierry, Douglas Bates, Mark Payne +1 more
Dear Mark, In case of a linear model you can create a new variable Y = R - ssb and model Y without offset instead of R with ssb as offset. That should give the same parameter estimates. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 Thierry.Onkelinx at inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-sig-mixed-models-bounces at r-project.org [mailto:r-sig-mixed-models-bounces at r-project.org] Namens Mark Payne Verzonden: dinsdag 11 november 2014 13:23 Aan: r-sig-mixed-models at r-project.org Onderwerp: [R-sig-ME] Offset() in gls() in nlme Hi, I am trying to use the following model formula in gls() in the nlme package: R ~ Turb + offset(ssb) Unfortunately, gls() seems to ignore the offset argument and give results that are identical to R ~ Turb This is not the case when I use lm() - however, I would like to include a corAR1() term as well, which is why I am using gls(). Is this known and intended behaviour? If so, is there a recommended workaround/alternative? Best wishes, Mark _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.
It may work if you use the offset argument instead of putting an offset term in the formula. The model-fitting code in R (and S before it) sometimes has the "there's more than one way to do it" approach of Perl. This is convenient for users but not for those writing the code. I believe we implemented the offset argument form. On Wed Nov 12 2014 at 2:52:30 AM ONKELINX, Thierry <Thierry.ONKELINX at inbo.be> wrote:
Dear Mark,
In case of a linear model you can create a new variable Y = R - ssb and
model Y without offset instead of R with ssb as offset. That should give
the same parameter estimates.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-sig-mixed-models-bounces at r-project.org [mailto:r-sig-mixed-models-
bounces at r-project.org] Namens Mark Payne
Verzonden: dinsdag 11 november 2014 13:23
Aan: r-sig-mixed-models at r-project.org
Onderwerp: [R-sig-ME] Offset() in gls() in nlme
Hi,
I am trying to use the following model formula in gls() in the nlme
package:
R ~ Turb + offset(ssb)
Unfortunately, gls() seems to ignore the offset argument and give results
that are identical to
R ~ Turb
This is not the case when I use lm() - however, I would like to include a
corAR1() term as well, which is why I am using gls().
Is this known and intended behaviour? If so, is there a recommended
workaround/alternative?
Best wishes,
Mark
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
4 days later
Hi Douglas,
Thanks for the reply - unfortunately there doesn't seem to be an offset
argument either in the latest version of nlme... :-(
> gls
function (model, data = sys.frame(sys.parent()), correlation = NULL,
weights = NULL, subset, method = c("REML", "ML"), na.action = na.fail,
control = list(), verbose = FALSE)
> packageDescription("nlme")
Package: nlme
Version: 3.1-118
Date: 2014-10-07
Mark
On 13/11/14 04:54, Douglas Bates wrote:
It may work if you use the offset argument instead of putting an offset
term in the formula. The model-fitting code in R (and S before it)
sometimes has the "there's more than one way to do it" approach of
Perl. This is convenient for users but not for those writing the code.
I believe we implemented the offset argument form.
On Wed Nov 12 2014 at 2:52:30 AM ONKELINX, Thierry
<Thierry.ONKELINX at inbo.be <mailto:Thierry.ONKELINX at inbo.be>> wrote:
Dear Mark,
In case of a linear model you can create a new variable Y = R - ssb
and model Y without offset instead of R with ssb as offset. That
should give the same parameter estimates.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for
Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be <mailto:Thierry.Onkelinx at inbo.be>
www.inbo.be <http://www.inbo.be>
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given
body of data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-sig-mixed-models-bounces at r-__project.org
<mailto:r-sig-mixed-models-bounces at r-project.org>
[mailto:r-sig-mixed-models-__bounces at r-project.org
<mailto:r-sig-mixed-models-bounces at r-project.org>] Namens Mark Payne
Verzonden: dinsdag 11 november 2014 13:23
Aan: r-sig-mixed-models at r-project.__org
<mailto:r-sig-mixed-models at r-project.org>
Onderwerp: [R-sig-ME] Offset() in gls() in nlme
Hi,
I am trying to use the following model formula in gls() in the nlme
package:
R ~ Turb + offset(ssb)
Unfortunately, gls() seems to ignore the offset argument and give
results that are identical to
R ~ Turb
This is not the case when I use lm() - however, I would like to
include a
corAR1() term as well, which is why I am using gls().
Is this known and intended behaviour? If so, is there a recommended
workaround/alternative?
Best wishes,
Mark
[[alternative HTML version deleted]]
_________________________________________________
R-sig-mixed-models at r-project.__org
<mailto:R-sig-mixed-models at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/r-sig-mixed-models
<https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
Dit bericht en eventuele bijlagen geven enkel de visie van de
schrijver weer en binden het INBO onder geen enkel beding, zolang
dit bericht niet bevestigd is door een geldig ondertekend document.
The views expressed in this message and any annex are purely those
of the writer and may not be regarded as stating an official
position of INBO, as long as the message is not confirmed by a duly
signed document.
_________________________________________________
R-sig-mixed-models at r-project.__org
<mailto:R-sig-mixed-models at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/r-sig-mixed-models
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In that case, I believe Thierry's solution is correct. For linear models, offsets are a convenience rather than a necessity.
On Sun, Nov 16, 2014 at 4:40 PM, Mark Payne <mpay at aqua.dtu.dk> wrote:
Hi Douglas, Thanks for the reply - unfortunately there doesn't seem to be an offset argument either in the latest version of nlme... :-(
gls
function (model, data = sys.frame(sys.parent()), correlation = NULL,
weights = NULL, subset, method = c("REML", "ML"), na.action = na.fail,
control = list(), verbose = FALSE)
packageDescription("nlme")
Package: nlme Version: 3.1-118 Date: 2014-10-07 Mark On 13/11/14 04:54, Douglas Bates wrote:
It may work if you use the offset argument instead of putting an offset
term in the formula. The model-fitting code in R (and S before it)
sometimes has the "there's more than one way to do it" approach of
Perl. This is convenient for users but not for those writing the code.
I believe we implemented the offset argument form.
On Wed Nov 12 2014 at 2:52:30 AM ONKELINX, Thierry
<Thierry.ONKELINX at inbo.be <mailto:Thierry.ONKELINX at inbo.be>> wrote:
Dear Mark,
In case of a linear model you can create a new variable Y = R - ssb
and model Y without offset instead of R with ssb as offset. That
should give the same parameter estimates.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for
Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be <mailto:Thierry.Onkelinx at inbo.be>
www.inbo.be <http://www.inbo.be>
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given
body of data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-sig-mixed-models-bounces at r-__project.org
<mailto:r-sig-mixed-models-bounces at r-project.org>
[mailto:r-sig-mixed-models-__bounces at r-project.org
<mailto:r-sig-mixed-models-bounces at r-project.org>] Namens Mark Payne
Verzonden: dinsdag 11 november 2014 13:23
Aan: r-sig-mixed-models at r-project.__org
<mailto:r-sig-mixed-models at r-project.org>
Onderwerp: [R-sig-ME] Offset() in gls() in nlme
Hi,
I am trying to use the following model formula in gls() in the nlme
package:
R ~ Turb + offset(ssb)
Unfortunately, gls() seems to ignore the offset argument and give
results that are identical to
R ~ Turb
This is not the case when I use lm() - however, I would like to
include a
corAR1() term as well, which is why I am using gls().
Is this known and intended behaviour? If so, is there a recommended
workaround/alternative?
Best wishes,
Mark
[[alternative HTML version deleted]]
_________________________________________________
R-sig-mixed-models at r-project.__org
<mailto:R-sig-mixed-models at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/r-sig-mixed-models
<https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * *
*
Dit bericht en eventuele bijlagen geven enkel de visie van de
schrijver weer en binden het INBO onder geen enkel beding, zolang
dit bericht niet bevestigd is door een geldig ondertekend document.
The views expressed in this message and any annex are purely those
of the writer and may not be regarded as stating an official
position of INBO, as long as the message is not confirmed by a duly
signed document.
_________________________________________________
R-sig-mixed-models at r-project.__org
<mailto:R-sig-mixed-models at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/r-sig-mixed-models
<https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models