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Dennis Fisher

2010-Aug-13 21:21 UTC

[R] Unable to retrieve residual sum of squares from nls output

Colleagues,

I am using "nls" successfully (2.11.1, OS X) but I am having
difficulties retrieving part of the output - residual sum of squares.  I have
assigned the output to FIT:> > FIT
> Nonlinear regression model
>   model:  NEWY ~ PMESOR + PAMPLITUDE * cos(2 * pi * (NEWX -
POFFSET)/PERIOD)
>    data:  parent.frame() 
>     PMESOR PAMPLITUDE    POFFSET 
>    1153.02   -1183.09      24.58 
>  residual sum-of-squares: 1815056
> 
> Number of iterations to convergence: 8 
> Achieved convergence tolerance: 1.643e-08 
As you can see, the object contains "residual sum-of-squares:
1815056".  However, I can't figure out how to grab that value.   The
tried using "str":> > str(FIT)
> List of 6
>  $ m          :List of 16
>   ..$ resid     :function ()  
>   ..$ fitted    :function ()  
>   ..$ formula   :function ()  
>   ..$ deviance  :function ()  
>   ..$ lhs       :function ()  
>   ..$ gradient  :function ()  
>   ..$ conv      :function ()  
>   ..$ incr      :function ()  
>   ..$ setVarying:function (vary = rep(TRUE, length(useParams)))  
>   ..$ setPars   :function (newPars)  
>   ..$ getPars   :function ()  
>   ..$ getAllPars:function ()  
>   ..$ getEnv    :function ()  
>   ..$ trace     :function ()  
>   ..$ Rmat      :function ()  
>   ..$ predict   :function (newdata = list(), qr = FALSE)  
>   ..- attr(*, "class")= chr "nlsModel"
>  $ convInfo   :List of 5
>   ..$ isConv     : logi TRUE
>   ..$ finIter    : int 8
>   ..$ finTol     : num 1.64e-08
>   ..$ stopCode   : int 0
>   ..$ stopMessage: chr "converged"
>  $ data       : language parent.frame()
>  $ call       : language nls(formula = NEWY ~ PMESOR + PAMPLITUDE * cos(2 *
pi * (NEWX -      POFFSET)/PERIOD), start = list(PMESOR = MESOR, PAMPLITUDE =
AMPLITUDE,  ...
>  $ dataClasses: Named chr "numeric"
>   ..- attr(*, "names")= chr "NEWX"
>  $ control    :List of 2
>   ..$ maxiter : num 1000
>   ..$ warnOnly: logi TRUE
>  - attr(*, "class")= chr "nls"
However, none of these elements appears to contain the residual sum of squares.
Help!  Thanks.

Dennis





Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com

Gabor Grothendieck

2010-Aug-13 21:32 UTC

head link

[R] Unable to retrieve residual sum of squares from nls output

On Fri, Aug 13, 2010 at 5:21 PM, Dennis Fisher <fisher at plessthan.com>
wrote:> Colleagues,
>
> I am using "nls" successfully (2.11.1, OS X) but I am having
difficulties retrieving part of the output - residual sum of squares. ?I have
assigned the output to FIT:
>> > FIT
>> Nonlinear regression model
>> ? model: ?NEWY ~ PMESOR + PAMPLITUDE * cos(2 * pi * (NEWX -
POFFSET)/PERIOD)
>> ? ?data: ?parent.frame()
>> ? ? PMESOR PAMPLITUDE ? ?POFFSET
>> ? ?1153.02 ? -1183.09 ? ? ?24.58
>> ?residual sum-of-squares: 1815056
>>
>> Number of iterations to convergence: 8
>> Achieved convergence tolerance: 1.643e-08
>
> As you can see, the object contains "residual sum-of-squares:
1815056". ?However, I can't figure out how to grab that value. ? The
tried using "str":
>> > str(FIT)
>> List of 6
>> ?$ m ? ? ? ? ?:List of 16
>> ? ..$ resid ? ? :function ()
>> ? ..$ fitted ? ?:function ()
>> ? ..$ formula ? :function ()
>> ? ..$ deviance ?:function ()
>> ? ..$ lhs ? ? ? :function ()
>> ? ..$ gradient ?:function ()
>> ? ..$ conv ? ? ?:function ()
>> ? ..$ incr ? ? ?:function ()
>> ? ..$ setVarying:function (vary = rep(TRUE, length(useParams)))
>> ? ..$ setPars ? :function (newPars)
>> ? ..$ getPars ? :function ()
>> ? ..$ getAllPars:function ()
>> ? ..$ getEnv ? ?:function ()
>> ? ..$ trace ? ? :function ()
>> ? ..$ Rmat ? ? ?:function ()
>> ? ..$ predict ? :function (newdata = list(), qr = FALSE)
>> ? ..- attr(*, "class")= chr "nlsModel"
>> ?$ convInfo ? :List of 5
>> ? ..$ isConv ? ? : logi TRUE
>> ? ..$ finIter ? ?: int 8
>> ? ..$ finTol ? ? : num 1.64e-08
>> ? ..$ stopCode ? : int 0
>> ? ..$ stopMessage: chr "converged"
>> ?$ data ? ? ? : language parent.frame()
>> ?$ call ? ? ? : language nls(formula = NEWY ~ PMESOR + PAMPLITUDE *
cos(2 * pi * (NEWX - ? ? ?POFFSET)/PERIOD), start = list(PMESOR = MESOR,
PAMPLITUDE = AMPLITUDE, ?...
>> ?$ dataClasses: Named chr "numeric"
>> ? ..- attr(*, "names")= chr "NEWX"
>> ?$ control ? ?:List of 2
>> ? ..$ maxiter : num 1000
>> ? ..$ warnOnly: logi TRUE
>> ?- attr(*, "class")= chr "nls"
>
> However, none of these elements appears to contain the residual sum of
squares.
> Help! ?Thanks.

Try:

   sum(resid(FIT)^2)

or

   FIT$m$deviance()

Jun Shen

2010-Aug-13 21:33 UTC

head link

[R] Unable to retrieve residual sum of squares from nls output

Hi, Dennis,

Does this give what you want?
>sum(resid(FIT)^2)
Jun

Senior Pharmacokineticist
Seventh Wave Labs
On Fri, Aug 13, 2010 at 4:21 PM, Dennis Fisher <fisher at plessthan.com>
wrote:> Colleagues,
>
> I am using "nls" successfully (2.11.1, OS X) but I am having
difficulties retrieving part of the output - residual sum of squares. ?I have
assigned the output to FIT:
>> > FIT
>> Nonlinear regression model
>> ? model: ?NEWY ~ PMESOR + PAMPLITUDE * cos(2 * pi * (NEWX -
POFFSET)/PERIOD)
>> ? ?data: ?parent.frame()
>> ? ? PMESOR PAMPLITUDE ? ?POFFSET
>> ? ?1153.02 ? -1183.09 ? ? ?24.58
>> ?residual sum-of-squares: 1815056
>>
>> Number of iterations to convergence: 8
>> Achieved convergence tolerance: 1.643e-08
>
> As you can see, the object contains "residual sum-of-squares:
1815056". ?However, I can't figure out how to grab that value. ? The
tried using "str":
>> > str(FIT)
>> List of 6
>> ?$ m ? ? ? ? ?:List of 16
>> ? ..$ resid ? ? :function ()
>> ? ..$ fitted ? ?:function ()
>> ? ..$ formula ? :function ()
>> ? ..$ deviance ?:function ()
>> ? ..$ lhs ? ? ? :function ()
>> ? ..$ gradient ?:function ()
>> ? ..$ conv ? ? ?:function ()
>> ? ..$ incr ? ? ?:function ()
>> ? ..$ setVarying:function (vary = rep(TRUE, length(useParams)))
>> ? ..$ setPars ? :function (newPars)
>> ? ..$ getPars ? :function ()
>> ? ..$ getAllPars:function ()
>> ? ..$ getEnv ? ?:function ()
>> ? ..$ trace ? ? :function ()
>> ? ..$ Rmat ? ? ?:function ()
>> ? ..$ predict ? :function (newdata = list(), qr = FALSE)
>> ? ..- attr(*, "class")= chr "nlsModel"
>> ?$ convInfo ? :List of 5
>> ? ..$ isConv ? ? : logi TRUE
>> ? ..$ finIter ? ?: int 8
>> ? ..$ finTol ? ? : num 1.64e-08
>> ? ..$ stopCode ? : int 0
>> ? ..$ stopMessage: chr "converged"
>> ?$ data ? ? ? : language parent.frame()
>> ?$ call ? ? ? : language nls(formula = NEWY ~ PMESOR + PAMPLITUDE *
cos(2 * pi * (NEWX - ? ? ?POFFSET)/PERIOD), start = list(PMESOR = MESOR,
PAMPLITUDE = AMPLITUDE, ?...
>> ?$ dataClasses: Named chr "numeric"
>> ? ..- attr(*, "names")= chr "NEWX"
>> ?$ control ? ?:List of 2
>> ? ..$ maxiter : num 1000
>> ? ..$ warnOnly: logi TRUE
>> ?- attr(*, "class")= chr "nls"
>
> However, none of these elements appears to contain the residual sum of
squares.
> Help! ?Thanks.
>
> Dennis
>
>
>
>
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone: 1-866-PLessThan (1-866-753-7784)
> Fax: 1-866-PLessThan (1-866-753-7784)
> www.PLessThan.com
>
> ______________________________________________
> R-help at 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.
>

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