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Dermot MacSweeney

2000-Oct-14 18:33 UTC

[R] Access to calculations in nls

Hi,

I would like to be able to access the calculated results from the nls package. 
Using the example in R, fm3DNase1 we can reurn certain parts of the 
calculations:
> coef(fm3DNase1)    Asym     xmid     scal 
2.345179 1.483089 1.041454 
> resid(fm3DNase1) [1] -0.0136806237 -0.0126806237  0.0089488569  0.0119488569 -0.0025803222
 [6]  0.0064196778  0.0026723396 -0.0003276604 -0.0187778127 -0.0237778127
[11]  0.0381369952  0.0201369952 -0.0335131004 -0.0035131004  0.0150122651
[16] -0.0049877349
attr(,"label")
[1] "Residuals"

What I would like to be able to return are the Std. Errors shown with the 
Parameter estimates below. Is there a command such as stderr(fm3DNase1) that 
would return:

[1] 0.07815 	0.08135		0.03227
> summary(fm3DNase1)
Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym  2.34518    0.07815   30.01 2.16e-13 ***
xmid  1.48309    0.08135   18.23 1.22e-10 ***
scal  1.04145    0.03227   32.27 8.50e-14 ***
---
Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'  0.1
` '  1

Residual standard error: 0.01919 on 13 degrees of freedom

Correlation of Parameter Estimates:
       Asym   xmid
xmid 0.9868       
scal 0.9008 0.9063

Thanks in Advance,

Dermot MacSweeney.

**************************************************************

Dermot MacSweeney			NMRC, 
Email: dsweeney at nmrc.ucc.ie		Lee Maltings, 
Tel: +353 21 904178			Prospect Row, 
Fax: +353 21 270271			Cork, 
WWW: http://nmrc.ucc.ie			Ireland

**************************************************************


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Prof Brian D Ripley

2000-Oct-14 20:18 UTC

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[R] Access to calculations in nls

On Sat, 14 Oct 2000, Dermot MacSweeney wrote:
> Hi,
> 
> I would like to be able to access the calculated results from the nls
package.
> Using the example in R, fm3DNase1 we can reurn certain parts of the 
> calculations:
> 
> > coef(fm3DNase1)
>     Asym     xmid     scal 
> 2.345179 1.483089 1.041454 
> 
> > resid(fm3DNase1)
>  [1] -0.0136806237 -0.0126806237  0.0089488569  0.0119488569 -0.0025803222
>  [6]  0.0064196778  0.0026723396 -0.0003276604 -0.0187778127 -0.0237778127
> [11]  0.0381369952  0.0201369952 -0.0335131004 -0.0035131004  0.0150122651
> [16] -0.0049877349
> attr(,"label")
> [1] "Residuals"
> 
> What I would like to be able to return are the Std. Errors shown with the 
> Parameter estimates below. Is there a command such as stderr(fm3DNase1)
that
> would return:
> 
> [1] 0.07815 	0.08135		0.03227
No, but summary itself returns them.  By convention summary methods
create a new object of class print.summary.foo which is then auto-printed.
So you wanted
> summary(fm3DNase1)$parameters[, 2]    Asym     xmid     scal 
0.078154 0.081353 0.032271 

(with names, or as.vector(...) if not).

As an aside, package MASS has a generic function vcov to pull out
variance-covariance estimates of coefficient estimates, so you can
do> vcov(fm3DNase1)         Asym      xmid      scal
Asym 0.006108 0.0062740 0.0022720
xmid 0.006274 0.0066183 0.0023794
scal 0.002272 0.0023794 0.0010414

too.  As it's generic, it works for most fitted model objects.
> 
> > summary(fm3DNase1)
> 
> Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
> 
> Parameters:
>      Estimate Std. Error t value Pr(>|t|)    
> Asym  2.34518    0.07815   30.01 2.16e-13 ***
> xmid  1.48309    0.08135   18.23 1.22e-10 ***
> scal  1.04145    0.03227   32.27 8.50e-14 ***
> ---
> Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'
0.1  ` '  1
> 
> Residual standard error: 0.01919 on 13 degrees of freedom
> 
> Correlation of Parameter Estimates:
>        Asym   xmid
> xmid 0.9868       
> scal 0.9008 0.9063
> 
> Thanks in Advance,
> 
> Dermot MacSweeney.
> 
> **************************************************************
> 
> Dermot MacSweeney			NMRC, 
> Email: dsweeney at nmrc.ucc.ie		Lee Maltings, 
> Tel: +353 21 904178			Prospect Row, 
> Fax: +353 21 270271			Cork, 
> WWW: http://nmrc.ucc.ie			Ireland
> 
> **************************************************************
> 
> 
>
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
>
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> 
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Rashid Nassar

2000-Oct-14 20:23 UTC

head link

[R] Access to calculations in nls

I hope the following helps (and that it is correct!):
> names(summary(fm3DNase1))[1] "formula"      "residuals"    "sigma"       
"df"
"cov.unscaled"
[6] "correlation"  "parameters"  
> summary(fm3DNase1)$sigma[1] 0.01919449
> summary(fm3DNase1)$parameters     Estimate Std. Error  t value     Pr(>|t|)
Asym 2.345179 0.07815378 30.00724 2.164935e-13
xmid 1.483089 0.08135307 18.23027 1.218523e-10
scal 1.041454 0.03227078 32.27237 8.504308e-14

# for the standard errors:
> summary(fm3DNase1)$parameters[,2]      Asym       xmid       scal 
0.07815378 0.08135307 0.03227078 

Rashid Nassar



On Sat, 14 Oct 2000, Dermot MacSweeney wrote:
> Date: Sat, 14 Oct 2000 19:33:17 +0100 (BST)
> From: Dermot MacSweeney <dsweeney at nmrc.ucc.ie>
> To: r-help at stat.math.ethz.ch
> Subject: [R] Access to calculations in nls
> 
> Hi,
> 
> I would like to be able to access the calculated results from the nls
package.
> Using the example in R, fm3DNase1 we can reurn certain parts of the 
> calculations:
> 
> > coef(fm3DNase1)
>     Asym     xmid     scal 
> 2.345179 1.483089 1.041454 
> 
> > resid(fm3DNase1)
>  [1] -0.0136806237 -0.0126806237  0.0089488569  0.0119488569 -0.0025803222
>  [6]  0.0064196778  0.0026723396 -0.0003276604 -0.0187778127 -0.0237778127
> [11]  0.0381369952  0.0201369952 -0.0335131004 -0.0035131004  0.0150122651
> [16] -0.0049877349
> attr(,"label")
> [1] "Residuals"
> 
> What I would like to be able to return are the Std. Errors shown with the 
> Parameter estimates below. Is there a command such as stderr(fm3DNase1)
that
> would return:
> 
> [1] 0.07815 	0.08135		0.03227
> 
> > summary(fm3DNase1)
> 
> Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
> 
> Parameters:
>      Estimate Std. Error t value Pr(>|t|)    
> Asym  2.34518    0.07815   30.01 2.16e-13 ***
> xmid  1.48309    0.08135   18.23 1.22e-10 ***
> scal  1.04145    0.03227   32.27 8.50e-14 ***
> ---
> Signif. codes:  0  `***'  0.001  `**'  0.01  `*'  0.05  `.'
0.1  ` '  1
> 
> Residual standard error: 0.01919 on 13 degrees of freedom
> 
> Correlation of Parameter Estimates:
>        Asym   xmid
> xmid 0.9868       
> scal 0.9008 0.9063
> 
> Thanks in Advance,
> 
> Dermot MacSweeney.
> 
> **************************************************************
> 
> Dermot MacSweeney			NMRC, 
> Email: dsweeney at nmrc.ucc.ie		Lee Maltings, 
> Tel: +353 21 904178			Prospect Row, 
> Fax: +353 21 270271			Cork, 
> WWW: http://nmrc.ucc.ie			Ireland
> 
> **************************************************************
> 
> 
>
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
>
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
> 
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at
stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._

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