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Daniel Malter

2008-Feb-26 07:25 UTC

[R] OLS standard errors

Hi,

the standard errors of the coefficients in two regressions that I computed
by hand and using lm() differ by about 1%. Can somebody help me to identify
the source of this difference? The coefficient estimates are the same, but
the standard errors differ. 

####Simulate data
	
	happiness=0
	income=0
	gender=(rep(c(0,1,1,0),25))
		for(i in 1:100){
  			happiness[i]=1000+i+rnorm(1,0,40)
 			income[i]=2*i+rnorm(1,0,40)
  			}

####Run lm()

	reg=lm(happiness~income+factor(gender))
	summary(reg)

####Compute coefficient estimates "by hand"

	x=cbind(income,gender)
	y=happiness

	z=as.matrix(cbind(rep(1,100),x))
	beta=solve(t(z)%*%z)%*%t(z)%*%y

####Compare estimates

	cbind(reg$coef,beta)  ##fine so far, they both look the same
	
	reg$coef[1]-beta[1]
	reg$coef[2]-beta[2]
	reg$coef[3]-beta[3]	##differences are too small to cause a 1%
difference

####Check predicted values

	estimates=c(beta[2],beta[3])

	predicted=estimates%*%t(x)
	predicted=as.vector(t(as.double(predicted+beta[1])))
	
	cbind(reg$fitted,predicted)		##inspect fitted values
	as.vector(reg$fitted-predicted)	##differences are marginal

#### Compute errors

	e=NA
	e2=NA
	for(i in 1:length(happiness)){
  		e[i]=y[i]-predicted[i]   ##for "hand-computed" regression
  		e2[i]=y[i]-reg$fitted[i] ##for lm() regression
  	}

#### Compute standard error of the coefficients

  sqrt(abs(var(e)*solve(t(z)%*%z)))	##for "hand-computed" regression
  sqrt(abs(var(e2)*solve(t(z)%*%z)))	##for lm() regression using e2 from
above

	##Both are the same

####Compare to lm() standard errors of the coefficients again

	summary(reg)


The diagonal elements of the variance/covariance matrices should be the
standard errors of the coefficients. Both are identical when computed by
hand. However, they differ from the standard errors reported in
summary(reg). The difference of 1% seems nonmarginal. Should I have
multiplied var(e)*solve(t(z)%*%z) by n and divided by n-1? But even if I do
this, I still observe a difference. Can anybody help me out what the source
of this difference is?

Cheers,
Daniel


-------------------------
cuncta stricte discussurus

Peter Dalgaard

2008-Feb-26 07:57 UTC

head link

[R] OLS standard errors

Daniel Malter wrote:> Hi,
>
> the standard errors of the coefficients in two regressions that I computed
> by hand and using lm() differ by about 1%. Can somebody help me to identify
> the source of this difference? The coefficient estimates are the same, but
> the standard errors differ. 
>
> ####Simulate data
> 	
> 	happiness=0
> 	income=0
> 	gender=(rep(c(0,1,1,0),25))
> 		for(i in 1:100){
>   			happiness[i]=1000+i+rnorm(1,0,40)
>  			income[i]=2*i+rnorm(1,0,40)
>   			}
>
> ####Run lm()
>
> 	reg=lm(happiness~income+factor(gender))
> 	summary(reg)
>
> ####Compute coefficient estimates "by hand"
>
> 	x=cbind(income,gender)
> 	y=happiness
>
> 	z=as.matrix(cbind(rep(1,100),x))
> 	beta=solve(t(z)%*%z)%*%t(z)%*%y
>
> ####Compare estimates
>
> 	cbind(reg$coef,beta)  ##fine so far, they both look the same
> 	
> 	reg$coef[1]-beta[1]
> 	reg$coef[2]-beta[2]
> 	reg$coef[3]-beta[3]	##differences are too small to cause a 1%
> difference
>
> ####Check predicted values
>
> 	estimates=c(beta[2],beta[3])
>
> 	predicted=estimates%*%t(x)
> 	predicted=as.vector(t(as.double(predicted+beta[1])))
> 	
> 	cbind(reg$fitted,predicted)		##inspect fitted values
> 	as.vector(reg$fitted-predicted)	##differences are marginal
>
> #### Compute errors
>
> 	e=NA
> 	e2=NA
> 	for(i in 1:length(happiness)){
>   		e[i]=y[i]-predicted[i]   ##for "hand-computed" regression
>   		e2[i]=y[i]-reg$fitted[i] ##for lm() regression
>   	}
>
> #### Compute standard error of the coefficients
>
>   sqrt(abs(var(e)*solve(t(z)%*%z)))	##for "hand-computed"
regression
>   sqrt(abs(var(e2)*solve(t(z)%*%z)))	##for lm() regression using e2 from
> above
>
> 	##Both are the same
>
> ####Compare to lm() standard errors of the coefficients again
>
> 	summary(reg)
>
>
> The diagonal elements of the variance/covariance matrices should be the
> standard errors of the coefficients. Both are identical when computed by
> hand. However, they differ from the standard errors reported in
> summary(reg). The difference of 1% seems nonmarginal. Should I have
> multiplied var(e)*solve(t(z)%*%z) by n and divided by n-1? But even if I do
> this, I still observe a difference. Can anybody help me out what the source
> of this difference is?
>
>   The degrees of freedom in a regression analysis is n minus the number of 
parameters, three in your case. I.e. the variance var(e) does not know 
about this and divides by n-1 where it should have been n-3, so.....
> Cheers,
> Daniel
>
>
> -------------------------
> cuncta stricte discussurus
>
> ______________________________________________
> 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.
>   

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

Prof Brian Ripley

2008-Feb-26 08:07 UTC

head link

[R] OLS standard errors

Please check your statistical methods lecture notes.  var(e) has divisor 
n-1, and that is not an unbiased estimator of the residual variance when 
'e' are residuals.  From summary.lm (and you are allowed to read the
code)

     rdf <- n - p
     if (is.na(z$df.residual) || rdf != z$df.residual)
         warning("residual degrees of freedom in object suggest this is not
an \"lm\" fit")
     p1 <- 1:p
     r <- z$residuals
     f <- z$fitted.values
     w <- z$weights
     if (is.null(w)) {
         mss <- if (attr(z$terms, "intercept"))
             sum((f - mean(f))^2)
         else sum(f^2)
         rss <- sum(r^2)
     }
     else {
         mss <- if (attr(z$terms, "intercept")) {
             m <- sum(w * f/sum(w))
             sum(w * (f - m)^2)
         }
         else sum(w * f^2)
         rss <- sum(w * r^2)
         r <- sqrt(w) * r
     }
     resvar <- rss/rdf

the correct divisor is n-p.  Since p=3 in your example, that explains a 2% 
difference in variances and hence a 1% difference in SEs.

On Tue, 26 Feb 2008, Daniel Malter wrote:
> Hi,
>
> the standard errors of the coefficients in two regressions that I computed
> by hand and using lm() differ by about 1%. Can somebody help me to identify
> the source of this difference? The coefficient estimates are the same, but
> the standard errors differ.
>
> ####Simulate data
>
> 	happiness=0
> 	income=0
> 	gender=(rep(c(0,1,1,0),25))
> 		for(i in 1:100){
>  			happiness[i]=1000+i+rnorm(1,0,40)
> 			income[i]=2*i+rnorm(1,0,40)
>  			}
>
> ####Run lm()
>
> 	reg=lm(happiness~income+factor(gender))
> 	summary(reg)
>
> ####Compute coefficient estimates "by hand"
>
> 	x=cbind(income,gender)
> 	y=happiness
>
> 	z=as.matrix(cbind(rep(1,100),x))
> 	beta=solve(t(z)%*%z)%*%t(z)%*%y
>
> ####Compare estimates
>
> 	cbind(reg$coef,beta)  ##fine so far, they both look the same
>
> 	reg$coef[1]-beta[1]
> 	reg$coef[2]-beta[2]
> 	reg$coef[3]-beta[3]	##differences are too small to cause a 1%
> difference
>
> ####Check predicted values
>
> 	estimates=c(beta[2],beta[3])
>
> 	predicted=estimates%*%t(x)
> 	predicted=as.vector(t(as.double(predicted+beta[1])))
>
> 	cbind(reg$fitted,predicted)		##inspect fitted values
> 	as.vector(reg$fitted-predicted)	##differences are marginal
>
> #### Compute errors
>
> 	e=NA
> 	e2=NA
> 	for(i in 1:length(happiness)){
>  		e[i]=y[i]-predicted[i]   ##for "hand-computed" regression
>  		e2[i]=y[i]-reg$fitted[i] ##for lm() regression
>  	}
>
> #### Compute standard error of the coefficients
>
>  sqrt(abs(var(e)*solve(t(z)%*%z)))	##for "hand-computed"
regression
>  sqrt(abs(var(e2)*solve(t(z)%*%z)))	##for lm() regression using e2 from
> above
>
> 	##Both are the same
>
> ####Compare to lm() standard errors of the coefficients again
>
> 	summary(reg)
>
>
> The diagonal elements of the variance/covariance matrices should be the
> standard errors of the coefficients. Both are identical when computed by
> hand. However, they differ from the standard errors reported in
> summary(reg). The difference of 1% seems nonmarginal. Should I have
> multiplied var(e)*solve(t(z)%*%z) by n and divided by n-1? But even if I do
> this, I still observe a difference. Can anybody help me out what the source
> of this difference is?
>
> Cheers,
> Daniel
>
>
> -------------------------
> cuncta stricte discussurus
>
> ______________________________________________
> 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.
>
-- 
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 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Viechtbauer Wolfgang (STAT)

2008-Feb-26 08:21 UTC

head link

[R] OLS standard errors

Try multiplying var(e) by n-1 and dividing by n-3 (97 are the degrees of freedom
for the sum of squares error in your example). Then it all matches up nicely.

Best,

-- 
Wolfgang Viechtbauer
?Department of Methodology and Statistics
?University of Maastricht, The Netherlands
?http://www.wvbauer.com/



----Original Message----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Daniel Malter Sent:
Tuesday, February 26, 2008 08:25 To: 'r-help'
Subject: [R] OLS standard errors
> Hi,
> 
> the standard errors of the coefficients in two regressions that I
> computed by hand and using lm() differ by about 1%. Can somebody help
> me to identify the source of this difference? The coefficient
> estimates are the same, but the standard errors differ.   
> 
> ####Simulate data
> 
> 	happiness=0
> 	income=0
> 	gender=(rep(c(0,1,1,0),25))
> 		for(i in 1:100){
>   			happiness[i]=1000+i+rnorm(1,0,40)
>  			income[i]=2*i+rnorm(1,0,40)
>   			}
> 
> ####Run lm()
> 
> 	reg=lm(happiness~income+factor(gender))
> 	summary(reg)
> 
> ####Compute coefficient estimates "by hand"
> 
> 	x=cbind(income,gender)
> 	y=happiness
> 
> 	z=as.matrix(cbind(rep(1,100),x))
> 	beta=solve(t(z)%*%z)%*%t(z)%*%y
> 
> ####Compare estimates
> 
> 	cbind(reg$coef,beta)  ##fine so far, they both look the same
> 
> 	reg$coef[1]-beta[1]
> 	reg$coef[2]-beta[2]
> 	reg$coef[3]-beta[3]	##differences are too small to cause a 1%
> difference
> 
> ####Check predicted values
> 
> 	estimates=c(beta[2],beta[3])
> 
> 	predicted=estimates%*%t(x)
> 	predicted=as.vector(t(as.double(predicted+beta[1])))
> 
> 	cbind(reg$fitted,predicted)		##inspect fitted values
> 	as.vector(reg$fitted-predicted)	##differences are marginal
> 
> #### Compute errors
> 
> 	e=NA
> 	e2=NA
> 	for(i in 1:length(happiness)){
>   		e[i]=y[i]-predicted[i]   ##for "hand-computed" regression
>   		e2[i]=y[i]-reg$fitted[i] ##for lm() regression
>   	}
> 
> #### Compute standard error of the coefficients
> 
>   sqrt(abs(var(e)*solve(t(z)%*%z)))	##for "hand-computed"
regression
>   sqrt(abs(var(e2)*solve(t(z)%*%z)))	##for lm() regression using e2
> from 
> above
> 
> 	##Both are the same
> 
> ####Compare to lm() standard errors of the coefficients again
> 
> 	summary(reg)
> 
> 
> The diagonal elements of the variance/covariance matrices should be
> the standard errors of the coefficients. Both are identical when
> computed by hand. However, they differ from the standard errors
> reported in summary(reg). The difference of 1% seems nonmarginal.
> Should I have multiplied var(e)*solve(t(z)%*%z) by n and divided by
> n-1? But even if I do this, I still observe a difference. Can anybody
> help me out what the source of this difference is?      
> 
> Cheers,
> Daniel
> 
> 
> -------------------------
> cuncta stricte discussurus
> 
> ______________________________________________
> 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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