[R] Other ways to lm() regression? (non-loop?)

Bert Gunter gunter.berton at gene.com
Mon Dec 26 17:00:21 CET 2011

Dear anonymous:

1. You may be more likely to get "useful tips" on this list if you
sign with your real name. It's friendlier.

2. If you are using R "14 hours/day." get and read a good R book. The
CRAN site or Amazon lists many; choose one or more that suits your

3. Read the R Help files carefully.  ?lm tells you that you do not
need a loop to fit many y's simultaneously:

"If response is a matrix a linear model is fitted separately by
least-squares to each column of the matrix. "

4. Loops are not necessarily so terrible. "apply" type functions are
basically loops, also; their chief advantage is often just code
readability, not efficiency.

5. For tasks such as yours, ?update methods are typically useful.


On Mon, Dec 26, 2011 at 4:29 AM, iliketurtles <isaacm200 at gmail.com> wrote:
> Hi, I'm quite new to R (1 month full time use so far). I have to run loop
> regressions VERY often in my work, so I would appreciate some new
> methodology that I'm not considering.
> #---------------------------------------------------------------------------------------------
> y<-matrix(rnorm(100),ncol=10,nrow=10)
> x<-matrix(rnorm(50),ncol=5,nrow=10)
> #Suppose I want to run the specification y=A+Bx+error, for each and every
> y[,n] onto each and every x[,n].
> #So with:
> ncol(y);ncol(x)
> #I should end up with 10*5=50 regressions in total.
> #I know how to do this fine:
> MISC1<-0
> for(i in 1:ncol(y)){
> for(j in 1:ncol(x)){
> reg<-lm(y[,i]~x[,j])
> MISC1<-cbind(MISC1,coef(reg)) #for coefficients
> }}
> coef<-matrix(MISC1[,-1],ncol=50)
> coef[,1];coef(lm(y[,1]~x[,1])) #test passed
> ncol(coef)                                #as desired, 50 regressions.
> #---------------------------------------------------------------------------------------------
> Now for my question: Is there easier or better methods of doing this? I know
> of a lapply method, but the only lapply way I know of for lm(..) is
> basically doing a lapply inside of a lapply, meaning it's exactly the same
> as the double loop above... I'm looking to escape from loops.
> Also, if any of you could share your top R tips that you've learned over the
> years, I'd really appreciate it. Tiny things like learning that array() and
> matrix() can have a 3rd dimension, learning of strsplit, etc.. have helped
> me immeasurably. (Not that I'm also googling for this stuff! I'm doing R 14
> hours a day!).
> Thanks.
> --
> View this message in context: http://r.789695.n4.nabble.com/Other-ways-to-lm-regression-non-loop-tp4234487p4234487.html
> Sent from the R help mailing list archive at Nabble.com.
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Bert Gunter
Genentech Nonclinical Biostatistics

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