[R-sig-eco] Linear Model of Data in Matrix Form

[Jane Shevtsov]

Thanks, but that doesn't quite work. Using your toy example gives an
error about variable lengths.

> z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6))
> z.melt <- melt(z)
> z.melt
  X1 X2 value
1  1  4     1
2  2  4     2
3  3  4     3
4  1  5     4
5  2  5     5
6  3  5     6
7  1  6     7
8  2  6     8
9  3  6     9
> lm(z ~ z.melt$X1 + z.melt$X2)
Error in model.frame.default(formula = z ~ z.melt$X1 + z.melt$X2,
drop.unused.levels = TRUE) :
  variable lengths differ (found for 'z.melt$X1')

I'm using R 2.12.0 on Windows and just installed the reshape package.

Jane

On Sun, Apr 3, 2011 at 3:40 PM, Ben Bolker <bbolker at gmail.com> wrote:
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> On 11-04-02 10:39 PM, Jane Shevtsov wrote:
>> I have data in matrix form from a parameter scan of a food web
>> simulation. (The matrix entry M[i,j] gives the variable of interest
>> for a web size i and connectance j.) How would I find an equation
>> expressing the variable of interest to web size and connectance? Can
>> lm() do it?
>>
>> Thanks,
>> Jane Shevtsov
>>
>
>  suppose your size and connectance vectors were sizevec and connvec.
> Then something like
>
> dimnames(M) <- list(sizevec,connvec)
> library(reshape)
> X <- melt(M)
> lm(value~X1+X2)
>
>  will do it.
>
>  Mini example:
>
>> z <- matrix(1:9,nrow=3,dimnames=list(1:3,4:6))
>> library(reshape)
> Loading required package: plyr
>
> Attaching package: 'reshape'
>
> The following object(s) are masked from 'package:plyr':
>
>    round_any
>
>> str(melt(z))
> 'data.frame':   9 obs. of  3 variables:
>  $ X1   : int  1 2 3 1 2 3 1 2 3
>  $ X2   : int  4 4 4 5 5 5 6 6 6
>  $ value: int  1 2 3 4 5 6 7 8 9
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-- 
-------------
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, <www.worldbeyondborders.org>
Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes

"In the long run, education intended to produce a molecular
geneticist, a systems ecologist, or an immunologist is inferior, both
for the individual and for society, than that intended to produce a
broadly educated person who has also written a dissertation." --John
Janovy, Jr., "On Becoming a Biologist"