[R-sig-eco] Linear Model of Data in Matrix Form
Jane Shevtsov
jane.eco at gmail.com
Mon Apr 4 05:28:07 CEST 2011
Thank you; that works!
Best,
Jane
On Sun, Apr 3, 2011 at 8:22 PM, Christian Roy <c_roy at ducks.ca> wrote:
> On Sun, Apr 3, 2011 at 11:05 PM, Jane Shevtsov <jane.eco at gmail.com> wrote:
>>
>> 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)
>
> In this example the syntax for your model is:
>> lm(z.melt$value ~ z.melt$X1 + z.melt$X2)
> Call:
> lm(formula = z.melt$value ~ z.melt$X1 + z.melt$X2)
> Coefficients:
> (Intercept) z.melt$X1 z.melt$X2
> -12 1 3
> Best,
> Chris
> -------
>>
>> 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:
>> > -----BEGIN PGP SIGNED MESSAGE-----
>> > Hash: SHA1
>> >
>> > 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
>> > -----BEGIN PGP SIGNATURE-----
>> > Version: GnuPG v1.4.10 (GNU/Linux)
>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>> >
>> > iEYEARECAAYFAk2Y90MACgkQc5UpGjwzenOmPQCdFAOGcxnzADXZNv9ikgDzJcPQ
>> > 3/IAn1ayn1HVOQOdlqFDPoq+Et6rR5nt
>> > =cfIQ
>> > -----END PGP SIGNATURE-----
>> >
>> > _______________________________________________
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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"
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
>
> --
> Christian Roy, Biol. Msc.
> Étudiant au Doctorat / Phd Student
> courriel: christian.roy.22 at ulaval.ca
> Université Laval, Faculté de foresterie, de géographie et de géomatique
>
--
-------------
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"
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