[R-sig-eco] R-sig-ecology Digest, (80/1): Binomial GLM: Is it the right way?

[Ludovico Frate]

Dear Class, thank you for your reply.
Maybe I have not been very clear in the exposition. I'll try to reformulate.

"the likelihood of colonizing or becoming extinct" is a proportion so the
binomial distribution should be still ok!

Considering only colonizing species, or arrivals, for a given plot. This
means that a species is not new in overall sampled flora but only for that
plot (i.e. *local* colonizer).

PLOTID;TRAITS;NUMBER OF NEW COLONIZERS;NUMBER OF SUCCESS;PROPORTION
1;	ChF;	4;	0;	0
1;	ChC;	4;	0;	0
1;	ChR;	4;	0;	0
1;	ChSC;4;	0;	0
1;	ChS;	4;	1;	0,25
1;	Ph;	4;	0;	0
1;	Geo;	4;	0;	0
1;	HeB;	4;	0;	0
1;	HeC;	4;	0;	0
1;	HeR;	4;	0;	0
1;	HeS;	4;	3;	0,75
1;	Th;   4;	0;	0
2;	ChF;	17;	0;	0
2;	ChC;	17;	0;	0
2;	ChR;	17;	1;	0,058823529
2;	ChSC;17;	0;	0
2;	ChS;	17;	2;	0,117647059
2;	Ph;	17;	0;	0
2;	Geo;	17;	1;	0,058823529
2;	HeB;	17;	0;	0
2;	HeC;	17;	0;	0
2;	HeR;	17;	2;	0,117647059
2;	HeS;	17;	7;	0,411764706
2;	Th;	17;	4;	0,235294118
3;	ChF;	16;	0;	0
3;	ChC;	16;	0;	0
3;	ChR;	16;	2;	0,125
3;	ChSC;16;	0;	0
3;	ChS;	16;	0;	0
3;	Ph;	16;	0;	0
3;	Geo;	16;	2;	0,125
3;	HeB;	16;	0;	0
3;	HeC;	16;	0;	0
3;	HeR;	16;	1;	0,0625
3;	HeS;	16;	9;	0,5625
3;	Th;	16;	2;	0,125
.       .       .       .
.       .       .       .
.       .       .       .
24    .       .       .


for example, in the table, the plot 1 has 4 new species found of which 1 is
a ChS and 3 are HeS with a proportion of 0.25 and 0.75 respectively.

In a GLM model, the response variable should be PROPORTION (that I have
improperly called PROBABILITY)

An hypothetical model could be:
M0<-glm(PROPORTION~TRAITS, family = binomial, weights = NUMBER OF NEW
COLONIZERS, data = ...)


Does it make sense?


For the second question, I agree with you that "the probability of a species
colonizing a plot not only depends on which life form that particular
species has".

Regards,
Ludovico



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