[R] problem with polr ?

From: Marc Girondot <marc.girondot_at_ese.u-psud.fr>
Date: Sat 11 Jun 2005 - 06:44:28 EST


I want to fit a multinomial model with logit link. For example let this matrix to be analyzed: male female aborted factor

10     12         1         1.2
14     14         4         1.3
15     12         3         1.4

(this is an example, not the true data which are far more complex...)

I suppose the correct function to analyze these data is polr from MASS library.

The data have been entered in a text file like this:

output factor n

m       1.2     10
f       1.2     12
a       1.2     1
m       1.3     14
f       1.3     14
a       1.3     4
m       1.4     15
f       1.4     12
a       1.4     3

However, after having performed the analysis, it appears this is not correct as the 3 outputs per experiment are not linked...

library(MASS)
dt.plr <- polr(output ~ factor, data=dt, weights=n)
> dt.pr1<-predict(dt.plr, , type="probs")
> dt.pr1

            a f m

1 0.09987167 0.4578184 0.4423099
2 0.09987167 0.4578184 0.4423099
3 0.09987167 0.4578184 0.4423099
4 0.09437078 0.4477902 0.4578390
5 0.09437078 0.4477902 0.4578390
6 0.09437078 0.4477902 0.4578390
7 0.08914287 0.4374067 0.4734505
8 0.08914287 0.4374067 0.4734505
9 0.08914287 0.4374067 0.4734505


---------------------------Another linked problem

Also, I don't understand what the meaning of the residual deviance that is displayed.
Let modify the file so that the model can also be analyzed using binomial model:

output factor n

m       1.2     10
f       1.2     12
a       1.2     0
m       1.3     14
f       1.3     14
a       1.3     0
m       1.4     15
f       1.4     12
a       1.4     0

dt.plr
Call:
polr(formula = output ~ factor, data = dt, weights = n)

Coefficients:

   factor
2.034848

Intercepts:

        a|f f|m
-16.306511 2.632410

Residual Deviance: 106.2304
AIC: 112.2304 whereas the corresponding scaled deviance for the binomial model (removing a column) is 1.842e-3...

-- 

__________________________________________________________
Marc Girondot, Pr
Laboratoire Ecologie, Systématique et Evolution
Equipe de Conservation des Populations et des Communautés
CNRS, ENGREF et Université Paris-Sud 11 , UMR 8079
Bâtiment 362
91405 Orsay Cedex, France

Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1 69 
15 56 96   e-mail: marc.girondot@ese.u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot
Fax in US: 1-425-732-6934

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Received on Sat Jun 11 06:47:40 2005

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