I have a problem with 3 classes requiring classification. I want to use multinomial logistic regression in a package nnet. The class result has 3 factors: P, Q, R. I want to consider Q as a basic factor.
So, I tried to write such contrasts:
P <- c(1,0,0)
R <- c(0,0,1)
contrasts(trainingLR$Class) <- cbind(P,R)
checked:
> contrasts(trainingLR$Class)
P R
P 1 0
Q 0 0
R 0 1
Now multinom():
library(nnet)
multinom(Class ~., data=trainingLR)
Output:
> multinom(Class ~., data=trainingLR)
initial value 180.172415
iter 10 value 34.990665
iter 20 value 11.765136
iter 30 value 0.162491
iter 40 value 0.000192
iter 40 value 0.000096
iter 40 value 0.000096
final value 0.000096
converged
Call:
multinom(formula = Class ~ ., data = trainingLR)
Coefficients:
(Intercept) IL8 IL17A IL23A IL23R
Q -116.2881 -16.562423 -34.80174 3.370051 6.422109
R 203.2414 6.918666 -34.40271 -10.233787 31.446915
EBI3 IL6ST IL12A IL12RB2 IL12B
Q -8.316808 12.75168 -7.880954 5.686425 -9.665776
R 5.135609 -20.48971 -2.093231 37.423452 14.669226
IL12RB1 IL27RA
Q -6.921755 -1.307048
R 15.552842 -7.063026
Residual Deviance: 0.0001922658
AIC: 48.00019
Question:
So, as you can see, since the class P did not appear in the output, this means that it was considered basic, being the first in alphabetical order, as expected when working with factor variables in R, and class Q was not considered as a basic level in In this case, how to make it the basis for two other levels?
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