CODEWITHSUNDEEP
rglmglmnet
Marcin
Marcin

Reputation: 8044

Why can't pass only 1 coulmn to glmnet when it is possible in glm function in R?

Why there is no possibility to pass only 1 explanatory variable to model in glmnet function from glmnet package when it is possible in glm function from base? Code and error are below:

> modelX<-glm( ifelse(train$cliks <1,0,1)~(sparseYY[,40]), family="binomial")
> summary(modelX)

Call:
glm(formula = ifelse(train$cliks < 1, 0, 1) ~ (sparseYY[, 40]), 
    family = "binomial")

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-0.2076  -0.2076  -0.2076  -0.2076   2.8641  

Coefficients:
               Estimate Std. Error  z value Pr(>|z|)    
(Intercept)    -3.82627    0.00823 -464.896   <2e-16 ***
sparseYY[, 40] -0.25844    0.15962   -1.619    0.105    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 146326  on 709677  degrees of freedom
Residual deviance: 146323  on 709676  degrees of freedom
AIC: 146327

Number of Fisher Scoring iterations: 6

> modelY<-glmnet( y =ifelse(train$cliks <1,0,1), x =(sparseYY[,40]), family="binomial"  )
Błąd wif (is.null(np) | (np[2] <= 1)) stop("x should be a matrix with 2 or more columns")

Upvotes: 7

Views: 6655

Answers (3)

tobsecret
tobsecret

Reputation: 2522

Here is an answer I got to this question from the maintainer of the package (Trevor Hastie):

glmnet is designed to select variables from a (large) collection. Allowing for 1 variable would have created a lot of edge case programming, and I was not interested in doing that. Sorry!

Upvotes: 12

CoderGuy123
CoderGuy123

Reputation: 6659

I don't know why, but it's some kind of internal limitation. It does not have to do with the family as Roman claimed above.

glmnet(x = as.matrix(iris[2:4]), y = as.matrix(iris[1]))
## long output
glmnet(x = as.matrix(iris[1]), y = as.matrix(iris[1]))
Error in glmnet(x = as.matrix(iris[2]), y = as.matrix(iris[1])) : 
  x should be a matrix with 2 or more columns

It's a simple check in the code https://github.com/cran/glmnet/blob/master/R/glmnet.R#L20

Upvotes: 1

Roman Luštrik
Roman Luštrik

Reputation: 70633

Because the documentation says so.

For family="binomial" should be either a factor with two levels, or a two-column matrix of counts or proportions (the second column is treated as the target class; for a factor, the last level in alphabetical order is the target class).

You have two options. Either construct a matrix where two columns represent counts, or, convert x into a factor with two levels.

Upvotes: -2

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