Error in model.frame.default(object, data, xlev = xlev) : object is not a matrix

r glmnet model.matrix
Faller picture Faller · Nov 18, 2016 · Viewed 20.2k times · Source

3 days old to R and can't figure out what I'm doing wrong. I'm trying to send some columns with two way interactions into a glmnet cox model. I have some data.frame() called dtable

Edit to make the code reproducible

xs<-c("Col1", "Col2", "Col3")
v<-c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, NA, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, NA, 25, 26, 27, 28, 29, 30)
df<-data.frame(matrix(v,ncol=3))
dm<-as.matrix(df)
dm<-matrix(dm[complete.cases(dm)], ncol=3)
colnames(dm)<-xs
dfdata<-data.frame(dm)
f<-as.formula(time~.*.)
xmatrix<-model.matrix(f, dfdata)[,-1]

When I run this I get the error

Error in model.frame.default(object, data, xlev = xlev) :    
object is not a matrix

Thanks in advance

Answer

Faller picture Faller · Nov 18, 2016

It's because of the formula: time~.*. In the data.frame() there is no time column for the formula to cross everything by.

Related questions

Big matrix to run glmnet()

I am having a problem to run glmnet lasso with a wide data set. My data has N=50, but p > 49000, all factors. So to run glmnet i have to create a model.matrix, BUT i just run out of …

Read More
R glmnet : "(list) object cannot be coerced to type 'double' "

I'm trying to use the glmnet package on a dataset. I'm using cv.glmnet() to get a lambda value for glmnet(). Here's the dataset and error message: > head(t2) X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 …

Read More
Extracting coefficient variable names from glmnet into a data.frame

I would like to extract the glmnet generated model coefficients and create a SQL query from them. The function coef(cv.glmnet.fit) yields a 'dgCMatrix' object. When I convert it to a matrix using as.matrix, the variable names …

Read More