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I have a fairly large dataset 1460(n)x81(p). About 38 variables are numeric and rest are factors with levels ranging from 2-30. I am using dummy.data.frame from dummies package to encode the factor variables to run PCA.

However, as I run the following code:

train_dummy <- dummy.data.frame(train, sep = ".", verbose = TRUE, all = TRUE) some of the colums are from the original dataset are removed.

Link to original training dataset: https://www.kaggle.com/c/house-prices-advanced-regression-techniques/data

A number of columns from the original dataset including response variable SalePrice are being dropped. Any ideas/suggestions on what to try?

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