library(recipes)
library(tidyverse)
library(AppliedPredictiveModeling)

data(AlzheimerDisease)
predictors %>%
  cbind(diagnosis) ->
  alzheimers

alzheimers %>%
  mutate(male = factor(male),
         Genotype = fct_infreq(fct_lump(Genotype, n=3))) ->
  alzheimers

# split data
alzheimers %>%
  initial_split(prop=.9) ->
  alz_split

alz_split %>%
  training() ->
  alz_train

alz_split %>%
  testing() ->
  alz_test

# scaling / basics process
alz_train %>%
  recipe(diagnosis ~ ., .)  %>%
  step_center(all_numeric()) %>%
  step_scale(all_numeric()) %>%
  prep(training=alz_train) ->
  alz_preprocess

# feature reduction
alz_preprocess %>%
  step_corr(all_numeric()) %>%
  step_nzv(all_predictors()) %>%
  step_zv(all_predictors()) %>%
  step_pca(all_numeric()) %>%
  step_upsample(diagnosis) %>%
  prep(training=alz_train, retain=TRUE) ->
  alz_preprocess

# prep training
alz_preprocess %>%
  juice(all_outcomes(), all_predictors()) ->
  alz_train_p

# prep test
alz_preprocess %>%
  bake(alz_test) ->
  alz_test_p