class: center, middle, title-slide # Reproducible preprocessing with recipes ## Happy Scientist Seminar ### Emil Hvitfeldt ### 2019-4-27 --- ``` ## Loading required package: dplyr ``` ``` ## ## Attaching package: 'dplyr' ``` ``` ## The following objects are masked from 'package:stats': ## ## filter, lag ``` ``` ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union ``` ``` ## ## Attaching package: 'recipes' ``` ``` ## The following object is masked from 'package:stats': ## ## step ``` <style>.orange { color: #EF8633; } .blue { color: #3381F7; } </style> <br> <br> ## What happens to the data between `read_data()` and `fit_model()`? --- ## Prices of 54,000 round cut diamonds ```r library(ggplot2) diamonds ``` ``` ## # A tibble: 53,940 x 10 ## carat cut color clarity depth table price x y z ## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> ## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43 ## 2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31 ## 3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31 ## 4 0.290 Premium I VS2 62.4 58 334 4.2 4.23 2.63 ## 5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75 ## 6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48 ## 7 0.24 Very Good I VVS1 62.3 57 336 3.95 3.98 2.47 ## 8 0.26 Very Good H SI1 61.9 55 337 4.07 4.11 2.53 ## 9 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49 ## 10 0.23 Very Good H VS1 59.4 61 338 4 4.05 2.39 ## # … with 53,930 more rows ``` --- ## Formula expression in modeling <code class ='r hljs remark-code'>model <- lm(<span style='color:#EF8633'>price</span> ~ <span style='color:#3381F7'>cut:color + carat + log(depth)</span>, <br> data = diamonds)</code> - Select .orange[outcome] & .blue[predictors] --- ## Formula expression in modeling <code class ='r hljs remark-code'>model <- lm(price ~ <span style='color:#EF8633'>cut:color</span> + carat + log(depth), <br> data = diamonds)</code> - Select outcome & predictors - .orange[Operators] to matrix of predictors --- ## Formula expression in modeling <code class ='r hljs remark-code'>model <- lm(price ~ cut:color + carat + <span style='color:#EF8633'>log(depth)</span>, <br> data = diamonds)</code> - Select outcome & predictors - Operators to matrix of predictors - .orange[Inline functions] --- ## Work under the hood - model.matrix ```r model.matrix(price ~ cut:color + carat + log(depth) + table, data = diamonds) ``` ``` ## Rows: 53,940 ## Columns: 39 ## $ `(Intercept)` <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,… ## $ carat <dbl> 0.23, 0.21, 0.23, 0.29, 0.31, 0.24, 0.24, 0.26,… ## $ `log(depth)` <dbl> 4.119037, 4.091006, 4.041295, 4.133565, 4.14788… ## $ table <dbl> 55, 61, 65, 58, 58, 57, 57, 55, 61, 61, 55, 56,… ## $ `cutFair:colorD` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutGood:colorD` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutVery Good:colorD` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutPremium:colorD` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutIdeal:colorD` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutFair:colorE` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,… ## $ `cutGood:colorE` <dbl> 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ... ``` --- ## Downsides - **Tidious typing with many variables** --- ## Downsides - Tedious typing with many variables - **Functions have to manually be applied to each variable** ```r lm(y ~ log(x01) + log(x02) + log(x03) + log(x04) + log(x05) + log(x06) + log(x07) + log(x08) + log(x09) + log(x10) + log(x11) + log(x12) + log(x13) + log(x14) + log(x15) + log(x16) + log(x17) + log(x18) + log(x19) + log(x20) + log(x21) + log(x22) + log(x23) + log(x24) + log(x25) + log(x26) + log(x27) + log(x28) + log(x29) + log(x30) + log(x31) + log(x32) + log(x33) + log(x34) + log(x35), data = dat) ``` --- ## Downsides - Tedious typing with many variables - Functions have to manually be applied to each variable - **Operations are constrained to single columns** ```r # Not possible lm(y ~ pca(x01, x02, x03, x04, x05), data = dat) ``` --- ## Downsides - Tedious typing with many variables - Functions have to manually be applied to each variable - Operations are constrained to single columns - **Everything happens at once** You can't apply multiple transformations to the same variable. --- ## Downsides - Tedious typing with many variables - Functions have to manually be applied to each variable - Operations are constrained to single columns - Everything happens at once - **Connected to the model, calculations are not saved between models** One could manually use `model.matrix` and pass the result to the modeling function. --- .center[  ] --- # Recipes New package to deal with this problem ### Benefits: - **Modular** --- # Recipes New package to deal with this problem ### Benefits: - Modular - **pipeable** --- # Recipes New package to deal with this problem ### Benefits: - Modular - pipeable - **Deferred evaluation** --- # Recipes New package to deal with this problem ### Benefits: - Modular - pipeable - Deferred evaluation - **Isolates test data from training data** --- # Recipes New package to deal with this problem ### Benefits: - Modular - pipeable - Deferred evaluation - Isolates test data from training data - **Can do things formulas can't** --- # Modularity and pipeability ```r price ~ cut + color + carat + log(depth) + table ``` Taking the formula from before we can rewrite it as the following recipe ```r rec <- recipe(price ~ cut + color + carat + depth + table, data = diamonds) %>% step_log(depth) %>% step_dummy(cut, color) ``` --- # Modularity and pipeability ```r price ~ cut + color + carat + log(depth) + table ``` Taking the formula from before we can rewrite it as the following recipe <code class ='r hljs remark-code'>rec <- recipe(<span style='color:#EF8633'>price ~ cut + color + carat + depth + table</span>, <br> data = diamonds) %>%<br> step_log(depth) %>%<br> step_dummy(cut, color)</code> .orange[formula] expression to specify variables --- # Modularity and pipeability ```r price ~ cut + color + carat + log(depth) + table ``` Taking the formula from before we can rewrite it as the following recipe <code class ='r hljs remark-code'>rec <- recipe(price ~ cut + color + carat + depth + table, <br> data = diamonds) %>%<br> <span style='color:#EF8633'>step_log(depth) %>%</span><br> step_dummy(cut, color)</code> then apply .orange[log] transformation on `depth` --- # Modularity and pipeability ```r price ~ cut + color + carat + log(depth) + table ``` Taking the formula from before we can rewrite it as the following recipe <code class ='r hljs remark-code'>rec <- recipe(price ~ cut + color + carat + depth + table, <br> data = diamonds) %>%<br> step_log(depth) %>%<br> <span style='color:#EF8633'>step_dummy(cut, color)</span></code> lastly we create .orange[dummy variables] from `cut` and `color` --- ## Deferred evaluation If we look at the recipe we created we don't see a dataset, but instead, we see a specification ```r rec ``` ``` ## Data Recipe ## ## Inputs: ## ## role #variables ## outcome 1 ## predictor 5 ## ## Operations: ## ## Log transformation on depth ## Dummy variables from cut, color ``` --- ## Deferred evaluation **recipes** gives a specification of the intent of what we want to do. No calculations have been carried out yet. First we need to `prep()` the recipe. This will calculate the sufficient statistics needed to perform each of the steps. ```r prepped_rec <- prep(rec) ``` --- ## Deferred evaluation ```r prepped_rec ``` ``` ## Data Recipe ## ## Inputs: ## ## role #variables ## outcome 1 ## predictor 5 ## ## Training data contained 53940 data points and no missing data. ## ## Operations: ## ## Log transformation on depth [trained] ## Dummy variables from cut, color [trained] ``` --- # Baking After we have prepped the recipe we can `bake()` it to apply all the transformations ```r bake(prepped_rec, new_data = diamonds) ``` ``` ## Rows: 53,940 ## Columns: 14 ## $ carat <dbl> 0.23, 0.21, 0.23, 0.29, 0.31, 0.24, 0.24, 0.26, 0.22, 0.23, 0… ## $ depth <dbl> 4.119037, 4.091006, 4.041295, 4.133565, 4.147885, 4.139955, 4… ## $ table <dbl> 55, 61, 65, 58, 58, 57, 57, 55, 61, 61, 55, 56, 61, 54, 62, 5… ## $ price <int> 326, 326, 327, 334, 335, 336, 336, 337, 337, 338, 339, 340, 3… ## $ cut_1 <dbl> 0.6324555, 0.3162278, -0.3162278, 0.3162278, -0.3162278, 0.00… ## $ cut_2 <dbl> 0.5345225, -0.2672612, -0.2672612, -0.2672612, -0.2672612, -0… ## $ cut_3 <dbl> 3.162278e-01, -6.324555e-01, 6.324555e-01, -6.324555e-01, 6.3… ## $ cut_4 <dbl> 0.1195229, -0.4780914, -0.4780914, -0.4780914, -0.4780914, 0.… ... ``` --- # Baking / Juicing Since the dataset is already calculated after running `prep()` can we use `juice()` to extract it ```r juice(prepped_rec) ``` ``` ## Rows: 53,940 ## Columns: 14 ## $ carat <dbl> 0.23, 0.21, 0.23, 0.29, 0.31, 0.24, 0.24, 0.26, 0.22, 0.23, 0… ## $ depth <dbl> 4.119037, 4.091006, 4.041295, 4.133565, 4.147885, 4.139955, 4… ## $ table <dbl> 55, 61, 65, 58, 58, 57, 57, 55, 61, 61, 55, 56, 61, 54, 62, 5… ## $ price <int> 326, 326, 327, 334, 335, 336, 336, 337, 337, 338, 339, 340, 3… ## $ cut_1 <dbl> 0.6324555, 0.3162278, -0.3162278, 0.3162278, -0.3162278, 0.00… ## $ cut_2 <dbl> 0.5345225, -0.2672612, -0.2672612, -0.2672612, -0.2672612, -0… ## $ cut_3 <dbl> 3.162278e-01, -6.324555e-01, 6.324555e-01, -6.324555e-01, 6.3… ## $ cut_4 <dbl> 0.1195229, -0.4780914, -0.4780914, -0.4780914, -0.4780914, 0.… ... ``` --- .center[ # recipes workflow ] <br> <br> <br> .huge[ .center[ ```r recipe -> prepare -> bake/juice (define) -> (estimate) -> (apply) ``` ] ] --- ## Isolates test & training data When working with data for predictive modeling it is important to make sure any information from the test data leaks into the training data. This is avoided by using **recipes** by making sure you only prep the recipe with the training dataset. --- # Can do things formulas can't --- # selectors .pull-left[ It can be annoying to manually specify variables by name. Use of selectors can greatly help you! ] .pull-right[ <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> step_dummy(all_nominal()) %>%<br> step_zv(all_numeric()) %>%<br> step_center(all_predictors())</code> ] --- # selectors .pull-left[ .orange[`all_nominal()`] is used to select all the nominal variables. ] .pull-right[ <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> step_dummy(<span style='color:#EF8633'>all_nominal()</span>) %>%<br> step_zv(all_numeric()) %>%<br> step_center(all_predictors())</code> ] --- # selectors .pull-left[ .orange[`all_numeric()`] is used to select all the numeric variables. Even the ones generated by .blue[`step_dummy()`] ] .pull-right[ <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> <span style='color:#3381F7'>step_dummy</span>(all_nominal()) %>%<br> step_zv(<span style='color:#EF8633'>all_numeric()</span>) %>%<br> step_center(all_predictors())</code> ] --- # selectors .pull-left[ .orange[`all_predictors()`] is used to select all predictor variables. Will not break even if a variable is removed with .blue[`step_zv()`] ] .pull-right[ <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> step_dummy(all_nominal()) %>%<br> <span style='color:#3381F7'>step_zv</span>(all_numeric()) %>%<br> step_center(<span style='color:#EF8633'>all_predictors()</span>)</code> ] --- # Roles .pull-left[ .orange[`update_role()`] can be used to give variables roles. That then can be selected with .blue[`has_role()`] Roles can also be set with `role = ` argument inside steps ] .pull-right[ <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> <span style='color:#EF8633'>update_role</span>(x, y, z, new_role = "size") %>%<br> step_log(<span style='color:#3381F7'>has_role</span>("size")) %>%<br> step_dummy(all_nominal()) %>%<br> step_zv(all_numeric()) %>%<br> step_center(all_predictors())</code> ] --- ## PCA extraction <code class ='r hljs remark-code'>rec <- recipe(price ~ ., data = diamonds) %>%<br> step_dummy(all_nominal()) %>%<br> step_scale(all_predictors()) %>%<br> step_center(all_predictors()) %>%<br> <span style='color:#EF8633'>step_pca</span>(all_predictors(), <span style='color:#3381F7'>threshold = 0.8</span>)</code> You can also write a recipe that extract enough .orange[principal components] to expain .blue[80% of the variance] Loadings will be kept in the prepped recipe to make sure other datasets are transformed correctly --- ## Imputation **recipes** does by default NOT deal with missing data. There are many steps to perform imputation, some include `step_knnimpute()`, `step_meanimpute()` and `step_medianimpute()` for numerics and `step_unknown()` for factors. --- class: title-slide <br> <br> <br> <br> <br> # Thank you!