Fitting and predicting with parsnip

These examples show how to fit and predict with different combinations of model, mode, and engine. As a reminder, in parsnip,

the model type differentiates basic modeling approaches, such as random forests, logistic regression, linear support vector machines, etc.,
the mode denotes in what kind of modeling context it will be used (most commonly, classification or regression), and
the computational engine indicates how the model is fit, such as with a specific R package implementation or even methods outside of R like Keras or Stan.

The following examples use consistent data sets throughout. For regression, we use the Chicago ridership data. For classification, we use an artificial data set for a binary example and the Palmer penguins data for a multiclass example.

`bart()` models

With the "dbarts" engine

Regression Example (`dbarts`)

We’ll model the ridership on the Chicago elevated trains as a function of the 14 day lagged ridership at two stations. The two predictors are in the same units (rides per day/1000) and do not need to be normalized. All but the last week of data are used for training. The last week will be predicted after the model is fit.

  library(tidymodels)

  ## ── Attaching packages ─────────────────────────── tidymodels 1.2.0.9000 ──

  ## ✔ broom        1.0.5          ✔ rsample      1.2.1     
  ## ✔ dials        1.2.1          ✔ tibble       3.2.1     
  ## ✔ dplyr        1.1.4          ✔ tidyr        1.3.1     
  ## ✔ infer        1.0.7          ✔ tune         1.2.1     
  ## ✔ modeldata    1.3.0          ✔ workflows    1.1.4     
  ## ✔ parsnip      1.2.1.9001     ✔ workflowsets 1.1.0     
  ## ✔ purrr        1.0.2          ✔ yardstick    1.3.1     
  ## ✔ recipes      1.0.10

  ## ── Conflicts ─────────────────────────────────── tidymodels_conflicts() ──
  ## ✖ purrr::discard() masks scales::discard()
  ## ✖ dplyr::filter()  masks stats::filter()
  ## ✖ dplyr::lag()     masks stats::lag()
  ## ✖ recipes::step()  masks stats::step()
  ## • Use suppressPackageStartupMessages() to eliminate package startup messages

  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  bt_reg_spec <- 
    bart(trees = 15) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("dbarts")
  bt_reg_spec

  ## BART Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   trees = 15
  ## 
  ## Computational engine: dbarts

Now we create the model fit object:

  set.seed(1)
  bt_reg_fit <- bt_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  bt_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ## `NULL`()

The holdout data can be predicted:

  predict(bt_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.1 
  ## 2 20.3 
  ## 3 21.3 
  ## 4 20.2 
  ## 5 19.4 
  ## 6  7.51
  ## 7  6.44

Classification Example (`dbarts`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  bt_cls_spec <- 
    bart(trees = 15) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("dbarts")
  bt_cls_spec

  ## 
  ## Call:
  ## NULL

Now we create the model fit object:

  set.seed(1)
  bt_cls_fit <- bt_cls_spec %>% fit(Class ~ ., data = data_train)
  bt_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ## `NULL`()

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(bt_cls_fit, data_test),
    predict(bt_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.352        0.648
  ##  2 Class1             0.823        0.177
  ##  3 Class1             0.497        0.503
  ##  4 Class2             0.509        0.491
  ##  5 Class2             0.434        0.566
  ##  6 Class2             0.185        0.815
  ##  7 Class1             0.663        0.337
  ##  8 Class2             0.392        0.608
  ##  9 Class1             0.967        0.033
  ## 10 Class2             0.095        0.905

`boost_tree()` models

With the "xgboost" engine

Regression Example (`xgboost`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  bt_reg_spec <- 
    boost_tree(trees = 15) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("xgboost")
  bt_reg_spec

  ## Boosted Tree Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   trees = 15
  ## 
  ## Computational engine: xgboost

Now we create the model fit object:

  set.seed(1)
  bt_reg_fit <- bt_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  bt_reg_fit

  ## parsnip model object
  ## 
  ## ##### xgb.Booster
  ## raw: 51.4 Kb 
  ## call:
  ##   xgboost::xgb.train(params = list(eta = 0.3, max_depth = 6, gamma = 0, 
  ##     colsample_bytree = 1, colsample_bynode = 1, min_child_weight = 1, 
  ##     subsample = 1), data = x$data, nrounds = 15, watchlist = x$watchlist, 
  ##     verbose = 0, nthread = 1, objective = "reg:squarederror")
  ## params (as set within xgb.train):
  ##   eta = "0.3", max_depth = "6", gamma = "0", colsample_bytree = "1", colsample_bynode = "1", min_child_weight = "1", subsample = "1", nthread = "1", objective = "reg:squarederror", validate_parameters = "TRUE"
  ## xgb.attributes:
  ##   niter
  ## callbacks:
  ##   cb.evaluation.log()
  ## # of features: 2 
  ## niter: 15
  ## nfeatures : 2 
  ## evaluation_log:
  ##      iter training_rmse
  ##     <num>         <num>
  ##         1     10.481475
  ##         2      7.620929
  ## ---                    
  ##        14      2.551943
  ##        15      2.531085

The holdout data can be predicted:

  predict(bt_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.6 
  ## 2 20.6 
  ## 3 20.2 
  ## 4 20.6 
  ## 5 19.3 
  ## 6  7.26
  ## 7  5.92

Classification Example (`xgboost`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  bt_cls_spec <- 
    boost_tree(trees = 15) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("xgboost")
  bt_cls_spec

  ## Boosted Tree Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   trees = 15
  ## 
  ## Computational engine: xgboost

Now we create the model fit object:

  set.seed(1)
  bt_cls_fit <- bt_cls_spec %>% fit(Class ~ ., data = data_train)
  bt_cls_fit

  ## parsnip model object
  ## 
  ## ##### xgb.Booster
  ## raw: 40.8 Kb 
  ## call:
  ##   xgboost::xgb.train(params = list(eta = 0.3, max_depth = 6, gamma = 0, 
  ##     colsample_bytree = 1, colsample_bynode = 1, min_child_weight = 1, 
  ##     subsample = 1), data = x$data, nrounds = 15, watchlist = x$watchlist, 
  ##     verbose = 0, nthread = 1, objective = "binary:logistic")
  ## params (as set within xgb.train):
  ##   eta = "0.3", max_depth = "6", gamma = "0", colsample_bytree = "1", colsample_bynode = "1", min_child_weight = "1", subsample = "1", nthread = "1", objective = "binary:logistic", validate_parameters = "TRUE"
  ## xgb.attributes:
  ##   niter
  ## callbacks:
  ##   cb.evaluation.log()
  ## # of features: 2 
  ## niter: 15
  ## nfeatures : 2 
  ## evaluation_log:
  ##      iter training_logloss
  ##     <num>            <num>
  ##         1        0.5524619
  ##         2        0.4730697
  ## ---                       
  ##        14        0.2523133
  ##        15        0.2490712

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(bt_cls_fit, data_test),
    predict(bt_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2            0.220        0.780 
  ##  2 Class1            0.931        0.0689
  ##  3 Class1            0.638        0.362 
  ##  4 Class1            0.815        0.185 
  ##  5 Class2            0.292        0.708 
  ##  6 Class2            0.120        0.880 
  ##  7 Class1            0.796        0.204 
  ##  8 Class2            0.392        0.608 
  ##  9 Class1            0.879        0.121 
  ## 10 Class2            0.0389       0.961

With the "C5.0" engine

Classification Example (`C5.0`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  bt_cls_spec <- 
    boost_tree(trees = 15) %>% 
    set_mode("classification") %>% 
    set_engine("C5.0")
  bt_cls_spec

  ## Boosted Tree Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   trees = 15
  ## 
  ## Computational engine: C5.0

Now we create the model fit object:

  set.seed(1)
  bt_cls_fit <- bt_cls_spec %>% fit(Class ~ ., data = data_train)
  bt_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ## C5.0.default(x = x, y = y, trials = 15, control
  ##  = C50::C5.0Control(minCases = 2, sample = 0))
  ## 
  ## Classification Tree
  ## Number of samples: 781 
  ## Number of predictors: 2 
  ## 
  ## Number of boosting iterations: 15 requested;  6 used due to early stopping
  ## Average tree size: 3.2 
  ## 
  ## Non-standard options: attempt to group attributes

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(bt_cls_fit, data_test),
    predict(bt_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.311        0.689
  ##  2 Class1             0.863        0.137
  ##  3 Class1             0.535        0.465
  ##  4 Class2             0.336        0.664
  ##  5 Class2             0.336        0.664
  ##  6 Class2             0.137        0.863
  ##  7 Class2             0.496        0.504
  ##  8 Class2             0.311        0.689
  ##  9 Class1             1            0    
  ## 10 Class2             0            1

`decision_tree()` models

With the "rpart" engine

Regression Example (`rpart`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  dt_reg_spec <- 
    decision_tree(tree_depth = 30) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("rpart")
  dt_reg_spec

  ## Decision Tree Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   tree_depth = 30
  ## 
  ## Computational engine: rpart

Now we create the model fit object:

  set.seed(1)
  dt_reg_fit <- dt_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  dt_reg_fit

  ## parsnip model object
  ## 
  ## n= 5691 
  ## 
  ## node), split, n, deviance, yval
  ##       * denotes terminal node
  ## 
  ## 1) root 5691 244958.800 13.615560  
  ##   2) Quincy_Wells< 2.737 1721  22973.630  5.194394  
  ##     4) Clark_Lake< 5.07 1116  13166.830  4.260215 *
  ##     5) Clark_Lake>=5.07 605   7036.349  6.917607 *
  ##   3) Quincy_Wells>=2.737 3970  47031.540 17.266140  
  ##     6) Clark_Lake< 17.6965 1940  16042.090 15.418210 *
  ##     7) Clark_Lake>=17.6965 2030  18033.560 19.032140 *

The holdout data can be predicted:

  predict(dt_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 19.0 
  ## 2 19.0 
  ## 3 19.0 
  ## 4 19.0 
  ## 5 19.0 
  ## 6  6.92
  ## 7  6.92

Classification Example (`rpart`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  dt_cls_spec <- 
    decision_tree(tree_depth = 30) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("rpart")
  dt_cls_spec

  ## Decision Tree Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   tree_depth = 30
  ## 
  ## Computational engine: rpart

Now we create the model fit object:

  set.seed(1)
  dt_cls_fit <- dt_cls_spec %>% fit(Class ~ ., data = data_train)
  dt_cls_fit

  ## parsnip model object
  ## 
  ## n= 781 
  ## 
  ## node), split, n, loss, yval, (yprob)
  ##       * denotes terminal node
  ## 
  ##  1) root 781 348 Class1 (0.5544174 0.4455826)  
  ##    2) B< 1.495535 400  61 Class1 (0.8475000 0.1525000) *
  ##    3) B>=1.495535 381  94 Class2 (0.2467192 0.7532808)  
  ##      6) B< 2.079458 191  70 Class2 (0.3664921 0.6335079)  
  ##       12) A>=2.572663 48  13 Class1 (0.7291667 0.2708333) *
  ##       13) A< 2.572663 143  35 Class2 (0.2447552 0.7552448) *
  ##      7) B>=2.079458 190  24 Class2 (0.1263158 0.8736842) *

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(dt_cls_fit, data_test),
    predict(dt_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.245        0.755
  ##  2 Class1             0.848        0.152
  ##  3 Class1             0.848        0.152
  ##  4 Class1             0.729        0.271
  ##  5 Class1             0.729        0.271
  ##  6 Class2             0.126        0.874
  ##  7 Class2             0.245        0.755
  ##  8 Class2             0.245        0.755
  ##  9 Class1             0.848        0.152
  ## 10 Class2             0.126        0.874

With the "C5.0" engine

Classification Example (`C5.0`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  dt_cls_spec <- 
    decision_tree(min_n = 2) %>% 
    set_mode("classification") %>% 
    set_engine("C5.0")
  dt_cls_spec

  ## Decision Tree Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   min_n = 2
  ## 
  ## Computational engine: C5.0

Now we create the model fit object:

  set.seed(1)
  dt_cls_fit <- dt_cls_spec %>% fit(Class ~ ., data = data_train)
  dt_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ## C5.0.default(x = x, y = y, trials = 1, control
  ##  = C50::C5.0Control(minCases = 2, sample = 0))
  ## 
  ## Classification Tree
  ## Number of samples: 781 
  ## Number of predictors: 2 
  ## 
  ## Tree size: 4 
  ## 
  ## Non-standard options: attempt to group attributes

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(dt_cls_fit, data_test),
    predict(dt_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.233        0.767
  ##  2 Class1             0.847        0.153
  ##  3 Class1             0.847        0.153
  ##  4 Class1             0.727        0.273
  ##  5 Class1             0.727        0.273
  ##  6 Class2             0.118        0.882
  ##  7 Class2             0.233        0.767
  ##  8 Class2             0.233        0.767
  ##  9 Class1             0.847        0.153
  ## 10 Class2             0.118        0.882

`gen_additive_mod()` models

With the "mgcv" engine

Regression Example (`mgcv`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  gam_reg_spec <- 
    gen_additive_mod(select_features = FALSE, adjust_deg_free = 10) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("mgcv")
  gam_reg_spec

  ## GAM Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   select_features = FALSE
  ##   adjust_deg_free = 10
  ## 
  ## Computational engine: mgcv

Now we create the model fit object:

  set.seed(1)
  gam_reg_fit <- gam_reg_spec %>% 
    fit(ridership ~ Clark_Lake + Quincy_Wells, data = Chicago_train)
  gam_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Family: gaussian 
  ## Link function: identity 
  ## 
  ## Formula:
  ## ridership ~ Clark_Lake + Quincy_Wells
  ## Total model degrees of freedom 3 
  ## 
  ## GCV score: 9.505245

The holdout data can be predicted:

  predict(gam_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.3 
  ## 2 20.5 
  ## 3 20.8 
  ## 4 20.5 
  ## 5 18.8 
  ## 6  7.45
  ## 7  7.02

Classification Example (`mgcv`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  gam_cls_spec <- 
    gen_additive_mod(select_features = FALSE, adjust_deg_free = 10) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("mgcv")
  gam_cls_spec

  ## GAM Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   select_features = FALSE
  ##   adjust_deg_free = 10
  ## 
  ## Computational engine: mgcv

Now we create the model fit object:

  set.seed(1)
  gam_cls_fit <- gam_cls_spec %>% fit(Class ~ A + B, data = data_train)
  gam_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Family: binomial 
  ## Link function: logit 
  ## 
  ## Formula:
  ## Class ~ A + B
  ## Total model degrees of freedom 3 
  ## 
  ## UBRE score: -0.07548008

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(gam_cls_fit, data_test),
    predict(gam_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.518      0.482  
  ##  2 Class1             0.909      0.0913 
  ##  3 Class1             0.648      0.352  
  ##  4 Class1             0.610      0.390  
  ##  5 Class2             0.443      0.557  
  ##  6 Class2             0.206      0.794  
  ##  7 Class1             0.708      0.292  
  ##  8 Class1             0.567      0.433  
  ##  9 Class1             0.994      0.00582
  ## 10 Class2             0.108      0.892

`linear_reg()` models

With the "lm" engine

Regression Example (`lm`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  linreg_reg_spec <- 
    linear_reg() %>% 
    set_engine("lm")
  linreg_reg_spec

  ## Linear Regression Model Specification (regression)
  ## 
  ## Computational engine: lm

Now we create the model fit object:

  set.seed(1)
  linreg_reg_fit <- linreg_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  linreg_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ## stats::lm(formula = ridership ~ ., data = data)
  ## 
  ## Coefficients:
  ##  (Intercept)    Clark_Lake  Quincy_Wells  
  ##       1.6624        0.7738        0.2557

The holdout data can be predicted:

  predict(linreg_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.3 
  ## 2 20.5 
  ## 3 20.8 
  ## 4 20.5 
  ## 5 18.8 
  ## 6  7.45
  ## 7  7.02

With the "glm" engine

Regression Example (`glm`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  linreg_reg_spec <- 
    linear_reg() %>% 
    set_engine("glm")
  linreg_reg_spec

  ## Linear Regression Model Specification (regression)
  ## 
  ## Computational engine: glm

Now we create the model fit object:

  set.seed(1)
  linreg_reg_fit <- linreg_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  linreg_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:  stats::glm(formula = ridership ~ ., family = stats::gaussian, 
  ##     data = data)
  ## 
  ## Coefficients:
  ##  (Intercept)    Clark_Lake  Quincy_Wells  
  ##       1.6624        0.7738        0.2557  
  ## 
  ## Degrees of Freedom: 5690 Total (i.e. Null);  5688 Residual
  ## Null Deviance:     245000 
  ## Residual Deviance: 53530   AIC: 28910

The holdout data can be predicted:

  predict(linreg_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.3 
  ## 2 20.5 
  ## 3 20.8 
  ## 4 20.5 
  ## 5 18.8 
  ## 6  7.45
  ## 7  7.02

With the "glmnet" engine

Regression Example (`glmnet`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  linreg_reg_spec <- 
    linear_reg(penalty = 0.1) %>% 
    set_engine("glmnet")
  linreg_reg_spec

  ## Linear Regression Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   penalty = 0.1
  ## 
  ## Computational engine: glmnet

Now we create the model fit object:

  set.seed(1)
  linreg_reg_fit <- linreg_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  linreg_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:  glmnet::glmnet(x = maybe_matrix(x), y = y, family = "gaussian") 
  ## 
  ##    Df  %Dev Lambda
  ## 1   0  0.00 5.7970
  ## 2   1 13.25 5.2820
  ## 3   1 24.26 4.8130
  ## 4   1 33.40 4.3850
  ## 5   1 40.98 3.9960
  ## 6   1 47.28 3.6410
  ## 7   1 52.51 3.3170
  ## 8   1 56.85 3.0220
  ## 9   1 60.45 2.7540
  ## 10  1 63.44 2.5090
  ## 11  1 65.92 2.2860
  ## 12  1 67.99 2.0830
  ## 13  1 69.70 1.8980
  ## 14  1 71.12 1.7300
  ## 15  1 72.30 1.5760
  ## 16  2 73.29 1.4360
  ## 17  2 74.11 1.3080
  ## 18  2 74.80 1.1920
  ## 19  2 75.37 1.0860
  ## 20  2 75.84 0.9897
  ## 21  2 76.23 0.9018
  ## 22  2 76.56 0.8217
  ## 23  2 76.83 0.7487
  ## 24  2 77.05 0.6822
  ## 25  2 77.24 0.6216
  ## 26  2 77.39 0.5664
  ## 27  2 77.52 0.5160
  ## 28  2 77.63 0.4702
  ## 29  2 77.72 0.4284
  ## 30  2 77.79 0.3904
  ## 31  2 77.85 0.3557
  ## 32  2 77.90 0.3241
  ## 33  2 77.94 0.2953
  ## 34  2 77.98 0.2691
  ## 35  2 78.01 0.2452
  ## 36  2 78.03 0.2234
  ## 37  2 78.05 0.2035
  ## 38  2 78.07 0.1855
  ## 39  2 78.08 0.1690
  ## 40  2 78.09 0.1540
  ## 41  2 78.10 0.1403
  ## 42  2 78.11 0.1278
  ## 43  2 78.12 0.1165
  ## 44  2 78.12 0.1061
  ## 45  2 78.13 0.0967
  ## 46  2 78.13 0.0881
  ## 47  2 78.13 0.0803
  ## 48  2 78.14 0.0732
  ## 49  2 78.14 0.0666
  ## 50  2 78.14 0.0607
  ## 51  2 78.14 0.0553
  ## 52  2 78.14 0.0504
  ## 53  2 78.14 0.0459
  ## 54  2 78.15 0.0419
  ## 55  2 78.15 0.0381

The holdout data can be predicted:

  predict(linreg_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.2 
  ## 2 20.4 
  ## 3 20.7 
  ## 4 20.4 
  ## 5 18.7 
  ## 6  7.57
  ## 7  7.15

With the "keras" engine

Regression Example (`keras`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  linreg_reg_spec <- 
    linear_reg(penalty = 0.1) %>% 
    set_engine("keras")
  linreg_reg_spec

  ## Linear Regression Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   penalty = 0.1
  ## 
  ## Computational engine: keras

Now we create the model fit object:

  set.seed(1)
  linreg_reg_fit <- linreg_reg_spec %>% fit(ridership ~ ., data = Chicago_train)

  ## Epoch 1/20
  ## 178/178 - 0s - loss: 756.3401 - 466ms/epoch - 3ms/step
  ## Epoch 2/20
  ## 178/178 - 0s - loss: 525.8923 - 168ms/epoch - 943us/step
  ## Epoch 3/20
  ## 178/178 - 0s - loss: 396.4454 - 154ms/epoch - 865us/step
  ## Epoch 4/20
  ## 178/178 - 0s - loss: 319.8469 - 164ms/epoch - 920us/step
  ## Epoch 5/20
  ## 178/178 - 0s - loss: 272.5901 - 152ms/epoch - 856us/step
  ## Epoch 6/20
  ## 178/178 - 0s - loss: 242.4278 - 151ms/epoch - 847us/step
  ## Epoch 7/20
  ## 178/178 - 0s - loss: 222.5514 - 148ms/epoch - 834us/step
  ## Epoch 8/20
  ## 178/178 - 0s - loss: 208.8100 - 149ms/epoch - 836us/step
  ## Epoch 9/20
  ## 178/178 - 0s - loss: 198.3248 - 149ms/epoch - 838us/step
  ## Epoch 10/20
  ## 178/178 - 0s - loss: 188.6236 - 150ms/epoch - 843us/step
  ## Epoch 11/20
  ## 178/178 - 0s - loss: 176.7256 - 149ms/epoch - 837us/step
  ## Epoch 12/20
  ## 178/178 - 0s - loss: 158.0104 - 150ms/epoch - 843us/step
  ## Epoch 13/20
  ## 178/178 - 0s - loss: 126.3732 - 150ms/epoch - 842us/step
  ## Epoch 14/20
  ## 178/178 - 0s - loss: 81.3748 - 149ms/epoch - 838us/step
  ## Epoch 15/20
  ## 178/178 - 0s - loss: 39.2055 - 149ms/epoch - 839us/step
  ## Epoch 16/20
  ## 178/178 - 0s - loss: 17.2765 - 149ms/epoch - 838us/step
  ## Epoch 17/20
  ## 178/178 - 0s - loss: 11.2830 - 152ms/epoch - 852us/step
  ## Epoch 18/20
  ## 178/178 - 0s - loss: 10.3650 - 150ms/epoch - 843us/step
  ## Epoch 19/20
  ## 178/178 - 0s - loss: 10.2656 - 149ms/epoch - 837us/step
  ## Epoch 20/20
  ## 178/178 - 0s - loss: 10.2522 - 149ms/epoch - 837us/step

  linreg_reg_fit

  ## parsnip model object
  ## 
  ## Model: "sequential"
  ## __________________________________________________________________________
  ##  Layer (type)                    Output Shape                 Param #     
  ## ==========================================================================
  ##  dense (Dense)                   (None, 1)                    3           
  ##  dense_1 (Dense)                 (None, 1)                    2           
  ## ==========================================================================
  ## Total params: 5 (20.00 Byte)
  ## Trainable params: 5 (20.00 Byte)
  ## Non-trainable params: 0 (0.00 Byte)
  ## __________________________________________________________________________

The holdout data can be predicted:

  predict(linreg_reg_fit, Chicago_test)

  ## 1/1 - 0s - 48ms/epoch - 48ms/step

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 19.7 
  ## 2 19.7 
  ## 3 20.0 
  ## 4 19.8 
  ## 5 18.2 
  ## 6  7.92
  ## 7  7.26

With the "stan" engine

Regression Example (`stan`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  linreg_reg_spec <- 
    linear_reg() %>% 
    set_engine("stan")
  linreg_reg_spec

  ## Linear Regression Model Specification (regression)
  ## 
  ## Computational engine: stan

Now we create the model fit object:

  set.seed(1)
  linreg_reg_fit <- linreg_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  linreg_reg_fit

  ## parsnip model object
  ## 
  ## stan_glm
  ##  family:       gaussian [identity]
  ##  formula:      ridership ~ .
  ##  observations: 5691
  ##  predictors:   3
  ## ------
  ##              Median MAD_SD
  ## (Intercept)  1.7    0.1   
  ## Clark_Lake   0.8    0.0   
  ## Quincy_Wells 0.3    0.1   
  ## 
  ## Auxiliary parameter(s):
  ##       Median MAD_SD
  ## sigma 3.1    0.0   
  ## 
  ## ------
  ## * For help interpreting the printed output see ?print.stanreg
  ## * For info on the priors used see ?prior_summary.stanreg

The holdout data can be predicted:

  predict(linreg_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.3 
  ## 2 20.5 
  ## 3 20.8 
  ## 4 20.5 
  ## 5 18.8 
  ## 6  7.45
  ## 7  7.02

`logistic_reg()` models

With the "glm" engine

Classification Example (`glm`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  logreg_cls_spec <- 
    logistic_reg() %>% 
    set_engine("glm")
  logreg_cls_spec

  ## Logistic Regression Model Specification (classification)
  ## 
  ## Computational engine: glm

Now we create the model fit object:

  set.seed(1)
  logreg_cls_fit <- logreg_cls_spec %>% fit(Class ~ ., data = data_train)
  logreg_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:  stats::glm(formula = Class ~ ., family = stats::binomial, data = data)
  ## 
  ## Coefficients:
  ## (Intercept)            A            B  
  ##      -3.755       -1.259        3.855  
  ## 
  ## Degrees of Freedom: 780 Total (i.e. Null);  778 Residual
  ## Null Deviance:     1073 
  ## Residual Deviance: 662.1   AIC: 668.1

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(logreg_cls_fit, data_test),
    predict(logreg_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.518      0.482  
  ##  2 Class1             0.909      0.0913 
  ##  3 Class1             0.648      0.352  
  ##  4 Class1             0.610      0.390  
  ##  5 Class2             0.443      0.557  
  ##  6 Class2             0.206      0.794  
  ##  7 Class1             0.708      0.292  
  ##  8 Class1             0.567      0.433  
  ##  9 Class1             0.994      0.00582
  ## 10 Class2             0.108      0.892

With the "glmnet" engine

Classification Example (`glmnet`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  logreg_cls_spec <- 
    logistic_reg(penalty = 0.1) %>% 
    set_engine("glmnet")
  logreg_cls_spec

  ## Logistic Regression Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   penalty = 0.1
  ## 
  ## Computational engine: glmnet

Now we create the model fit object:

  set.seed(1)
  logreg_cls_fit <- logreg_cls_spec %>% fit(Class ~ ., data = data_train)
  logreg_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:  glmnet::glmnet(x = maybe_matrix(x), y = y, family = "binomial") 
  ## 
  ##    Df  %Dev   Lambda
  ## 1   0  0.00 0.308500
  ## 2   1  4.76 0.281100
  ## 3   1  8.75 0.256100
  ## 4   1 12.13 0.233300
  ## 5   1 15.01 0.212600
  ## 6   1 17.50 0.193700
  ## 7   1 19.64 0.176500
  ## 8   1 21.49 0.160800
  ## 9   1 23.10 0.146500
  ## 10  1 24.49 0.133500
  ## 11  1 25.71 0.121700
  ## 12  1 26.76 0.110900
  ## 13  1 27.67 0.101000
  ## 14  1 28.46 0.092030
  ## 15  1 29.15 0.083860
  ## 16  1 29.74 0.076410
  ## 17  1 30.25 0.069620
  ## 18  1 30.70 0.063430
  ## 19  1 31.08 0.057800
  ## 20  1 31.40 0.052660
  ## 21  1 31.68 0.047990
  ## 22  1 31.92 0.043720
  ## 23  1 32.13 0.039840
  ## 24  2 32.70 0.036300
  ## 25  2 33.50 0.033070
  ## 26  2 34.18 0.030140
  ## 27  2 34.78 0.027460
  ## 28  2 35.29 0.025020
  ## 29  2 35.72 0.022800
  ## 30  2 36.11 0.020770
  ## 31  2 36.43 0.018930
  ## 32  2 36.71 0.017250
  ## 33  2 36.96 0.015710
  ## 34  2 37.16 0.014320
  ## 35  2 37.34 0.013050
  ## 36  2 37.49 0.011890
  ## 37  2 37.62 0.010830
  ## 38  2 37.73 0.009868
  ## 39  2 37.82 0.008992
  ## 40  2 37.90 0.008193
  ## 41  2 37.97 0.007465
  ## 42  2 38.02 0.006802
  ## 43  2 38.07 0.006198
  ## 44  2 38.11 0.005647
  ## 45  2 38.15 0.005145
  ## 46  2 38.18 0.004688
  ## 47  2 38.20 0.004272
  ## 48  2 38.22 0.003892
  ## 49  2 38.24 0.003547
  ## 50  2 38.25 0.003231
  ## 51  2 38.26 0.002944
  ## 52  2 38.27 0.002683
  ## 53  2 38.28 0.002444
  ## 54  2 38.29 0.002227
  ## 55  2 38.29 0.002029
  ## 56  2 38.30 0.001849
  ## 57  2 38.30 0.001685
  ## 58  2 38.31 0.001535
  ## 59  2 38.31 0.001399
  ## 60  2 38.31 0.001275
  ## 61  2 38.31 0.001161
  ## 62  2 38.32 0.001058
  ## 63  2 38.32 0.000964
  ## 64  2 38.32 0.000879
  ## 65  2 38.32 0.000800

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(logreg_cls_fit, data_test),
    predict(logreg_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.530        0.470
  ##  2 Class1             0.713        0.287
  ##  3 Class1             0.616        0.384
  ##  4 Class2             0.416        0.584
  ##  5 Class2             0.417        0.583
  ##  6 Class2             0.288        0.712
  ##  7 Class1             0.554        0.446
  ##  8 Class1             0.557        0.443
  ##  9 Class1             0.820        0.180
  ## 10 Class2             0.206        0.794

With the "keras" engine

Classification Example (`keras`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  logreg_cls_spec <- 
    logistic_reg(penalty = 0.1) %>% 
    set_engine("keras")
  logreg_cls_spec

  ## Logistic Regression Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   penalty = 0.1
  ## 
  ## Computational engine: keras

Now we create the model fit object:

  set.seed(1)
  logreg_cls_fit <- logreg_cls_spec %>% fit(Class ~ ., data = data_train)

  ## Epoch 1/20
  ## 25/25 - 0s - loss: 1.3291 - 380ms/epoch - 15ms/step
  ## Epoch 2/20
  ## 25/25 - 0s - loss: 1.2536 - 23ms/epoch - 938us/step
  ## Epoch 3/20
  ## 25/25 - 0s - loss: 1.1870 - 23ms/epoch - 938us/step
  ## Epoch 4/20
  ## 25/25 - 0s - loss: 1.1256 - 23ms/epoch - 934us/step
  ## Epoch 5/20
  ## 25/25 - 0s - loss: 1.0727 - 24ms/epoch - 962us/step
  ## Epoch 6/20
  ## 25/25 - 0s - loss: 1.0241 - 23ms/epoch - 938us/step
  ## Epoch 7/20
  ## 25/25 - 0s - loss: 0.9821 - 24ms/epoch - 949us/step
  ## Epoch 8/20
  ## 25/25 - 0s - loss: 0.9442 - 24ms/epoch - 947us/step
  ## Epoch 9/20
  ## 25/25 - 0s - loss: 0.9108 - 24ms/epoch - 947us/step
  ## Epoch 10/20
  ## 25/25 - 0s - loss: 0.8810 - 25ms/epoch - 990us/step
  ## Epoch 11/20
  ## 25/25 - 0s - loss: 0.8560 - 24ms/epoch - 959us/step
  ## Epoch 12/20
  ## 25/25 - 0s - loss: 0.8336 - 24ms/epoch - 956us/step
  ## Epoch 13/20
  ## 25/25 - 0s - loss: 0.8138 - 24ms/epoch - 964us/step
  ## Epoch 14/20
  ## 25/25 - 0s - loss: 0.7973 - 24ms/epoch - 957us/step
  ## Epoch 15/20
  ## 25/25 - 0s - loss: 0.7827 - 24ms/epoch - 949us/step
  ## Epoch 16/20
  ## 25/25 - 0s - loss: 0.7695 - 27ms/epoch - 1ms/step
  ## Epoch 17/20
  ## 25/25 - 0s - loss: 0.7588 - 26ms/epoch - 1ms/step
  ## Epoch 18/20
  ## 25/25 - 0s - loss: 0.7488 - 26ms/epoch - 1ms/step
  ## Epoch 19/20
  ## 25/25 - 0s - loss: 0.7405 - 27ms/epoch - 1ms/step
  ## Epoch 20/20
  ## 25/25 - 0s - loss: 0.7330 - 25ms/epoch - 1ms/step

  logreg_cls_fit

  ## parsnip model object
  ## 
  ## Model: "sequential_1"
  ## __________________________________________________________________________
  ##  Layer (type)                    Output Shape                 Param #     
  ## ==========================================================================
  ##  dense_2 (Dense)                 (None, 1)                    3           
  ##  dense_3 (Dense)                 (None, 2)                    4           
  ## ==========================================================================
  ## Total params: 7 (28.00 Byte)
  ## Trainable params: 7 (28.00 Byte)
  ## Non-trainable params: 0 (0.00 Byte)
  ## __________________________________________________________________________

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(logreg_cls_fit, data_test),
    predict(logreg_cls_fit, data_test, type = "prob")
  )

  ## 1/1 - 0s - 31ms/epoch - 31ms/step
  ## 1/1 - 0s - 13ms/epoch - 13ms/step

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.339        0.661
  ##  2 Class2             0.350        0.650
  ##  3 Class2             0.418        0.582
  ##  4 Class2             0.133        0.867
  ##  5 Class2             0.200        0.800
  ##  6 Class2             0.146        0.854
  ##  7 Class2             0.261        0.739
  ##  8 Class2             0.357        0.643
  ##  9 Class2             0.201        0.799
  ## 10 Class2             0.105        0.895

With the "LiblineaR" engine

Classification Example (`LiblineaR`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  logreg_cls_spec <- 
    logistic_reg(penalty = 0.1) %>% 
    set_engine("LiblineaR")
  logreg_cls_spec

  ## Logistic Regression Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   penalty = 0.1
  ## 
  ## Computational engine: LiblineaR

Now we create the model fit object:

  set.seed(1)
  logreg_cls_fit <- logreg_cls_spec %>% fit(Class ~ ., data = data_train)
  logreg_cls_fit

  ## parsnip model object
  ## 
  ## $TypeDetail
  ## [1] "L2-regularized logistic regression primal (L2R_LR)"
  ## 
  ## $Type
  ## [1] 0
  ## 
  ## $W
  ##             A         B     Bias
  ## [1,] 1.219818 -3.759034 3.674861
  ## 
  ## $Bias
  ## [1] 1
  ## 
  ## $ClassNames
  ## [1] Class1 Class2
  ## Levels: Class1 Class2
  ## 
  ## $NbClass
  ## [1] 2
  ## 
  ## attr(,"class")
  ## [1] "LiblineaR"

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(logreg_cls_fit, data_test),
    predict(logreg_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.517      0.483  
  ##  2 Class1             0.904      0.0964 
  ##  3 Class1             0.645      0.355  
  ##  4 Class1             0.604      0.396  
  ##  5 Class2             0.442      0.558  
  ##  6 Class2             0.210      0.790  
  ##  7 Class1             0.702      0.298  
  ##  8 Class1             0.565      0.435  
  ##  9 Class1             0.993      0.00667
  ## 10 Class2             0.112      0.888

With the "stan" engine

Classification Example (`stan`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  logreg_cls_spec <- 
    logistic_reg() %>% 
    set_engine("stan")
  logreg_cls_spec

  ## Logistic Regression Model Specification (classification)
  ## 
  ## Computational engine: stan

Now we create the model fit object:

  set.seed(1)
  logreg_cls_fit <- logreg_cls_spec %>% fit(Class ~ ., data = data_train)
  logreg_cls_fit

  ## parsnip model object
  ## 
  ## stan_glm
  ##  family:       binomial [logit]
  ##  formula:      Class ~ .
  ##  observations: 781
  ##  predictors:   3
  ## ------
  ##             Median MAD_SD
  ## (Intercept) -3.8    0.3  
  ## A           -1.3    0.2  
  ## B            3.9    0.3  
  ## 
  ## ------
  ## * For help interpreting the printed output see ?print.stanreg
  ## * For info on the priors used see ?prior_summary.stanreg

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(logreg_cls_fit, data_test),
    predict(logreg_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.518      0.482  
  ##  2 Class1             0.909      0.0909 
  ##  3 Class1             0.650      0.350  
  ##  4 Class1             0.609      0.391  
  ##  5 Class2             0.443      0.557  
  ##  6 Class2             0.206      0.794  
  ##  7 Class1             0.708      0.292  
  ##  8 Class1             0.568      0.432  
  ##  9 Class1             0.994      0.00580
  ## 10 Class2             0.108      0.892

`mars()` models

With the "earth" engine

Regression Example (`earth`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  mars_reg_spec <- 
    mars(prod_degree = 1, prune_method = "backward") %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("earth")
  mars_reg_spec

  ## MARS Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   prod_degree = 1
  ##   prune_method = backward
  ## 
  ## Computational engine: earth

Now we create the model fit object:

  set.seed(1)
  mars_reg_fit <- mars_reg_spec %>% fit(ridership ~ ., data = Chicago_train)

  ## 
  ## Attaching package: 'plotrix'

  ## The following object is masked from 'package:scales':
  ## 
  ##     rescale

  mars_reg_fit

  ## parsnip model object
  ## 
  ## Selected 5 of 6 terms, and 2 of 2 predictors
  ## Termination condition: RSq changed by less than 0.001 at 6 terms
  ## Importance: Clark_Lake, Quincy_Wells
  ## Number of terms at each degree of interaction: 1 4 (additive model)
  ## GCV 9.085818    RSS 51543.98    GRSq 0.7889881    RSq 0.789581

The holdout data can be predicted:

  predict(mars_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.4 
  ## 2 20.7 
  ## 3 21.0 
  ## 4 20.7 
  ## 5 19.0 
  ## 6  7.99
  ## 7  6.68

Classification Example (`earth`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  mars_cls_spec <- 
    mars(prod_degree = 1, prune_method = "backward") %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("earth")
  mars_cls_spec

  ## MARS Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   prod_degree = 1
  ##   prune_method = backward
  ## 
  ## Computational engine: earth

Now we create the model fit object:

  set.seed(1)
  mars_cls_fit <- mars_cls_spec %>% fit(Class ~ ., data = data_train)
  mars_cls_fit

  ## parsnip model object
  ## 
  ## GLM (family binomial, link logit):
  ##  nulldev  df       dev  df   devratio     AIC iters converged
  ##  1073.43 780   632.723 775      0.411   644.7     5         1
  ## 
  ## Earth selected 6 of 13 terms, and 2 of 2 predictors
  ## Termination condition: Reached nk 21
  ## Importance: B, A
  ## Number of terms at each degree of interaction: 1 5 (additive model)
  ## Earth GCV 0.1334948    RSS 101.3432    GRSq 0.461003    RSq 0.4747349

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(mars_cls_fit, data_test),
    predict(mars_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2            0.332       0.668  
  ##  2 Class1            0.845       0.155  
  ##  3 Class1            0.585       0.415  
  ##  4 Class1            0.690       0.310  
  ##  5 Class2            0.483       0.517  
  ##  6 Class2            0.318       0.682  
  ##  7 Class1            0.661       0.339  
  ##  8 Class2            0.398       0.602  
  ##  9 Class1            0.990       0.00972
  ## 10 Class2            0.0625      0.938

`mlp()` models

With the "nnet" engine

Regression Example (`nnet`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  mlp_reg_spec <- 
    mlp(penalty = 0, epochs = 100) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("nnet")
  mlp_reg_spec

  ## Single Layer Neural Network Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   penalty = 0
  ##   epochs = 100
  ## 
  ## Computational engine: nnet

Now we create the model fit object:

  set.seed(1)
  mlp_reg_fit <- mlp_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  mlp_reg_fit

  ## parsnip model object
  ## 
  ## a 2-5-1 network with 21 weights
  ## inputs: Clark_Lake Quincy_Wells 
  ## output(s): ridership 
  ## options were - linear output units

The holdout data can be predicted:

  predict(mlp_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.5 
  ## 2 20.8 
  ## 3 21.1 
  ## 4 20.8 
  ## 5 18.8 
  ## 6  8.09
  ## 7  6.22

Classification Example (`nnet`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  mlp_cls_spec <- 
    mlp(penalty = 0, epochs = 100) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("nnet")
  mlp_cls_spec

  ## Single Layer Neural Network Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   penalty = 0
  ##   epochs = 100
  ## 
  ## Computational engine: nnet

Now we create the model fit object:

  set.seed(1)
  mlp_cls_fit <- mlp_cls_spec %>% fit(Class ~ ., data = data_train)
  mlp_cls_fit

  ## parsnip model object
  ## 
  ## a 2-5-1 network with 21 weights
  ## inputs: A B 
  ## output(s): Class 
  ## options were - entropy fitting

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(mlp_cls_fit, data_test),
    predict(mlp_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.364        0.636
  ##  2 Class1             0.691        0.309
  ##  3 Class1             0.577        0.423
  ##  4 Class1             0.686        0.314
  ##  5 Class2             0.466        0.534
  ##  6 Class2             0.339        0.661
  ##  7 Class1             0.670        0.330
  ##  8 Class2             0.384        0.616
  ##  9 Class1             0.692        0.308
  ## 10 Class2             0.330        0.670

With the "keras" engine

Regression Example (`keras`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  mlp_reg_spec <- 
    mlp(penalty = 0, epochs = 20) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("keras")
  mlp_reg_spec

  ## Single Layer Neural Network Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   penalty = 0
  ##   epochs = 20
  ## 
  ## Computational engine: keras

Now we create the model fit object:

  set.seed(1)
  mlp_reg_fit <- mlp_reg_spec %>% fit(ridership ~ ., data = Chicago_train)

  ## Epoch 1/20
  ## 178/178 - 0s - loss: 227.1692 - 447ms/epoch - 3ms/step
  ## Epoch 2/20
  ## 178/178 - 0s - loss: 195.0656 - 158ms/epoch - 889us/step
  ## Epoch 3/20
  ## 178/178 - 0s - loss: 179.2528 - 156ms/epoch - 878us/step
  ## Epoch 4/20
  ## 178/178 - 0s - loss: 167.7030 - 158ms/epoch - 890us/step
  ## Epoch 5/20
  ## 178/178 - 0s - loss: 158.9285 - 165ms/epoch - 929us/step
  ## Epoch 6/20
  ## 178/178 - 0s - loss: 151.0857 - 158ms/epoch - 886us/step
  ## Epoch 7/20
  ## 178/178 - 0s - loss: 143.8481 - 156ms/epoch - 877us/step
  ## Epoch 8/20
  ## 178/178 - 0s - loss: 137.0743 - 157ms/epoch - 883us/step
  ## Epoch 9/20
  ## 178/178 - 0s - loss: 130.6889 - 157ms/epoch - 881us/step
  ## Epoch 10/20
  ## 178/178 - 0s - loss: 124.6528 - 157ms/epoch - 883us/step
  ## Epoch 11/20
  ## 178/178 - 0s - loss: 118.9300 - 159ms/epoch - 895us/step
  ## Epoch 12/20
  ## 178/178 - 0s - loss: 113.4896 - 157ms/epoch - 882us/step
  ## Epoch 13/20
  ## 178/178 - 0s - loss: 108.3090 - 156ms/epoch - 876us/step
  ## Epoch 14/20
  ## 178/178 - 0s - loss: 103.3597 - 157ms/epoch - 882us/step
  ## Epoch 15/20
  ## 178/178 - 0s - loss: 98.6057 - 157ms/epoch - 882us/step
  ## Epoch 16/20
  ## 178/178 - 0s - loss: 94.0230 - 156ms/epoch - 879us/step
  ## Epoch 17/20
  ## 178/178 - 0s - loss: 89.5978 - 156ms/epoch - 879us/step
  ## Epoch 18/20
  ## 178/178 - 0s - loss: 85.2963 - 157ms/epoch - 883us/step
  ## Epoch 19/20
  ## 178/178 - 0s - loss: 81.0430 - 168ms/epoch - 943us/step
  ## Epoch 20/20
  ## 178/178 - 0s - loss: 76.8973 - 158ms/epoch - 887us/step

  mlp_reg_fit

  ## parsnip model object
  ## 
  ## Model: "sequential_2"
  ## __________________________________________________________________________
  ##  Layer (type)                    Output Shape                 Param #     
  ## ==========================================================================
  ##  dense_4 (Dense)                 (None, 5)                    15          
  ##  dense_5 (Dense)                 (None, 1)                    6           
  ## ==========================================================================
  ## Total params: 21 (84.00 Byte)
  ## Trainable params: 21 (84.00 Byte)
  ## Non-trainable params: 0 (0.00 Byte)
  ## __________________________________________________________________________

The holdout data can be predicted:

  predict(mlp_reg_fit, Chicago_test)

  ## 1/1 - 0s - 30ms/epoch - 30ms/step

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1  7.78
  ## 2  7.78
  ## 3  7.78
  ## 4  7.78
  ## 5  7.78
  ## 6  7.12
  ## 7  6.97

Classification Example (`keras`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  mlp_cls_spec <- 
    mlp(penalty = 0, epochs = 20) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("keras")
  mlp_cls_spec

  ## Single Layer Neural Network Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   penalty = 0
  ##   epochs = 20
  ## 
  ## Computational engine: keras

Now we create the model fit object:

  set.seed(1)
  mlp_cls_fit <- mlp_cls_spec %>% fit(Class ~ ., data = data_train)

  ## Epoch 1/20
  ## 25/25 - 0s - loss: 0.7280 - 347ms/epoch - 14ms/step
  ## Epoch 2/20
  ## 25/25 - 0s - loss: 0.7196 - 25ms/epoch - 1ms/step
  ## Epoch 3/20
  ## 25/25 - 0s - loss: 0.7124 - 24ms/epoch - 957us/step
  ## Epoch 4/20
  ## 25/25 - 0s - loss: 0.7059 - 24ms/epoch - 959us/step
  ## Epoch 5/20
  ## 25/25 - 0s - loss: 0.7005 - 24ms/epoch - 963us/step
  ## Epoch 6/20
  ## 25/25 - 0s - loss: 0.6957 - 24ms/epoch - 977us/step
  ## Epoch 7/20
  ## 25/25 - 0s - loss: 0.6913 - 25ms/epoch - 984us/step
  ## Epoch 8/20
  ## 25/25 - 0s - loss: 0.6874 - 25ms/epoch - 982us/step
  ## Epoch 9/20
  ## 25/25 - 0s - loss: 0.6837 - 25ms/epoch - 980us/step
  ## Epoch 10/20
  ## 25/25 - 0s - loss: 0.6802 - 24ms/epoch - 974us/step
  ## Epoch 11/20
  ## 25/25 - 0s - loss: 0.6770 - 118ms/epoch - 5ms/step
  ## Epoch 12/20
  ## 25/25 - 0s - loss: 0.6739 - 25ms/epoch - 1ms/step
  ## Epoch 13/20
  ## 25/25 - 0s - loss: 0.6709 - 24ms/epoch - 978us/step
  ## Epoch 14/20
  ## 25/25 - 0s - loss: 0.6679 - 25ms/epoch - 984us/step
  ## Epoch 15/20
  ## 25/25 - 0s - loss: 0.6649 - 25ms/epoch - 986us/step
  ## Epoch 16/20
  ## 25/25 - 0s - loss: 0.6620 - 24ms/epoch - 974us/step
  ## Epoch 17/20
  ## 25/25 - 0s - loss: 0.6590 - 24ms/epoch - 977us/step
  ## Epoch 18/20
  ## 25/25 - 0s - loss: 0.6560 - 26ms/epoch - 1ms/step
  ## Epoch 19/20
  ## 25/25 - 0s - loss: 0.6530 - 24ms/epoch - 973us/step
  ## Epoch 20/20
  ## 25/25 - 0s - loss: 0.6499 - 24ms/epoch - 971us/step

  mlp_cls_fit

  ## parsnip model object
  ## 
  ## Model: "sequential_3"
  ## __________________________________________________________________________
  ##  Layer (type)                    Output Shape                 Param #     
  ## ==========================================================================
  ##  dense_6 (Dense)                 (None, 5)                    15          
  ##  dense_7 (Dense)                 (None, 2)                    12          
  ## ==========================================================================
  ## Total params: 27 (108.00 Byte)
  ## Trainable params: 27 (108.00 Byte)
  ## Non-trainable params: 0 (0.00 Byte)
  ## __________________________________________________________________________

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(mlp_cls_fit, data_test),
    predict(mlp_cls_fit, data_test, type = "prob")
  )

  ## 1/1 - 0s - 31ms/epoch - 31ms/step
  ## 1/1 - 0s - 13ms/epoch - 13ms/step

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.532        0.468
  ##  2 Class1             0.585        0.415
  ##  3 Class1             0.568        0.432
  ##  4 Class2             0.465        0.535
  ##  5 Class2             0.479        0.521
  ##  6 Class2             0.442        0.558
  ##  7 Class1             0.524        0.476
  ##  8 Class1             0.542        0.458
  ##  9 Class1             0.596        0.404
  ## 10 Class2             0.418        0.582

`multinom_reg()` models

With the "glmnet" engine

Classification Example (`glmnet`)

We’ll predict the island where the penguins were observed with two variables in the same unit (mm): bill length and bill depth.

library(tidymodels)
tidymodels_prefer()
data(penguins)

penguins <- penguins %>% select(island, starts_with("bill_"))
penguins_train <- penguins[-c(21, 153, 31, 277, 1), ]
penguins_test  <- penguins[ c(21, 153, 31, 277, 1), ]

We can define the model with specific parameters:

mr_cls_spec <- 
  multinom_reg(penalty = 0.1) %>% 
  set_engine("glmnet")
mr_cls_spec

## Multinomial Regression Model Specification (classification)
## 
## Main Arguments:
##   penalty = 0.1
## 
## Computational engine: glmnet

Now we create the model fit object:

set.seed(1)
mr_cls_fit <- mr_cls_spec %>% fit(island ~ ., data = penguins_train)
mr_cls_fit

## parsnip model object
## 
## 
## Call:  glmnet::glmnet(x = maybe_matrix(x), y = y, family = "multinomial") 
## 
##    Df  %Dev  Lambda
## 1   0  0.00 0.31730
## 2   1  3.43 0.28910
## 3   1  6.30 0.26340
## 4   1  8.74 0.24000
## 5   1 10.83 0.21870
## 6   1 12.62 0.19930
## 7   1 14.17 0.18160
## 8   1 15.51 0.16540
## 9   1 16.67 0.15070
## 10  1 17.68 0.13740
## 11  1 18.56 0.12520
## 12  2 19.93 0.11400
## 13  2 21.31 0.10390
## 14  2 22.50 0.09467
## 15  2 23.52 0.08626
## 16  2 24.40 0.07860
## 17  2 25.16 0.07162
## 18  2 25.81 0.06526
## 19  2 26.37 0.05946
## 20  2 26.86 0.05418
## 21  2 27.27 0.04936
## 22  2 27.63 0.04498
## 23  2 27.94 0.04098
## 24  2 28.21 0.03734
## 25  2 28.44 0.03402
## 26  2 28.63 0.03100
## 27  2 28.80 0.02825
## 28  2 28.94 0.02574
## 29  2 29.06 0.02345
## 30  2 29.17 0.02137
## 31  2 29.26 0.01947
## 32  2 29.33 0.01774
## 33  2 29.39 0.01616
## 34  2 29.45 0.01473
## 35  2 29.49 0.01342
## 36  2 29.53 0.01223
## 37  2 29.56 0.01114
## 38  2 29.59 0.01015
## 39  2 29.61 0.00925
## 40  2 29.63 0.00843
## 41  2 29.65 0.00768
## 42  2 29.67 0.00700
## 43  2 29.68 0.00638
## 44  2 29.69 0.00581
## 45  2 29.70 0.00529
## 46  2 29.71 0.00482
## 47  2 29.71 0.00439
## 48  2 29.72 0.00400
## 49  2 29.72 0.00365
## 50  2 29.73 0.00332
## 51  2 29.73 0.00303
## 52  2 29.74 0.00276
## 53  2 29.74 0.00251
## 54  2 29.74 0.00229
## 55  2 29.75 0.00209
## 56  2 29.75 0.00190
## 57  2 29.75 0.00173
## 58  2 29.75 0.00158
## 59  2 29.75 0.00144
## 60  2 29.75 0.00131

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

bind_cols(
  predict(mr_cls_fit, penguins_test),
  predict(mr_cls_fit, penguins_test, type = "prob")
)

## # A tibble: 5 × 4
##   .pred_class .pred_Biscoe .pred_Dream .pred_Torgersen
##   <fct>              <dbl>       <dbl>           <dbl>
## 1 Dream              0.339      0.448           0.214 
## 2 Biscoe             0.879      0.0882          0.0331
## 3 Biscoe             0.539      0.317           0.144 
## 4 Dream              0.403      0.435           0.162 
## 5 Dream              0.297      0.481           0.221

With the "keras" engine

Classification Example (`keras`)

We’ll predict the island where the penguins were observed with two variables in the same unit (mm): bill length and bill depth.

library(tidymodels)
tidymodels_prefer()
data(penguins)

penguins <- penguins %>% select(island, starts_with("bill_"))
penguins_train <- penguins[-c(21, 153, 31, 277, 1), ]
penguins_test  <- penguins[ c(21, 153, 31, 277, 1), ]

We can define the model with specific parameters:

mr_cls_spec <- 
  multinom_reg(penalty = 0.1) %>% 
  set_engine("keras")
mr_cls_spec

## Multinomial Regression Model Specification (classification)
## 
## Main Arguments:
##   penalty = 0.1
## 
## Computational engine: keras

Now we create the model fit object:

set.seed(1)
mr_cls_fit <- mr_cls_spec %>% fit(island ~ ., data = penguins_train)

## Epoch 1/20
## 11/11 - 0s - loss: 19.0873 - 345ms/epoch - 31ms/step
## Epoch 2/20
## 11/11 - 0s - loss: 18.4665 - 11ms/epoch - 1ms/step
## Epoch 3/20
## 11/11 - 0s - loss: 17.8459 - 11ms/epoch - 1ms/step
## Epoch 4/20
## 11/11 - 0s - loss: 17.2520 - 11ms/epoch - 1ms/step
## Epoch 5/20
## 11/11 - 0s - loss: 16.6553 - 11ms/epoch - 1ms/step
## Epoch 6/20
## 11/11 - 0s - loss: 16.0837 - 11ms/epoch - 1ms/step
## Epoch 7/20
## 11/11 - 0s - loss: 15.5205 - 11ms/epoch - 1ms/step
## Epoch 8/20
## 11/11 - 0s - loss: 14.9723 - 11ms/epoch - 1ms/step
## Epoch 9/20
## 11/11 - 0s - loss: 14.4344 - 11ms/epoch - 1ms/step
## Epoch 10/20
## 11/11 - 0s - loss: 13.9115 - 11ms/epoch - 1ms/step
## Epoch 11/20
## 11/11 - 0s - loss: 13.4085 - 11ms/epoch - 1ms/step
## Epoch 12/20
## 11/11 - 0s - loss: 12.9193 - 11ms/epoch - 1ms/step
## Epoch 13/20
## 11/11 - 0s - loss: 12.4340 - 11ms/epoch - 1ms/step
## Epoch 14/20
## 11/11 - 0s - loss: 11.9760 - 11ms/epoch - 999us/step
## Epoch 15/20
## 11/11 - 0s - loss: 11.5234 - 11ms/epoch - 1ms/step
## Epoch 16/20
## 11/11 - 0s - loss: 11.0957 - 11ms/epoch - 997us/step
## Epoch 17/20
## 11/11 - 0s - loss: 10.6776 - 11ms/epoch - 1ms/step
## Epoch 18/20
## 11/11 - 0s - loss: 10.2835 - 11ms/epoch - 1ms/step
## Epoch 19/20
## 11/11 - 0s - loss: 9.9111 - 11ms/epoch - 1ms/step
## Epoch 20/20
## 11/11 - 0s - loss: 9.5595 - 11ms/epoch - 1ms/step

mr_cls_fit

## parsnip model object
## 
## Model: "sequential_4"
## __________________________________________________________________________
##  Layer (type)                    Output Shape                 Param #     
## ==========================================================================
##  dense_8 (Dense)                 (None, 1)                    3           
##  dense_9 (Dense)                 (None, 3)                    6           
## ==========================================================================
## Total params: 9 (36.00 Byte)
## Trainable params: 9 (36.00 Byte)
## Non-trainable params: 0 (0.00 Byte)
## __________________________________________________________________________

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

bind_cols(
  predict(mr_cls_fit, penguins_test),
  predict(mr_cls_fit, penguins_test, type = "prob")
)

## 1/1 - 0s - 29ms/epoch - 29ms/step
## 1/1 - 0s - 13ms/epoch - 13ms/step

## # A tibble: 5 × 4
##   .pred_class .pred_Biscoe .pred_Dream .pred_Torgersen
##   <fct>              <dbl>       <dbl>           <dbl>
## 1 Dream           8.36e-18           1        1.41e-11
## 2 Dream           3.16e-21           1        9.95e-14
## 3 Dream           1.76e-18           1        5.29e-12
## 4 Dream           1.33e-21           1        5.77e-14
## 5 Dream           2.16e-18           1        6.02e-12

With the "nnet" engine

Classification Example (`nnet`)

We’ll predict the island where the penguins were observed with two variables in the same unit (mm): bill length and bill depth.

library(tidymodels)
tidymodels_prefer()
data(penguins)

penguins <- penguins %>% select(island, starts_with("bill_"))
penguins_train <- penguins[-c(21, 153, 31, 277, 1), ]
penguins_test  <- penguins[ c(21, 153, 31, 277, 1), ]

We can define the model with specific parameters:

mr_cls_spec <- 
  multinom_reg(penalty = 0.1) %>% 
  set_engine("nnet")
mr_cls_spec

## Multinomial Regression Model Specification (classification)
## 
## Main Arguments:
##   penalty = 0.1
## 
## Computational engine: nnet

Now we create the model fit object:

set.seed(1)
mr_cls_fit <- mr_cls_spec %>% fit(island ~ ., data = penguins_train)
mr_cls_fit

## parsnip model object
## 
## Call:
## nnet::multinom(formula = island ~ ., data = data, decay = ~0.1, 
##     trace = FALSE)
## 
## Coefficients:
##           (Intercept) bill_length_mm bill_depth_mm
## Dream       -8.243575     -0.0580960     0.6168318
## Torgersen   -1.610588     -0.2789588     0.6978480
## 
## Residual Deviance: 502.5009 
## AIC: 514.5009

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

bind_cols(
  predict(mr_cls_fit, penguins_test),
  predict(mr_cls_fit, penguins_test, type = "prob")
)

## # A tibble: 5 × 4
##   .pred_class .pred_Biscoe .pred_Dream .pred_Torgersen
##   <fct>              <dbl>       <dbl>           <dbl>
## 1 Dream              0.193      0.450          0.357  
## 2 Biscoe             0.937      0.0582         0.00487
## 3 Biscoe             0.462      0.364          0.174  
## 4 Dream              0.450      0.495          0.0556 
## 5 Dream              0.183      0.506          0.311

`nearest_neighbor()` models

With the "kknn" engine

Regression Example (`kknn`)

library(tidymodels)
tidymodels_prefer()
data(Chicago)

n <- nrow(Chicago)
Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)

Chicago_train <- Chicago[1:(n - 7), ]
Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

knn_reg_spec <-
  nearest_neighbor(neighbors = 5, weight_func = "triangular") %>%
  # This model can be used for classification or regression, so set mode
  set_mode("regression") %>%
  set_engine("kknn")
knn_reg_spec

## K-Nearest Neighbor Model Specification (regression)
## 
## Main Arguments:
##   neighbors = 5
##   weight_func = triangular
## 
## Computational engine: kknn

Now we create the model fit object:

knn_reg_fit <- knn_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
knn_reg_fit

## parsnip model object
## 
## 
## Call:
## kknn::train.kknn(formula = ridership ~ ., data = data, ks = min_rows(5,     data, 5), kernel = ~"triangular")
## 
## Type of response variable: continuous
## minimal mean absolute error: 1.79223
## Minimal mean squared error: 11.21809
## Best kernel: triangular
## Best k: 5

The holdout data can be predicted:

predict(knn_reg_fit, Chicago_test)

## # A tibble: 7 × 1
##   .pred
##   <dbl>
## 1 20.5 
## 2 21.1 
## 3 21.4 
## 4 21.8 
## 5 19.5 
## 6  7.83
## 7  5.54

Classification Example (`kknn`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

library(tidymodels)
tidymodels_prefer()
data(two_class_dat)

data_train <- two_class_dat[-(1:10), ]
data_test  <- two_class_dat[  1:10 , ]

Since there are two classes, we’ll use an odd number of neighbors to avoid ties:

knn_cls_spec <-
  nearest_neighbor(neighbors = 11, weight_func = "triangular") %>%
  # This model can be used for classification or regression, so set mode
  set_mode("classification") %>%
  set_engine("kknn")
knn_cls_spec

## K-Nearest Neighbor Model Specification (classification)
## 
## Main Arguments:
##   neighbors = 11
##   weight_func = triangular
## 
## Computational engine: kknn

Now we create the model fit object:

knn_cls_fit <- knn_cls_spec %>% fit(Class ~ ., data = data_train)
knn_cls_fit

## parsnip model object
## 
## 
## Call:
## kknn::train.kknn(formula = Class ~ ., data = data, ks = min_rows(11,     data, 5), kernel = ~"triangular")
## 
## Type of response variable: nominal
## Minimal misclassification: 0.1869398
## Best kernel: triangular
## Best k: 11

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

bind_cols(
  predict(knn_cls_fit, data_test),
  predict(knn_cls_fit, data_test, type = "prob")
)

## # A tibble: 10 × 3
##    .pred_class .pred_Class1 .pred_Class2
##    <fct>              <dbl>        <dbl>
##  1 Class2            0.177       0.823  
##  2 Class1            0.995       0.00515
##  3 Class1            0.590       0.410  
##  4 Class1            0.770       0.230  
##  5 Class2            0.333       0.667  
##  6 Class2            0.182       0.818  
##  7 Class1            0.692       0.308  
##  8 Class2            0.400       0.600  
##  9 Class1            0.814       0.186  
## 10 Class2            0.0273      0.973

`rand_forest()` models

With the "ranger" engine

Regression Example (`ranger`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  rf_reg_spec <- 
    rand_forest(trees = 200, min_n = 5) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("ranger")
  rf_reg_spec

  ## Random Forest Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   trees = 200
  ##   min_n = 5
  ## 
  ## Computational engine: ranger

Now we create the model fit object:

  set.seed(1)
  rf_reg_fit <- rf_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  rf_reg_fit

  ## parsnip model object
  ## 
  ## Ranger result
  ## 
  ## Call:
  ##  ranger::ranger(x = maybe_data_frame(x), y = y, num.trees = ~200,      min.node.size = min_rows(~5, x), num.threads = 1, verbose = FALSE,      seed = sample.int(10^5, 1)) 
  ## 
  ## Type:                             Regression 
  ## Number of trees:                  200 
  ## Sample size:                      5691 
  ## Number of independent variables:  2 
  ## Mtry:                             1 
  ## Target node size:                 5 
  ## Variable importance mode:         none 
  ## Splitrule:                        variance 
  ## OOB prediction error (MSE):       9.72953 
  ## R squared (OOB):                  0.7739986

The holdout data can be predicted:

  predict(rf_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.4 
  ## 2 21.5 
  ## 3 20.8 
  ## 4 21.6 
  ## 5 19.4 
  ## 6  7.32
  ## 7  6.03

Classification Example (`ranger`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  rf_cls_spec <- 
    rand_forest(trees = 200, min_n = 5) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("ranger")
  rf_cls_spec

  ## Random Forest Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   trees = 200
  ##   min_n = 5
  ## 
  ## Computational engine: ranger

Now we create the model fit object:

  set.seed(1)
  rf_cls_fit <- rf_cls_spec %>% fit(Class ~ ., data = data_train)
  rf_cls_fit

  ## parsnip model object
  ## 
  ## Ranger result
  ## 
  ## Call:
  ##  ranger::ranger(x = maybe_data_frame(x), y = y, num.trees = ~200,      min.node.size = min_rows(~5, x), num.threads = 1, verbose = FALSE,      seed = sample.int(10^5, 1), probability = TRUE) 
  ## 
  ## Type:                             Probability estimation 
  ## Number of trees:                  200 
  ## Sample size:                      781 
  ## Number of independent variables:  2 
  ## Mtry:                             1 
  ## Target node size:                 5 
  ## Variable importance mode:         none 
  ## Splitrule:                        gini 
  ## OOB prediction error (Brier s.):  0.1534794

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(rf_cls_fit, data_test),
    predict(rf_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2           0.274         0.725 
  ##  2 Class1           0.928         0.0716
  ##  3 Class2           0.497         0.503 
  ##  4 Class1           0.703         0.297 
  ##  5 Class2           0.302         0.698 
  ##  6 Class2           0.151         0.849 
  ##  7 Class1           0.701         0.299 
  ##  8 Class1           0.592         0.409 
  ##  9 Class1           0.752         0.248 
  ## 10 Class2           0.00225       0.998

With the "randomForest" engine

Regression Example (`randomForest`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  rf_reg_spec <- 
    rand_forest(trees = 200, min_n = 5) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("randomForest")
  rf_reg_spec

  ## Random Forest Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   trees = 200
  ##   min_n = 5
  ## 
  ## Computational engine: randomForest

Now we create the model fit object:

  set.seed(1)
  rf_reg_fit <- rf_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  rf_reg_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ##  randomForest(x = maybe_data_frame(x), y = y, ntree = ~200, nodesize = min_rows(~5,      x)) 
  ##                Type of random forest: regression
  ##                      Number of trees: 200
  ## No. of variables tried at each split: 1
  ## 
  ##           Mean of squared residuals: 9.696736
  ##                     % Var explained: 77.47

The holdout data can be predicted:

  predict(rf_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.4 
  ## 2 21.6 
  ## 3 20.9 
  ## 4 21.6 
  ## 5 19.3 
  ## 6  7.33
  ## 7  6.16

Classification Example (`randomForest`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  rf_cls_spec <- 
    rand_forest(trees = 200, min_n = 5) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("randomForest")
  rf_cls_spec

  ## Random Forest Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   trees = 200
  ##   min_n = 5
  ## 
  ## Computational engine: randomForest

Now we create the model fit object:

  set.seed(1)
  rf_cls_fit <- rf_cls_spec %>% fit(Class ~ ., data = data_train)
  rf_cls_fit

  ## parsnip model object
  ## 
  ## 
  ## Call:
  ##  randomForest(x = maybe_data_frame(x), y = y, ntree = ~200, nodesize = min_rows(~5,      x)) 
  ##                Type of random forest: classification
  ##                      Number of trees: 200
  ## No. of variables tried at each split: 1
  ## 
  ##         OOB estimate of  error rate: 19.72%
  ## Confusion matrix:
  ##        Class1 Class2 class.error
  ## Class1    363     70   0.1616628
  ## Class2     84    264   0.2413793

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(rf_cls_fit, data_test),
    predict(rf_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class2             0.23         0.77 
  ##  2 Class1             0.95         0.05 
  ##  3 Class1             0.59         0.41 
  ##  4 Class1             0.75         0.25 
  ##  5 Class2             0.305        0.695
  ##  6 Class2             0.105        0.895
  ##  7 Class1             0.685        0.315
  ##  8 Class1             0.63         0.37 
  ##  9 Class1             0.79         0.21 
  ## 10 Class2             0.02         0.98

`svm_linear()` models

With the "LiblineaR" engine

Regression Example (`LiblineaR`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  svm_reg_spec <- 
    svm_linear(cost = 1, margin = 0.1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("LiblineaR")
  svm_reg_spec

  ## Linear Support Vector Machine Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ##   margin = 0.1
  ## 
  ## Computational engine: LiblineaR

Now we create the model fit object:

  set.seed(1)
  svm_reg_fit <- svm_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
  svm_reg_fit

  ## parsnip model object
  ## 
  ## $TypeDetail
  ## [1] "L2-regularized L2-loss support vector regression primal (L2R_L2LOSS_SVR)"
  ## 
  ## $Type
  ## [1] 11
  ## 
  ## $W
  ##      Clark_Lake Quincy_Wells       Bias
  ## [1,]  0.8277352    0.3430336 0.05042585
  ## 
  ## $Bias
  ## [1] 1
  ## 
  ## $NbClass
  ## [1] 2
  ## 
  ## attr(,"class")
  ## [1] "LiblineaR"

The holdout data can be predicted:

  predict(svm_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 20.6 
  ## 2 20.8 
  ## 3 21.1 
  ## 4 20.8 
  ## 5 18.9 
  ## 6  6.40
  ## 7  5.90

Classification Example (`LiblineaR`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  svm_cls_spec <- 
    svm_linear(cost = 1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("LiblineaR")
  svm_cls_spec

  ## Linear Support Vector Machine Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ## 
  ## Computational engine: LiblineaR

Now we create the model fit object:

  set.seed(1)
  svm_cls_fit <- svm_cls_spec %>% fit(Class ~ ., data = data_train)
  svm_cls_fit

  ## parsnip model object
  ## 
  ## $TypeDetail
  ## [1] "L2-regularized L2-loss support vector classification dual (L2R_L2LOSS_SVC_DUAL)"
  ## 
  ## $Type
  ## [1] 1
  ## 
  ## $W
  ##              A         B     Bias
  ## [1,] 0.4067922 -1.314783 1.321851
  ## 
  ## $Bias
  ## [1] 1
  ## 
  ## $ClassNames
  ## [1] Class1 Class2
  ## Levels: Class1 Class2
  ## 
  ## $NbClass
  ## [1] 2
  ## 
  ## attr(,"class")
  ## [1] "LiblineaR"

The holdout data can be predicted for hard class predictions.

  predict(svm_cls_fit, data_test)

  ## # A tibble: 10 × 1
  ##    .pred_class
  ##    <fct>      
  ##  1 Class1     
  ##  2 Class1     
  ##  3 Class1     
  ##  4 Class1     
  ##  5 Class2     
  ##  6 Class2     
  ##  7 Class1     
  ##  8 Class1     
  ##  9 Class1     
  ## 10 Class2

With the "kernlab" engine

Regression Example (`kernlab`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  svm_reg_spec <- 
    svm_linear(cost = 1, margin = 0.1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("kernlab")
  svm_reg_spec

  ## Linear Support Vector Machine Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ##   margin = 0.1
  ## 
  ## Computational engine: kernlab

Now we create the model fit object:

  set.seed(1)
  svm_reg_fit <- svm_reg_spec %>% fit(ridership ~ ., data = Chicago_train)

  ##  Setting default kernel parameters

  svm_reg_fit

  ## parsnip model object
  ## 
  ## Support Vector Machine object of class "ksvm" 
  ## 
  ## SV type: eps-svr  (regression) 
  ##  parameter : epsilon = 0.1  cost C = 1 
  ## 
  ## Linear (vanilla) kernel function. 
  ## 
  ## Number of Support Vectors : 2283 
  ## 
  ## Objective Function Value : -825.1632 
  ## Training error : 0.226456

The holdout data can be predicted:

  predict(svm_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 21.0 
  ## 2 21.2 
  ## 3 21.5 
  ## 4 21.2 
  ## 5 19.4 
  ## 6  6.87
  ## 7  6.41

Classification Example (`kernlab`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  svm_cls_spec <- 
    svm_linear(cost = 1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("kernlab")
  svm_cls_spec

  ## Linear Support Vector Machine Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ## 
  ## Computational engine: kernlab

Now we create the model fit object:

  set.seed(1)
  svm_cls_fit <- svm_cls_spec %>% fit(Class ~ ., data = data_train)

  ##  Setting default kernel parameters

  svm_cls_fit

  ## parsnip model object
  ## 
  ## Support Vector Machine object of class "ksvm" 
  ## 
  ## SV type: C-svc  (classification) 
  ##  parameter : cost C = 1 
  ## 
  ## Linear (vanilla) kernel function. 
  ## 
  ## Number of Support Vectors : 353 
  ## 
  ## Objective Function Value : -349.425 
  ## Training error : 0.174136 
  ## Probability model included.

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(svm_cls_fit, data_test),
    predict(svm_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.517      0.483  
  ##  2 Class1             0.904      0.0956 
  ##  3 Class1             0.645      0.355  
  ##  4 Class1             0.610      0.390  
  ##  5 Class2             0.445      0.555  
  ##  6 Class2             0.212      0.788  
  ##  7 Class1             0.704      0.296  
  ##  8 Class1             0.565      0.435  
  ##  9 Class1             0.994      0.00646
  ## 10 Class2             0.114      0.886

`svm_poly()` models

With the "kernlab" engine

Regression Example (`kernlab`)

  library(tidymodels)
  tidymodels_prefer()
  data(Chicago)
  
  n <- nrow(Chicago)
  Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)
  
  Chicago_train <- Chicago[1:(n - 7), ]
  Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

  svm_reg_spec <- 
    svm_poly(cost = 1, margin = 0.1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("regression") %>% 
    set_engine("kernlab")
  svm_reg_spec

  ## Polynomial Support Vector Machine Model Specification (regression)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ##   margin = 0.1
  ## 
  ## Computational engine: kernlab

Now we create the model fit object:

  set.seed(1)
  svm_reg_fit <- svm_reg_spec %>% fit(ridership ~ ., data = Chicago_train)

  ##  Setting default kernel parameters

  svm_reg_fit

  ## parsnip model object
  ## 
  ## Support Vector Machine object of class "ksvm" 
  ## 
  ## SV type: eps-svr  (regression) 
  ##  parameter : epsilon = 0.1  cost C = 1 
  ## 
  ## Polynomial kernel function. 
  ##  Hyperparameters : degree =  1  scale =  1  offset =  1 
  ## 
  ## Number of Support Vectors : 2283 
  ## 
  ## Objective Function Value : -825.1628 
  ## Training error : 0.226471

The holdout data can be predicted:

  predict(svm_reg_fit, Chicago_test)

  ## # A tibble: 7 × 1
  ##   .pred
  ##   <dbl>
  ## 1 21.0 
  ## 2 21.2 
  ## 3 21.5 
  ## 4 21.2 
  ## 5 19.4 
  ## 6  6.87
  ## 7  6.41

Classification Example (`kernlab`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

  library(tidymodels)
  tidymodels_prefer()
  data(two_class_dat)
  
  data_train <- two_class_dat[-(1:10), ]
  data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

  svm_cls_spec <- 
    svm_poly(cost = 1) %>% 
    # This model can be used for classification or regression, so set mode
    set_mode("classification") %>% 
    set_engine("kernlab")
  svm_cls_spec

  ## Polynomial Support Vector Machine Model Specification (classification)
  ## 
  ## Main Arguments:
  ##   cost = 1
  ## 
  ## Computational engine: kernlab

Now we create the model fit object:

  set.seed(1)
  svm_cls_fit <- svm_cls_spec %>% fit(Class ~ ., data = data_train)

  ##  Setting default kernel parameters

  svm_cls_fit

  ## parsnip model object
  ## 
  ## Support Vector Machine object of class "ksvm" 
  ## 
  ## SV type: C-svc  (classification) 
  ##  parameter : cost C = 1 
  ## 
  ## Polynomial kernel function. 
  ##  Hyperparameters : degree =  1  scale =  1  offset =  1 
  ## 
  ## Number of Support Vectors : 353 
  ## 
  ## Objective Function Value : -349.425 
  ## Training error : 0.174136 
  ## Probability model included.

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

  bind_cols(
    predict(svm_cls_fit, data_test),
    predict(svm_cls_fit, data_test, type = "prob")
  )

  ## # A tibble: 10 × 3
  ##    .pred_class .pred_Class1 .pred_Class2
  ##    <fct>              <dbl>        <dbl>
  ##  1 Class1             0.517      0.483  
  ##  2 Class1             0.904      0.0956 
  ##  3 Class1             0.645      0.355  
  ##  4 Class1             0.610      0.390  
  ##  5 Class2             0.445      0.555  
  ##  6 Class2             0.212      0.788  
  ##  7 Class1             0.704      0.296  
  ##  8 Class1             0.565      0.435  
  ##  9 Class1             0.994      0.00646
  ## 10 Class2             0.114      0.886

`svm_rbf()` models

With the "kernlab" engine

Regression Example (`kernlab`)

library(tidymodels)
tidymodels_prefer()
data(Chicago)

n <- nrow(Chicago)
Chicago <- Chicago %>% select(ridership, Clark_Lake, Quincy_Wells)

Chicago_train <- Chicago[1:(n - 7), ]
Chicago_test <- Chicago[(n - 6):n, ]

We can define the model with specific parameters:

svm_reg_spec <- 
  svm_rbf(cost = 1, margin = 0.1) %>% 
  # This model can be used for classification or regression, so set mode
  set_mode("regression") %>% 
  set_engine("kernlab")
svm_reg_spec

## Radial Basis Function Support Vector Machine Model Specification (regression)
## 
## Main Arguments:
##   cost = 1
##   margin = 0.1
## 
## Computational engine: kernlab

Now we create the model fit object:

set.seed(1)
svm_reg_fit <- svm_reg_spec %>% fit(ridership ~ ., data = Chicago_train)
svm_reg_fit

## parsnip model object
## 
## Support Vector Machine object of class "ksvm" 
## 
## SV type: eps-svr  (regression) 
##  parameter : epsilon = 0.1  cost C = 1 
## 
## Gaussian Radial Basis kernel function. 
##  Hyperparameter : sigma =  10.8262370251485 
## 
## Number of Support Vectors : 2233 
## 
## Objective Function Value : -746.584 
## Training error : 0.205567

The holdout data can be predicted:

predict(svm_reg_fit, Chicago_test)

## # A tibble: 7 × 1
##   .pred
##   <dbl>
## 1 20.7 
## 2 21.2 
## 3 21.3 
## 4 21.1 
## 5 19.4 
## 6  6.77
## 7  6.13

Classification Example (`kernlab`)

The example data has two predictors and an outcome with two classes. Both predictors are in the same units.

library(tidymodels)
tidymodels_prefer()
data(two_class_dat)

data_train <- two_class_dat[-(1:10), ]
data_test  <- two_class_dat[  1:10 , ]

We can define the model with specific parameters:

svm_cls_spec <- 
  svm_rbf(cost = 1) %>% 
  # This model can be used for classification or regression, so set mode
  set_mode("classification") %>% 
  set_engine("kernlab")
svm_cls_spec

## Radial Basis Function Support Vector Machine Model Specification (classification)
## 
## Main Arguments:
##   cost = 1
## 
## Computational engine: kernlab

Now we create the model fit object:

set.seed(1)
svm_cls_fit <- svm_cls_spec %>% fit(Class ~ ., data = data_train)
svm_cls_fit

## parsnip model object
## 
## Support Vector Machine object of class "ksvm" 
## 
## SV type: C-svc  (classification) 
##  parameter : cost C = 1 
## 
## Gaussian Radial Basis kernel function. 
##  Hyperparameter : sigma =  1.63216688499952 
## 
## Number of Support Vectors : 327 
## 
## Objective Function Value : -294.4344 
## Training error : 0.169014 
## Probability model included.

The holdout data can be predicted for both hard class predictions and probabilities. We’ll bind these together into one tibble:

bind_cols(
  predict(svm_cls_fit, data_test),
  predict(svm_cls_fit, data_test, type = "prob")
)

## # A tibble: 10 × 3
##    .pred_class .pred_Class1 .pred_Class2
##    <fct>              <dbl>        <dbl>
##  1 Class2             0.238       0.762 
##  2 Class1             0.905       0.0950
##  3 Class1             0.619       0.381 
##  4 Class1             0.879       0.121 
##  5 Class1             0.641       0.359 
##  6 Class2             0.153       0.847 
##  7 Class1             0.745       0.255 
##  8 Class2             0.313       0.687 
##  9 Class1             0.878       0.122 
## 10 Class2             0.137       0.863

bart() models

Regression Example (dbarts)

Classification Example (dbarts)

boost_tree() models

Regression Example (xgboost)

Classification Example (xgboost)

Classification Example (C5.0)

decision_tree() models

Regression Example (rpart)

Classification Example (rpart)

Classification Example (C5.0)

gen_additive_mod() models

Regression Example (mgcv)

Classification Example (mgcv)

linear_reg() models

Regression Example (lm)

Regression Example (glm)

Regression Example (glmnet)

Regression Example (keras)

Regression Example (stan)

logistic_reg() models

Classification Example (glm)

Classification Example (glmnet)

Classification Example (keras)

Classification Example (LiblineaR)

Classification Example (stan)

mars() models

Regression Example (earth)

Classification Example (earth)

mlp() models

Regression Example (nnet)

Classification Example (nnet)

Regression Example (keras)

Classification Example (keras)

multinom_reg() models

Classification Example (glmnet)

Classification Example (keras)

Classification Example (nnet)

nearest_neighbor() models

Regression Example (kknn)

Classification Example (kknn)

rand_forest() models

Regression Example (ranger)

Classification Example (ranger)

Regression Example (randomForest)

Classification Example (randomForest)

svm_linear() models

Regression Example (LiblineaR)

Classification Example (LiblineaR)

Regression Example (kernlab)

Classification Example (kernlab)

svm_poly() models

Regression Example (kernlab)

Classification Example (kernlab)

svm_rbf() models

Regression Example (kernlab)

Classification Example (kernlab)

`bart()` models

Regression Example (`dbarts`)

Classification Example (`dbarts`)

`boost_tree()` models

Regression Example (`xgboost`)

Classification Example (`xgboost`)

Classification Example (`C5.0`)

`decision_tree()` models

Regression Example (`rpart`)

Classification Example (`rpart`)

Classification Example (`C5.0`)

`gen_additive_mod()` models

Regression Example (`mgcv`)

Classification Example (`mgcv`)

`linear_reg()` models

Regression Example (`lm`)

Regression Example (`glm`)

Regression Example (`glmnet`)

Regression Example (`keras`)

Regression Example (`stan`)

`logistic_reg()` models

Classification Example (`glm`)

Classification Example (`glmnet`)

Classification Example (`keras`)

Classification Example (`LiblineaR`)

Classification Example (`stan`)

`mars()` models

Regression Example (`earth`)

Classification Example (`earth`)

`mlp()` models

Regression Example (`nnet`)

Classification Example (`nnet`)

Regression Example (`keras`)

Classification Example (`keras`)

`multinom_reg()` models

Classification Example (`glmnet`)

Classification Example (`keras`)

Classification Example (`nnet`)

`nearest_neighbor()` models

Regression Example (`kknn`)

Classification Example (`kknn`)

`rand_forest()` models

Regression Example (`ranger`)

Classification Example (`ranger`)

Regression Example (`randomForest`)

Classification Example (`randomForest`)

`svm_linear()` models

Regression Example (`LiblineaR`)

Classification Example (`LiblineaR`)

Regression Example (`kernlab`)

Classification Example (`kernlab`)

`svm_poly()` models

Regression Example (`kernlab`)

Classification Example (`kernlab`)

`svm_rbf()` models

Regression Example (`kernlab`)

Classification Example (`kernlab`)