Package 'rules'

Title: Model Wrappers for Rule-Based Models
Description: Bindings for additional models for use with the 'parsnip' package. Models include prediction rule ensembles (Friedman and Popescu, 2008) <doi:10.1214/07-AOAS148>, C5.0 rules (Quinlan, 1992 ISBN: 1558602380), and Cubist (Kuhn and Johnson, 2013) <doi:10.1007/978-1-4614-6849-3>.
Authors: Emil Hvitfeldt [aut, cre] , Max Kuhn [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <[email protected]>
License: MIT + file LICENSE
Version: 1.0.2.9000
Built: 2024-11-15 06:24:26 UTC
Source: https://github.com/tidymodels/rules

Help Index

Parameter functions for Cubist models

Description

Committee-based models enact a boosting-like procedure to produce ensembles. committees parameter is for the number of models in the ensembles while max_rules can be used to limit the number of possible rules.

Usage

committees(range = c(1L, 100L), trans = NULL)

max_rules(range = c(1L, 500L), trans = NULL)

Arguments

range

A two-element vector holding the defaults for the smallest and largest possible values, respectively.
trans

A trans object from the scales package, such as scales::log10_trans() or scales::reciprocal_trans(). If not provided, the default is used which matches the units used in range. If no transformation, NULL.

Value

A function with classes "quant_param" and "param"

Examples

committees()
committees(4:5)

max_rules()

multi_predict() methods for rule-based models

Description

multi_predict() methods for rule-based models

Usage

## S3 method for class ''_cubist''
multi_predict(object, new_data, type = NULL, neighbors = NULL, ...)

## S3 method for class ''_xrf''
multi_predict(object, new_data, type = NULL, penalty = NULL, ...)

Arguments

object

A model_fit object.
new_data

A rectangular data object, such as a data frame.
type

A single character value or NULL. This argument is ignored in the method for ⁠_cubist⁠ objects and is handled internally (since type = "numeric" is always used).
neighbors

A numeric vector of neighbors values between zero and nine.
...

Not currently used.
penalty

Non-negative penalty values.

Turn C5.0 and rule-based models into tidy tibbles

Description

Turn C5.0 and rule-based models into tidy tibbles

Usage

## S3 method for class 'C5.0'
tidy(x, trees = x$trials["Actual"], ...)

## S3 method for class 'cubist'
tidy(x, committees = x$committee, ...)

## S3 method for class 'xrf'
tidy(x, penalty = NULL, unit = c("rules", "columns"), ...)

Arguments

x

A Cubist, C5.0, or xrf object.
trees

The number of boosting iterations to tidy (defaults to the entire ensemble).
...

Not currently used.
committees

The number of committees to tidy (defaults to the entire ensemble).
penalty

A single numeric value for the lambda penalty value.
unit

What data should be returned? For unit = 'rules', each row corresponds to a rule. For unit = 'columns', each row is a predictor column. The latter can be helpful when determining variable importance.

Details

The outputs for these tidy functions are different since the model structures are different.

Let’s look at Cubist and RuleFit first, using the Ames data, then C5.0 with a different data set.

An example using the Ames data

First we will fit a Cubist model and tidy it: 

library(tidymodels)
library(rules)
library(rlang)

data(ames, package = "modeldata")

ames <- ames %>% 
  mutate(Sale_Price = log10(Sale_Price)) %>% 
  select(Sale_Price, Longitude, Latitude, Central_Air)

cb_fit <-
  cubist_rules(committees = 10) %>%
  set_engine("Cubist") %>%
  fit(Sale_Price ~ ., data = ames)

cb_res <- tidy(cb_fit)

cb_res

## # A tibble: 223 x 5
##    committee rule_num rule                                    estimate statistic
##        <int>    <int> <chr>                                   <list>   <list>   
##  1         1        1 ( Central_Air == 'N' ) & ( Latitude <=~ <tibble> <tibble> 
##  2         1        2 ( Latitude <= 41.992611 ) & ( Latitude~ <tibble> <tibble> 
##  3         1        3 ( Central_Air == 'N' ) & ( Latitude > ~ <tibble> <tibble> 
##  4         1        4 ( Latitude <= 42.026997 ) & ( Longitud~ <tibble> <tibble> 
##  5         1        5 ( Longitude > -93.63002 ) & ( Latitude~ <tibble> <tibble> 
##  6         1        6 ( Latitude <= 42.035858 ) & ( Longitud~ <tibble> <tibble> 
##  7         1        7 ( Latitude <= 42.024029 ) & ( Latitude~ <tibble> <tibble> 
##  8         1        8 ( Longitude > -93.602348 ) & ( Latitud~ <tibble> <tibble> 
##  9         1        9 ( Latitude <= 41.991756 ) & ( Longitud~ <tibble> <tibble> 
## 10         1       10 ( Latitude > 42.041813 ) & ( Longitude~ <tibble> <tibble> 
## # i 213 more rows

Since Cubist fits linear regressions within the data from each rule, the coefficients are in the estimate column and other information are in statistic: 

cb_res$estimate[[1]]

## # A tibble: 3 x 2
##   term        estimate
##   <chr>          <dbl>
## 1 (Intercept)  -509.  
## 2 Longitude      -5.05
## 3 Latitude        0.99

cb_res$statistic[[1]]

## # A tibble: 1 x 6
##   num_conditions coverage  mean   min   max error
##            <dbl>    <dbl> <dbl> <dbl> <dbl> <dbl>
## 1              3       38  4.87  4.12  5.22 0.149

Note that we can get the data for this rule by using rlang::parse_expr() with it: 

rule_1_expr <- parse_expr(cb_res$rule[1])
rule_1_expr

## (Central_Air == "N") & (Latitude <= 42.026997) & (Longitude > 
##     -93.639572)

then use it to get the data back: 

filter(ames, !!rule_1_expr)

## # A tibble: 38 x 4
##    Sale_Price Longitude Latitude Central_Air
##         <dbl>     <dbl>    <dbl> <fct>      
##  1       5.04     -93.6     42.0 N          
##  2       4.74     -93.6     42.0 N          
##  3       4.75     -93.6     42.0 N          
##  4       4.54     -93.6     42.0 N          
##  5       4.64     -93.6     42.0 N          
##  6       5.22     -93.6     42.0 N          
##  7       4.80     -93.6     42.0 N          
##  8       4.99     -93.6     42.0 N          
##  9       5.09     -93.6     42.0 N          
## 10       4.89     -93.6     42.0 N          
## # i 28 more rows

Now let’s fit a RuleFit model. First, we’ll use a recipe to convert the Central Air predictor to an indicator: 

xrf_reg_mod <-
  rule_fit(trees = 3, penalty = .001) %>%
  set_engine("xrf") %>%
  set_mode("regression")
# Make dummy variables since xgboost will not

ames_rec <-
  recipe(Sale_Price ~ ., data = ames) %>%
  step_dummy(Central_Air) %>%
  step_zv(all_predictors())

ames_processed <- prep(ames_rec) %>% bake(new_data = NULL)

xrf_reg_fit <-
  xrf_reg_mod %>%
  fit(Sale_Price ~ ., data = ames_processed)

xrf_rule_res <- tidy(xrf_reg_fit, penalty = .001)

xrf_rule_res

## # A tibble: 8 x 3
##   rule_id       rule                                                    estimate
##   <chr>         <chr>                                                      <dbl>
## 1 (Intercept)   ( TRUE )                                                 16.4   
## 2 Central_Air_Y ( Central_Air_Y )                                         0.0567
## 3 Latitude      ( Latitude )                                             -0.424 
## 4 Longitude     ( Longitude )                                            -0.0694
## 5 r1_1          ( Longitude <  -93.6299744 )                              0.102 
## 6 r2_3          ( Central_Air_Y <  0.5 ) & ( Latitude <  42.0460129 )    -0.136 
## 7 r2_5          ( Latitude >= 42.0460129 ) & ( Longitude <  -93.650901~   0.302 
## 8 r2_6          ( Latitude >= 42.0460129 ) & ( Longitude >= -93.650901~   0.0853

Here, the focus is on the model coefficients produced by glmnet. We can also break down the results and sort them by the original predictor columns: 

tidy(xrf_reg_fit, penalty = .001, unit = "columns")

## # A tibble: 11 x 3
##    rule_id       term          estimate
##    <chr>         <chr>            <dbl>
##  1 r1_1          Longitude       0.102 
##  2 r2_3          Latitude       -0.136 
##  3 r2_5          Latitude        0.302 
##  4 r2_6          Latitude        0.0853
##  5 r2_3          Central_Air_Y  -0.136 
##  6 r2_5          Longitude       0.302 
##  7 r2_6          Longitude       0.0853
##  8 (Intercept)   (Intercept)    16.4   
##  9 Longitude     Longitude      -0.0694
## 10 Latitude      Latitude       -0.424 
## 11 Central_Air_Y Central_Air_Y   0.0567

C5.0 classification models

Here, we’ll use the Palmer penguin data: 

data(penguins, package = "modeldata")

penguins <- drop_na(penguins)

First, let’s fit a boosted rule-based model and tidy: 

rule_model <- 
  C5_rules(trees = 3) %>% 
  fit(island ~ ., data = penguins)

rule_info <- tidy(rule_model)

rule_info

## # A tibble: 25 x 4
##    trial rule_num rule                                                 statistic
##    <int>    <int> <chr>                                                <list>   
##  1     1        1 ( bill_length_mm > 37.5 )                            <tibble> 
##  2     1        2 ( species == 'Chinstrap' )                           <tibble> 
##  3     1        3 ( body_mass_g > 3200 ) & ( body_mass_g < 3700 ) & (~ <tibble> 
##  4     1        4 ( flipper_length_mm < 193 )                          <tibble> 
##  5     1        5 ( species == 'Adelie' ) & ( bill_length_mm > 38.299~ <tibble> 
##  6     1        6 ( bill_length_mm < 40.799999 ) & ( bill_depth_mm > ~ <tibble> 
##  7     1        7 ( species == 'Adelie' ) & ( bill_length_mm > 41.599~ <tibble> 
##  8     1        8 ( species == 'Adelie' ) & ( bill_depth_mm > 18.9 ) ~ <tibble> 
##  9     2        1 ( species == 'Gentoo' )                              <tibble> 
## 10     2        2 ( body_mass_g > 3700 ) & ( sex == 'female' )         <tibble> 
## # i 15 more rows

# The statistic column has the pre-computed data about the 
# data covered by the rule:
rule_info$statistic[[1]]

## # A tibble: 1 x 4
##   num_conditions coverage  lift class 
##            <dbl>    <dbl> <dbl> <chr> 
## 1              1      286  1.10 Biscoe

Tree-based models can also be tidied. Rather than saving the results in a recursive tree structure, we can show the paths to each of the terminal nodes (which is just a rule).

Let’s fit a model and tidy: 

tree_model <- 
  boost_tree(trees = 3) %>% 
  set_engine("C5.0") %>% 
  set_mode("classification") %>% 
  fit(island ~ ., data = penguins)

tree_info <- tidy(tree_model)

tree_info

## # A tibble: 34 x 4
##    trial  node rule                                                    statistic
##    <int> <int> <chr>                                                   <list>   
##  1     1     1 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  2     1     2 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  3     1     3 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  4     1     4 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  5     1     5 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  6     1     6 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  7     1     7 "( species %in% c(\"Adelie\") ) & ( sex == \"female\" ~ <tibble> 
##  8     1     8 "( species %in% c(\"Adelie\") ) & ( sex == \"male\" ) ~ <tibble> 
##  9     1     9 "( species %in% c(\"Adelie\") ) & ( sex == \"male\" ) ~ <tibble> 
## 10     1    10 "( species %in% c(\"Adelie\") ) & ( sex == \"male\" ) ~ <tibble> 
## # i 24 more rows

# The statistic column has the class breakdown:
tree_info$statistic[[1]]

## # A tibble: 3 x 2
##   value     count
##   <chr>     <dbl>
## 1 Biscoe        3
## 2 Dream         1
## 3 Torgersen     0

Note that C5.0 models can have fractional estimates of counts in the terminal nodes.