Apply 5
Alden Dimick
2025-03-25
Goal is to predict the spam emails
Import data
library(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
## ✔ purrr 1.0.2
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(correlationfunnel)## ══ correlationfunnel Tip #2 ════════════════════════════════════════════════════
## Clean your NA's prior to using `binarize()`.
## Missing values and cleaning data are critical to getting great correlations. :)data <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/main/data/2023/2023-08-15/spam.csv')## Rows: 4601 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): yesno
## dbl (6): crl.tot, dollar, bang, money, n000, make
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.data %>% skimr::skim()| Name | Piped data |
| Number of rows | 4601 |
| Number of columns | 7 |
| _______________________ | |
| Column type frequency: | |
| character | 1 |
| numeric | 6 |
| ________________________ | |
| Group variables | None |
Variable type: character
| skim_variable | n_missing | complete_rate | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| yesno | 0 | 1 | 1 | 1 | 0 | 2 | 0 |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| crl.tot | 0 | 1 | 283.29 | 606.35 | 1 | 35 | 95 | 266.00 | 15841.00 | ▇▁▁▁▁ |
| dollar | 0 | 1 | 0.08 | 0.25 | 0 | 0 | 0 | 0.05 | 6.00 | ▇▁▁▁▁ |
| bang | 0 | 1 | 0.27 | 0.82 | 0 | 0 | 0 | 0.32 | 32.48 | ▇▁▁▁▁ |
| money | 0 | 1 | 0.09 | 0.44 | 0 | 0 | 0 | 0.00 | 12.50 | ▇▁▁▁▁ |
| n000 | 0 | 1 | 0.10 | 0.35 | 0 | 0 | 0 | 0.00 | 5.45 | ▇▁▁▁▁ |
| make | 0 | 1 | 0.10 | 0.31 | 0 | 0 | 0 | 0.00 | 4.54 | ▇▁▁▁▁ |
clean data
data_clean <- data %>%
# Address factors imported as numeric
# mutate(across(where(is.character), as.factor)) %>%
mutate(yesno = as.factor(yesno))skimr::skim(data)| Name | data |
| Number of rows | 4601 |
| Number of columns | 7 |
| _______________________ | |
| Column type frequency: | |
| character | 1 |
| numeric | 6 |
| ________________________ | |
| Group variables | None |
Variable type: character
| skim_variable | n_missing | complete_rate | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| yesno | 0 | 1 | 1 | 1 | 0 | 2 | 0 |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| crl.tot | 0 | 1 | 283.29 | 606.35 | 1 | 35 | 95 | 266.00 | 15841.00 | ▇▁▁▁▁ |
| dollar | 0 | 1 | 0.08 | 0.25 | 0 | 0 | 0 | 0.05 | 6.00 | ▇▁▁▁▁ |
| bang | 0 | 1 | 0.27 | 0.82 | 0 | 0 | 0 | 0.32 | 32.48 | ▇▁▁▁▁ |
| money | 0 | 1 | 0.09 | 0.44 | 0 | 0 | 0 | 0.00 | 12.50 | ▇▁▁▁▁ |
| n000 | 0 | 1 | 0.10 | 0.35 | 0 | 0 | 0 | 0.00 | 5.45 | ▇▁▁▁▁ |
| make | 0 | 1 | 0.10 | 0.31 | 0 | 0 | 0 | 0.00 | 4.54 | ▇▁▁▁▁ |
Explore data
data %>% count(yesno)## # A tibble: 2 × 2
## yesno n
## <chr> <int>
## 1 n 2788
## 2 y 1813data %>%
ggplot(aes(yesno)) +
geom_bar()
yesno vs. dollar
data %>%
ggplot(aes(yesno, dollar)) +
geom_boxplot()
correlation plot
# step 1: binarize
data_binarized <- data %>%
select(-money) %>%
binarize()
data_binarized %>% glimpse()## Rows: 4,601
## Columns: 15
## $ `crl.tot__-Inf_35` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0…
## $ crl.tot__35_95 <dbl> 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
## $ crl.tot__95_266 <dbl> 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1…
## $ crl.tot__266_Inf <dbl> 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0…
## $ `dollar__-Inf_0.052` <dbl> 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 1…
## $ dollar__0.052_Inf <dbl> 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0…
## $ `bang__-Inf_0.315` <dbl> 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0…
## $ bang__0.315_Inf <dbl> 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1…
## $ n000__0 <dbl> 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1…
## $ `n000__-OTHER` <dbl> 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0…
## $ make__0 <dbl> 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1…
## $ make__0.1 <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
## $ `make__-OTHER` <dbl> 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0…
## $ yesno__n <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
## $ yesno__y <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…# step 2: correlation
data_correlation <- data_binarized %>%
correlate(yesno__y)
data_correlation## # A tibble: 15 × 3
## feature bin correlation
## <fct> <chr> <dbl>
## 1 yesno n -1
## 2 yesno y 1
## 3 dollar -Inf_0.052 -0.566
## 4 dollar 0.052_Inf 0.566
## 5 bang -Inf_0.315 -0.490
## 6 bang 0.315_Inf 0.490
## 7 n000 0 -0.419
## 8 n000 -OTHER 0.419
## 9 crl.tot -Inf_35 -0.360
## 10 crl.tot 266_Inf 0.299
## 11 make 0 -0.239
## 12 make -OTHER 0.223
## 13 crl.tot 95_266 0.145
## 14 crl.tot 35_95 -0.0818
## 15 make 0.1 0.0803# step 3: plot
data_correlation %>%
correlationfunnel::plot_correlation_funnel()
Model building
Split data
library(tidymodels)## ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ──## ✔ broom 1.0.7 ✔ rsample 1.2.1
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## ✔ parsnip 1.3.0 ✔ yardstick 1.3.2
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## • Use suppressPackageStartupMessages() to eliminate package startup messagesset.seed(1234)
data_clean <- data_clean %>% sample_n(100)
data_split <- initial_split(data_clean, strata = yesno)
data_train <- training(data_split)
data_test <- testing(data_split)
data_cv <- rsample::vfold_cv(data_train, strata = yesno)
data_cv## # 10-fold cross-validation using stratification
## # A tibble: 10 × 2
## splits id
## <list> <chr>
## 1 <split [66/8]> Fold01
## 2 <split [66/8]> Fold02
## 3 <split [66/8]> Fold03
## 4 <split [66/8]> Fold04
## 5 <split [67/7]> Fold05
## 6 <split [67/7]> Fold06
## 7 <split [67/7]> Fold07
## 8 <split [67/7]> Fold08
## 9 <split [67/7]> Fold09
## 10 <split [67/7]> Fold10Preprocess data
library(themis)
xgboost_rec <- recipes::recipe(yesno ~ ., data = data_train) %>%
step_dummy(all_nominal_predictors()) %>%
step_smote(yesno)
xgboost_rec %>% prep() %>% juice() %>% glimpse()## Rows: 88
## Columns: 7
## $ crl.tot <dbl> 50, 10, 8, 15, 15, 67, 5, 17, 600, 146, 322, 5, 8, 201, 9, 7, …
## $ dollar <dbl> 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,…
## $ bang <dbl> 0.175, 0.000, 0.000, 0.000, 0.000, 0.000, 3.260, 0.773, 0.017,…
## $ money <dbl> 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.…
## $ n000 <dbl> 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.…
## $ make <dbl> 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.11, 0.00, 0.…
## $ yesno <fct> n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n,…Specify model
xgboost_spec <-
boost_tree(trees = tune()) %>%
set_mode("classification") %>%
set_engine("xgboost")
xgboost_workflow <-
workflow() %>%
add_recipe(xgboost_rec) %>%
add_model(xgboost_spec) Tune hyperparameters
doParallel::registerDoParallel()
set.seed(65677)
xgboost_tune <-
tune_grid(xgboost_workflow,
resamples = data_cv,
grid = 5)