Apply 7
Spencer Murrin
2024-03-26
Import Data
members <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-09-22/members.csv')## Rows: 76519 Columns: 21
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (10): expedition_id, member_id, peak_id, peak_name, season, sex, citizen...
## dbl (5): year, age, highpoint_metres, death_height_metres, injury_height_me...
## lgl (6): hired, success, solo, oxygen_used, died, injured
##
## 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.skimr::skim(members)| Name | members |
| Number of rows | 76519 |
| Number of columns | 21 |
| _______________________ | |
| Column type frequency: | |
| character | 10 |
| logical | 6 |
| numeric | 5 |
| ________________________ | |
| Group variables | None |
Variable type: character
| skim_variable | n_missing | complete_rate | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| expedition_id | 0 | 1.00 | 9 | 9 | 0 | 10350 | 0 |
| member_id | 0 | 1.00 | 12 | 12 | 0 | 76518 | 0 |
| peak_id | 0 | 1.00 | 4 | 4 | 0 | 391 | 0 |
| peak_name | 15 | 1.00 | 4 | 25 | 0 | 390 | 0 |
| season | 0 | 1.00 | 6 | 7 | 0 | 5 | 0 |
| sex | 2 | 1.00 | 1 | 1 | 0 | 2 | 0 |
| citizenship | 10 | 1.00 | 2 | 23 | 0 | 212 | 0 |
| expedition_role | 21 | 1.00 | 4 | 25 | 0 | 524 | 0 |
| death_cause | 75413 | 0.01 | 3 | 27 | 0 | 12 | 0 |
| injury_type | 74807 | 0.02 | 3 | 27 | 0 | 11 | 0 |
Variable type: logical
| skim_variable | n_missing | complete_rate | mean | count |
|---|---|---|---|---|
| hired | 0 | 1 | 0.21 | FAL: 60788, TRU: 15731 |
| success | 0 | 1 | 0.38 | FAL: 47320, TRU: 29199 |
| solo | 0 | 1 | 0.00 | FAL: 76398, TRU: 121 |
| oxygen_used | 0 | 1 | 0.24 | FAL: 58286, TRU: 18233 |
| died | 0 | 1 | 0.01 | FAL: 75413, TRU: 1106 |
| injured | 0 | 1 | 0.02 | FAL: 74806, TRU: 1713 |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| year | 0 | 1.00 | 2000.36 | 14.78 | 1905 | 1991 | 2004 | 2012 | 2019 | ▁▁▁▃▇ |
| age | 3497 | 0.95 | 37.33 | 10.40 | 7 | 29 | 36 | 44 | 85 | ▁▇▅▁▁ |
| highpoint_metres | 21833 | 0.71 | 7470.68 | 1040.06 | 3800 | 6700 | 7400 | 8400 | 8850 | ▁▁▆▃▇ |
| death_height_metres | 75451 | 0.01 | 6592.85 | 1308.19 | 400 | 5800 | 6600 | 7550 | 8830 | ▁▁▂▇▆ |
| injury_height_metres | 75510 | 0.01 | 7049.91 | 1214.24 | 400 | 6200 | 7100 | 8000 | 8880 | ▁▁▂▇▇ |
data_clean <- members %>%
# Treat missing values
select(-death_cause, -injury_type, -highpoint_metres, -death_height_metres, -injury_height_metres, -peak_id) %>%
na.omit() %>%
# Log Transform Variables with pos-skewed Distribution
mutate(across(where(is.logical), as.factor))# Step 1: Prepare data
data_binarized_tbl <- data_clean %>%
select(-peak_name, -expedition_id) %>%
binarize()
data_binarized_tbl %>% glimpse()## Rows: 72,985
## Columns: 55
## $ `member_id__KANG10101-01` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `member_id__-OTHER` <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ `year__-Inf_1992` <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ year__1992_2004 <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ year__2004_2012 <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ year__2012_Inf <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ season__Autumn <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, …
## $ season__Spring <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, …
## $ season__Winter <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `season__-OTHER` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ sex__F <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ sex__M <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ `age__-Inf_29` <dbl> 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, …
## $ age__29_36 <dbl> 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, …
## $ age__36_44 <dbl> 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, …
## $ age__44_Inf <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Australia <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Austria <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Canada <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__China <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__France <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, …
## $ citizenship__Germany <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__India <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Italy <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Japan <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Nepal <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Netherlands <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__New_Zealand <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Poland <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Russia <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__S_Korea <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Spain <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__Switzerland <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__UK <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ citizenship__USA <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, …
## $ citizenship__W_Germany <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, …
## $ `citizenship__-OTHER` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ expedition_role__Climber <dbl> 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, …
## $ expedition_role__Deputy_Leader <dbl> 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ expedition_role__Exp_Doctor <dbl> 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `expedition_role__H-A_Worker` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ expedition_role__Leader <dbl> 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `expedition_role__-OTHER` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, …
## $ hired__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ hired__TRUE <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ success__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, …
## $ success__TRUE <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, …
## $ solo__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ `solo__-OTHER` <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ oxygen_used__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ oxygen_used__TRUE <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ died__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ died__TRUE <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ injured__FALSE <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ injured__TRUE <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …# Step 2: Correlate
data_corr_tbl <- data_binarized_tbl %>%
correlate(died__TRUE)## Warning: correlate(): [Data Imbalance Detected] Consider sampling to balance the classes more than 5%
## Column with imbalance: died__TRUEdata_corr_tbl## # A tibble: 55 × 3
## feature bin correlation
## <fct> <chr> <dbl>
## 1 died FALSE -1
## 2 died TRUE 1
## 3 year -Inf_1992 0.0519
## 4 success FALSE 0.0332
## 5 success TRUE -0.0332
## 6 year 2004_2012 -0.0211
## 7 year 2012_Inf -0.0208
## 8 sex F -0.0168
## 9 sex M 0.0168
## 10 citizenship USA -0.0154
## # ℹ 45 more rows# Step 3: Plot
data_corr_tbl %>%
plot_correlation_funnel()## Warning: ggrepel: 27 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
Build Model
Split Data
library(tidymodels)## ── Attaching packages ────────────────────────────────────── tidymodels 1.1.1 ──## ✔ broom 1.0.5 ✔ rsample 1.2.0
## ✔ dials 1.2.0 ✔ tune 1.1.2
## ✔ infer 1.0.6 ✔ workflows 1.1.3
## ✔ modeldata 1.3.0 ✔ workflowsets 1.0.1
## ✔ parsnip 1.1.1 ✔ yardstick 1.3.0## ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
## ✖ scales::discard() masks purrr::discard()
## ✖ dplyr::filter() masks stats::filter()
## ✖ recipes::fixed() masks stringr::fixed()
## ✖ dplyr::lag() masks stats::lag()
## ✖ xgboost::slice() masks dplyr::slice()
## ✖ yardstick::spec() masks readr::spec()
## ✖ recipes::step() masks stats::step()
## • Dig deeper into tidy modeling with R at https://www.tmwr.org#set.seed(2543)
#data_clean <- data_clean %>% group_by(died) %>% sample_n(50) %>% ungroup()
data_split <- initial_split(data_clean, strata = died)
data_train <- training(data_split)
data_test <- testing(data_split)
data_cv <- rsample::vfold_cv(data_train, strata = died)
data_cv## # 10-fold cross-validation using stratification
## # A tibble: 10 × 2
## splits id
## <list> <chr>
## 1 <split [49264/5474]> Fold01
## 2 <split [49264/5474]> Fold02
## 3 <split [49264/5474]> Fold03
## 4 <split [49264/5474]> Fold04
## 5 <split [49264/5474]> Fold05
## 6 <split [49264/5474]> Fold06
## 7 <split [49264/5474]> Fold07
## 8 <split [49264/5474]> Fold08
## 9 <split [49265/5473]> Fold09
## 10 <split [49265/5473]> Fold10Preprocess Data
library(themis)
xgboost_rec <- recipes::recipe(died ~ ., data = data_train) %>%
update_role(member_id, new_role = "ID") %>%
step_other(expedition_id, threshold = 0.1) %>%
step_dummy(all_nominal_predictors()) %>%
step_zv(all_predictors()) %>%
step_normalize(all_numeric_predictors())
#xgboost_rec <- recipes::recipe(died ~ ., data = data_train) %>%
#update_role(member_id, new_role = "ID") %>%
#step_other(expedition_id, threshold = 0.1) %>%
#step_dummy(all_nominal_predictors()) %>%
#step_zv(all_predictors()) %>%
#step_normalize(all_numeric_predictors()) %>%
#step_smote(died)
xgboost_rec %>% prep() %>% juice() %>% glimpse()## New names:
## • `expedition_role_Climber.Guide` -> `expedition_role_Climber.Guide...718`
## • `expedition_role_Climber.Sirdar` -> `expedition_role_Climber.Sirdar...719`
## • `expedition_role_Climber.Guide` -> `expedition_role_Climber.Guide...734`
## • `expedition_role_Climber.Sirdar` -> `expedition_role_Climber.Sirdar...742`## Rows: 54,738
## Columns: 1,015
## $ member_id <fct> AMAD78301-01, AMAD78301-02, …
## $ year <dbl> -1.632223, -1.632223, -1.632…
## $ age <dbl> 0.25707113, 0.35352171, -0.9…
## $ died <fct> FALSE, FALSE, FALSE, FALSE, …
## $ expedition_id_other <dbl> 0.03654288, 0.03654288, 0.03…
## $ peak_name_Ama.Dablam <dbl> 2.794147, 2.794147, 2.794147…
## $ peak_name_Amotsang <dbl> -0.01351734, -0.01351734, -0…
## $ peak_name_Amphu.Gyabjen <dbl> -0.01417724, -0.01417724, -0…
## $ peak_name_Amphu.I <dbl> -0.01130911, -0.01130911, -0…
## $ peak_name_Amphu.Middle <dbl> -0.008548648, -0.008548648, …
## $ peak_name_Anidesh.Chuli <dbl> -0.01130911, -0.01130911, -0…
## $ peak_name_Annapurna.I <dbl> -0.1508557, -0.1508557, -0.1…
## $ peak_name_Annapurna.I.East <dbl> -0.0230232, -0.0230232, -0.0…
## $ peak_name_Annapurna.I.Middle <dbl> -0.02456063, -0.02456063, -0…
## $ peak_name_Annapurna.II <dbl> -0.05380316, -0.05380316, -0…
## $ peak_name_Annapurna.III <dbl> -0.06146161, -0.06146161, -0…
## $ peak_name_Annapurna.IV <dbl> -0.1034853, -0.1034853, -0.1…
## $ peak_name_Annapurna.South <dbl> -0.05259445, -0.05259445, -0…
## $ peak_name_Api.Main <dbl> -0.03873326, -0.03873326, -0…
## $ peak_name_Arniko.Chuli <dbl> -0.02704209, -0.02704209, -0…
## $ peak_name_Bamongo <dbl> -0.01282356, -0.01282356, -0…
## $ peak_name_Baruntse <dbl> -0.172794, -0.172794, -0.172…
## $ peak_name_Baudha <dbl> -0.01813674, -0.01813674, -0…
## $ peak_name_Beding.Go <dbl> -0.01209006, -0.01209006, -0…
## $ peak_name_Bhairab.Takura <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Bhemdang.Ri <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Bhrikuti <dbl> -0.04446234, -0.04446234, -0…
## $ peak_name_Bhrikuti.Shail <dbl> -0.02529441, -0.02529441, -0…
## $ peak_name_Bhulu.Lhasa <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Bijora.Hiunchuli <dbl> -0.01282356, -0.01282356, -0…
## $ peak_name_Bobaye <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Boktoh <dbl> -0.008548648, -0.008548648, …
## $ peak_name_Burke.Kang <dbl> -0.02005165, -0.02005165, -0…
## $ peak_name_Chago <dbl> -0.01130911, -0.01130911, -0…
## $ peak_name_Chako <dbl> -0.01655605, -0.01655605, -0…
## $ peak_name_Chamar.Kang <dbl> -0.009557766, -0.009557766, …
## $ peak_name_Chamar.North <dbl> -0.02005165, -0.02005165, -0…
## $ peak_name_Chamlang <dbl> -0.03629139, -0.03629139, -0…
## $ peak_name_Chandi.Himal <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Changla <dbl> -0.01813674, -0.01813674, -0…
## $ peak_name_Changtse <dbl> -0.03340093, -0.03340093, -0…
## $ peak_name_Changwathang <dbl> -0.02418541, -0.02418541, -0…
## $ peak_name_Chaw.Peak <dbl> -0.009557766, -0.009557766, …
## $ peak_name_Chekigo <dbl> -0.01130911, -0.01130911, -0…
## $ peak_name_Cheo.Himal <dbl> -0.01762558, -0.01762558, -0…
## $ peak_name_Chhiv.Himal <dbl> -0.009557766, -0.009557766, …
## $ peak_name_Chhochenphu.Himal <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Chhopa.Bamare <dbl> -0.01130911, -0.01130911, -0…
## $ peak_name_Chhuboche <dbl> -0.008548648, -0.008548648, …
## $ peak_name_Chhukung.Ri <dbl> -0.01813674, -0.01813674, -0…
## $ peak_name_Chhukung.Tse <dbl> -0.008548648, -0.008548648, …
## $ peak_name_Cho.Oyu <dbl> -0.364381, -0.364381, -0.364…
## $ peak_name_Cho.Polu <dbl> -0.01655605, -0.01655605, -0…
## $ peak_name_Chobuje <dbl> -0.02179924, -0.02179924, -0…
## $ peak_name_Cholatse <dbl> -0.03943651, -0.03943651, -0…
## $ peak_name_Chukyima.Go <dbl> -0.01709917, -0.01709917, -0…
## $ peak_name_Chulu.Central <dbl> -0.01209006, -0.01209006, -0…
## $ peak_name_Chulu.West <dbl> -0.01351734, -0.01351734, -0…
## $ peak_name_Chumbu <dbl> -0.0104701, -0.0104701, -0.0…
## $ peak_name_Churen.Himal.Central <dbl> -0.0230232, -0.0230232, -0.0…
## $ peak_name_Churen.Himal.East <dbl> -0.0296253, -0.0296253, -0.0…
## $ peak_name_Churen.Himal.West <dbl> -0.03654288, -0.03654288, -0…
## $ peak_name_Danga <dbl> -0.009557766, -0.009557766, …
## $ peak_name_Danphe.Shail <dbl> -0.0230232, -0.0230232, -0.0…
## $ peak_name_Dhampus <dbl> -0.03825729, -0.03825729, -0…
## $ peak_name_Dhaulagiri.I <dbl> -0.187288, -0.187288, -0.187…
## $ peak_name_Dhaulagiri.II <dbl> -0.0408069, -0.0408069, -0.0…
## $ peak_name_Dhaulagiri.III <dbl> -0.02221471, -0.02221471, -0…
## $ peak_name_Dhaulagiri.IV <dbl> -0.03966818, -0.03966818, -0…
## $ peak_name_Dhaulagiri.V <dbl> -0.02456063, -0.02456063, -0…
## $ peak_name_Dhaulagiri.VI <dbl> -0.02529441, -0.02529441, -0…
## $ peak_name_Dhechyan.Khang <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Dingjung.North <dbl> -0.01209006, -0.01209006, -0…
## $ peak_name_Dingjung.Ri <dbl> -0.006044697, -0.006044697, …
## $ peak_name_Dolma.Khang <dbl> -0.03171401, -0.03171401, -0…
## $ peak_name_Dome.Kang <dbl> -0.0186339, -0.0186339, -0.0…
## $ peak_name_Domo <dbl> -0.004274207, -0.004274207, …
## $ peak_name_Dorje.Lhakpa <dbl> -0.05189126, -0.05189126, -0…
## $ peak_name_Dragmorpa.Ri <dbl> -0.01599452, -0.01599452, -0…
## $ peak_name_Drangnag.Ri <dbl> -0.02094365, -0.02094365, -0…
## $ peak_name_Drohmo <dbl> -0.02137572, -0.02137572, -0…
## $ peak_name_Dudh.Kundali <dbl> -0.01351734, -0.01351734, -0…
## $ peak_name_Dzanye <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Dzanye.II <dbl> -0.009557766, -0.009557766, …
## $ peak_name_Dzasampatse <dbl> -0.01209006, -0.01209006, -0…
## $ peak_name_Everest <dbl> -0.6363742, -0.6363742, -0.6…
## $ peak_name_Fang <dbl> -0.0352676, -0.0352676, -0.0…
## $ peak_name_Firnkopf <dbl> -0.01351734, -0.01351734, -0…
## $ peak_name_Firnkopf.West <dbl> -0.007403279, -0.007403279, …
## $ peak_name_Futi.Himal <dbl> -0.004274207, -0.004274207, …
## $ peak_name_Gama.Peak <dbl> -0.01282356, -0.01282356, -0…
## $ peak_name_Ganchenpo <dbl> -0.03228607, -0.03228607, -0…
## $ peak_name_Gandharva.Chuli <dbl> -0.004274207, -0.004274207, …
## $ peak_name_Ganesh.I <dbl> -0.02670168, -0.02670168, -0…
## $ peak_name_Ganesh.II <dbl> -0.03113149, -0.03113149, -0…
## $ peak_name_Ganesh.III <dbl> -0.02418541, -0.02418541, -0…
## $ peak_name_Ganesh.IV <dbl> -0.03083611, -0.03083611, -0…
## $ peak_name_Ganesh.V <dbl> -0.0205025, -0.0205025, -0.0…
## $ peak_name_Ganesh.VI <dbl> -0.01480777, -0.01480777, -0…
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## $ expedition_role_Film.Support <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Film.support.crew <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Film.team <dbl> -0.01130911, -0.01130911, -0…
## $ expedition_role_Film.Team <dbl> -0.04213302, -0.04213302, -0…
## $ expedition_role_Film.Team.Leader <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Film.Team.Liaison <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Film.Team.Exp.Doctor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Food <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Food.Manager <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Foods <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_General.Advisor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_General.Commander <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_General.Director <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_General.Leader <dbl> -0.01599452, -0.01599452, -0…
## $ expedition_role_General.Manager <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_H.A.Assistant <dbl> -0.07131701, -0.07131701, -0…
## $ expedition_role_H.A.Assistant..Guide <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_H.A.Assistant..Guide. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_H.A.Cameraman <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_H.A.Cook <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_H.A.Exp.Doctor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_H.A.Rope.Fixer <dbl> -0.01541256, -0.01541256, -0…
## $ expedition_role_H.A.Worder <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_H.A.Worker <dbl> -0.4646899, -0.4646899, -0.4…
## $ expedition_role_H.A.Worker..Cook. <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_H.A.Worker.Climber <dbl> -0.01599452, -0.01599452, -0…
## $ expedition_role_H.A.Worker.Cook <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_H.A.Worker.Kitchen.Boy <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_H.W.Worker <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_HA.Cook <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_HA.Worker <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Hang.glider.Pilot <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Head.of.Organization <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Helicopter.Tech <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_High.Altitude.Doctor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Historian <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Honorary.Leader <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Icefall.Doctor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Interpreter <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Intrepreter <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Joint.Leader <dbl> -0.01209006, -0.01209006, -0…
## $ expedition_role_Journalist <dbl> -0.02670168, -0.02670168, -0…
## $ expedition_role_Journalist.Photographer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Kayaker <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Kitchen.Boy <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Kitchen.Staff <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Ladder.Removal <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader <dbl> 2.5229073, -0.3963609, -0.39…
## $ expedition_role_Leader..2nd.smt.group. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Admin. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..BC.only. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Czech. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..French. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Group.1. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Group.2. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..I. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Ktm.only. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Lhotse.S.Face. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Lhotse.W.Face. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..nomimal. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Nominal. <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Leader..S. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..South.side. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Swiss. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Tawoche. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Tibetan.Staff. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..until.BC. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..until.C1. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Xixa.also. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader...Exp.Doctor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.of.Hankuk.Grp <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.of.Jap..Mbrs <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.of.KPNU.Grp <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..BC.Manager <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Leader..Exp.Doctor <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Leader..Manager <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader..Organizer <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Leader. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.Adv.BC.Manager <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.BC.Manager <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_Leader.BC.Mgr <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.Exp.Doctor <dbl> -0.02221471, -0.02221471, -0…
## $ expedition_role_Leader.Film.Team <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.Instructor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leader.Scientist <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Leader.Transport <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Leaer <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Lhotse.Climber <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Liaison.Officer <dbl> -0.01209006, -0.01209006, -0…
## $ expedition_role_Logistics.Supervisor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Manager <dbl> -0.01282356, -0.01282356, -0…
## $ expedition_role_Media.Coordinator <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Media.Officer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Medical.Officer <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Medical.Research <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Medical.Team <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Member <dbl> -0.06438789, -0.06438789, -0…
## $ expedition_role_Member..ABC.N.Col. <dbl> -0.01130911, -0.01130911, -0…
## $ expedition_role_Member.Instructor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Meteorologist <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Mgr...Climbing.Ldr <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Movie.Team <dbl> -0.0104701, -0.0104701, -0.0…
## $ expedition_role_Naike <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Non.Climber <dbl> -0.01282356, -0.01282356, -0…
## $ expedition_role_Non.member <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Organiser <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Organizer <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Organizer...Med.Off <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Original.Leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Photo.Team <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Photographer <dbl> -0.01709917, -0.01709917, -0…
## $ expedition_role_Physiologist <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Pilot <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Piotr.Czeslaw <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Police.Leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Porter <dbl> -0.01282356, -0.01282356, -0…
## $ expedition_role_President <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Press.Correspondent <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Programme.Director <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Radio.Officer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Radio.Operator <dbl> -0.0186339, -0.0186339, -0.0…
## $ expedition_role_Radio.Operator..BC. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Radio.Technician <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Reporter <dbl> -0.01599452, -0.01599452, -0…
## $ expedition_role_Reporter.Team <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Research <dbl> -0.01209006, -0.01209006, -0…
## $ expedition_role_Research.Doctor <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Researcher <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Rope.Team <dbl> -0.01709917, -0.01709917, -0…
## $ expedition_role_Rope.Team.H.A.Assistant <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Rope.fixing <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Scientific.Coordinator <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Scientific.Team <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_Scientist <dbl> -0.02221471, -0.02221471, -0…
## $ expedition_role_Secretary <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Secretary.interpreter <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Signal.Officer <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Sirdar <dbl> -0.07595662, -0.07595662, -0…
## $ expedition_role_Sirdar.Climber <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Sirdar.Climbing.Ldr <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Sirder <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Ski.Team <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Ski.Team.Leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Skiing.Demonstrator <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Staff.Photographer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Staff.Writer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Student.Leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Support <dbl> -0.0205025, -0.0205025, -0.0…
## $ expedition_role_Support.Climber <dbl> -0.01599452, -0.01599452, -0…
## $ expedition_role_Support.Crew <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Support.member <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Support.Member <dbl> -0.01417724, -0.01417724, -0…
## $ expedition_role_Support.Member..N.side. <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Support.Member..S.side. <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Support.Member..S. <dbl> -0.0104701, -0.0104701, -0.0…
## $ expedition_role_Surveyor <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Tactician <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Team.Historian <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Team.Leader..N. <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Team.Leader..S. <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Technical.Advisor <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Temporary.Leader <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Trainer <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_Transport <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_Transport.Manager <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Transport.Officer <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_Transport.Offier <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Transportation <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Trekker <dbl> -0.01762558, -0.01762558, -0…
## $ expedition_role_Trekking.Leader <dbl> -0.006044697, -0.006044697, …
## $ expedition_role_TV...Radio.Team <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_TV.Cameraman <dbl> -0.008548648, -0.008548648, …
## $ expedition_role_TV.Crew <dbl> -0.007403279, -0.007403279, …
## $ expedition_role_TV.Producer <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_TV.Reporter <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Vice.Leader <dbl> -0.009557766, -0.009557766, …
## $ expedition_role_Video.Editor <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Winch.Operator.at.C1 <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_Wireless.Operator <dbl> -0.004274207, -0.004274207, …
## $ expedition_role_xClimber <dbl> -0.004274207, -0.004274207, …
## $ hired_TRUE. <dbl> -0.4857769, -0.4857769, -0.4…
## $ success_TRUE. <dbl> -0.7881515, -0.7881515, -0.7…
## $ solo_TRUE. <dbl> -0.0408069, -0.0408069, -0.0…
## $ oxygen_used_TRUE. <dbl> -0.5675703, -0.5675703, -0.5…
## $ injured_TRUE. <dbl> -0.1509823, -0.1509823, -0.1…Specify Model
library(usemodels)
usemodels::use_xgboost(died ~ ., data = data_train)## xgboost_recipe <-
## recipe(formula = died ~ ., data = data_train) %>%
## step_zv(all_predictors())
##
## xgboost_spec <-
## boost_tree(trees = tune(), min_n = tune(), tree_depth = tune(), learn_rate = tune(),
## loss_reduction = tune(), sample_size = tune()) %>%
## set_mode("classification") %>%
## set_engine("xgboost")
##
## xgboost_workflow <-
## workflow() %>%
## add_recipe(xgboost_recipe) %>%
## add_model(xgboost_spec)
##
## set.seed(36638)
## xgboost_tune <-
## tune_grid(xgboost_workflow, resamples = stop("add your rsample object"), grid = stop("add number of candidate points"))xgboost_spec <-
boost_tree(trees = tune()) %>%
set_mode("classification") %>%
set_engine("xgboost")
xgboost_workflow <-
workflow() %>%
add_recipe(xgboost_rec) %>%
add_model(xgboost_spec) Tune Hyperparmeters
doParallel::registerDoParallel()
set.seed(24817)
xgboost_tune <-
tune_grid(xgboost_workflow,
resamples = data_cv,
grid = 5,
control = control_grid(save_pred = TRUE))Evaluate Models
tune::show_best(xgboost_tune, metric = "roc_auc")## # A tibble: 5 × 7
## trees .metric .estimator mean n std_err .config
## <int> <chr> <chr> <dbl> <int> <dbl> <chr>
## 1 232 roc_auc binary 0.776 10 0.00740 Preprocessor1_Model1
## 2 784 roc_auc binary 0.758 10 0.00736 Preprocessor1_Model2
## 3 1209 roc_auc binary 0.755 10 0.00699 Preprocessor1_Model4
## 4 1191 roc_auc binary 0.755 10 0.00704 Preprocessor1_Model3
## 5 1975 roc_auc binary 0.748 10 0.00739 Preprocessor1_Model5# Update the model by selecting the best hyper-parameters
xgboost_fw <- tune::finalize_workflow(xgboost_workflow,
tune::select_best(xgboost_tune, metric = "roc_auc"))
# Fit the model on the entire training data and test it on the test data
data_fit <- tune::last_fit(xgboost_fw, data_split)## New names:
## New names:
## → A | warning: ! There are new levels in a factor: Mardi Himal, ! There are new
## levels in a factor: Austria/Brazil, UK/Italy, Poland/Canada, Canada/UK,
## France/Algeria, New Zealand/UK, Turkmenistan, Chile/Sweden, Canada/Russia,
## UK/Iceland, Botswana, Netherlands/Switzerland, and Italy/Slovenia, ! There are
## new levels in a factor: Climber/Kayaker, Team Mgr, Trainer, Leader (II),
## Treasurer, Exp Doctor, BC Mgr, Deputy Leader (Xixa), Airdrop Team, Charge of
## publicity, Treasurer/Transport, Producer, Director, Press Director, Leader
## (Honorable), Technical Manager, Leader Scientist, Asst BC Manager, Leader
## (American), C1 Manager, Communications, …, Climber (Pvt), and Exp Docter
## There were issues with some computations A: x1
## There were issues with some computations A: x1
##
## • `expedition_role_Climber.Guide` -> `expedition_role_Climber.Guide...718`
## • `expedition_role_Climber.Sirdar` -> `expedition_role_Climber.Sirdar...719`
## • `expedition_role_Climber.Guide` -> `expedition_role_Climber.Guide...734`
## • `expedition_role_Climber.Sirdar` -> `expedition_role_Climber.Sirdar...742`tune::collect_metrics(data_fit)## # A tibble: 2 × 4
## .metric .estimator .estimate .config
## <chr> <chr> <dbl> <chr>
## 1 accuracy binary 0.988 Preprocessor1_Model1
## 2 roc_auc binary 0.784 Preprocessor1_Model1tune::collect_predictions(data_fit) %>%
ggplot(aes(died, .pred_TRUE)) +
geom_point(alpha = 0.3, fill = "midnightblue") +
geom_abline(lty = 2, color = "gray50") +
coord_fixed() 