# Import Data

library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.3     ✔ readr     2.1.4
## ✔ forcats   1.0.0     ✔ stringr   1.5.0
## ✔ ggplot2   3.4.3     ✔ tibble    3.2.1
## ✔ lubridate 1.9.3     ✔ tidyr     1.3.0
## ✔ purrr     1.0.2     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
data <- 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.
data %>% skimr::skim()
Data summary
Name Piped data
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 ▁▁▂▇▇

Goal: Predict the death on Nepal Himalaya climbers

Issues with data:

Cleaning Data

# Treating missing values
data_clean <- data %>% 
    select(-death_cause, -injury_type, -death_height_metres, -injury_height_metres) %>%
    na.omit()

Explore Data

data_clean %>% count(died)
## # A tibble: 2 × 2
##   died      n
##   <lgl> <int>
## 1 FALSE 51639
## 2 TRUE    744
data_clean %>%
    ggplot(aes(died)) +
    geom_bar()

Died vs. expedition_role

top_10_exp_role_vec <- data_clean %>% 
    count(expedition_role, sort = TRUE) %>% 
    head(10) %>% 
    pull(expedition_role)

# Relationship between pay and attrition
data_clean %>%
    filter(expedition_role %in% top_10_exp_role_vec) %>%
    count(died, expedition_role) %>%
    ggplot(aes(died, expedition_role, fill = n)) +
    geom_tile()

Relationship in all variables with Correlation plot

library(correlationfunnel)
## ══ correlationfunnel Tip #3 ════════════════════════════════════════════════════
## Using `binarize()` with data containing many columns or many rows can increase dimensionality substantially.
## Try subsetting your data column-wise or row-wise to avoid creating too many columns.
## You can always make a big problem smaller by sampling. :)
 # Step 1: Binarize
data_binarized <- data_clean %>%
    select(-member_id) %>% # ID variable
    binarize()

data_binarized %>% glimpse()
## Rows: 52,383
## Columns: 82
## $ expedition_id__HIML13308       <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `expedition_id__-OTHER`        <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ peak_id__AMAD                  <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ peak_id__ANN1                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__BARU                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__CHOY                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__DHA1                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__EVER                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__HIML                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__KANG                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__LHOT                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__MAKA                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__MANA                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_id__PUMO                  <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `peak_id__-OTHER`              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Ama_Dablam          <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ peak_name__Annapurna_I         <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Baruntse            <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Cho_Oyu             <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Dhaulagiri_I        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Everest             <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Himlung_Himal       <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Kangchenjunga       <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Lhotse              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Makalu              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Manaslu             <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ peak_name__Pumori              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `peak_name__-OTHER`            <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `year__-Inf_1997`              <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ year__1997_2007                <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ year__2007_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, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ season__Spring                 <dbl> 0, 0, 0, 0, 0, 1, 1, 1, 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, 1, 0, 1, 0, 0, 1, 0, 0, 1, …
## $ age__29_36                     <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, …
## $ age__36_43                     <dbl> 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, …
## $ age__43_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, 0, 0, 0, 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__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, 1, 1, 1, 1, 1, 1, 1, …
## $ `citizenship__-OTHER`          <dbl> 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, …
## $ expedition_role__Climber       <dbl> 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 1, 0, …
## $ expedition_role__Deputy_Leader <dbl> 1, 0, 0, 0, 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> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `expedition_role__-OTHER`      <dbl> 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, …
## $ hired__0                       <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ hired__1                       <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ `highpoint_metres__-Inf_6750`  <dbl> 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ highpoint_metres__6750_7400    <dbl> 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ highpoint_metres__7400_8450    <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ highpoint_metres__8450_Inf     <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ success__0                     <dbl> 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ success__1                     <dbl> 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ solo__0                        <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__0                 <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ oxygen_used__1                 <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ died__0                        <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ died__1                        <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ injured__0                     <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ injured__1                     <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
# Step 2: Correlation
data_correlation <- data_binarized %>%
    correlate(died__1)
## Warning: correlate(): [Data Imbalance Detected] Consider sampling to balance the classes more than 5%
##   Column with imbalance: died__1
data_correlation
## # A tibble: 82 × 3
##    feature   bin         correlation
##    <fct>     <chr>             <dbl>
##  1 died      0               -1     
##  2 died      1                1     
##  3 year      -Inf_1997        0.0843
##  4 success   0                0.0562
##  5 success   1               -0.0562
##  6 peak_id   ANN1             0.0431
##  7 peak_name Annapurna_I      0.0431
##  8 year      2012_Inf        -0.0330
##  9 peak_id   AMAD            -0.0323
## 10 peak_name Ama_Dablam      -0.0323
## # ℹ 72 more rows
# Step 3: Plot
data_correlation %>%
    correlationfunnel::plot_correlation_funnel()
## Warning: ggrepel: 45 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps