noiris: Data sets

library(tidyverse)

hd0 = readr::read_csv('data-raw/heart-disease/heart.csv')


tidyext::describe_all(hd0)

heart_disease = hd0 %>%
  mutate(
    sex = factor(sex, labels = c('female', 'male')),
    cp = factor(cp, labels = c('typical angina', 'atypical angina', 'non-anginal pain', 'asymptomatic')),
    fbs = factor(fbs, labels = c('lt_120', 'gt_120')),
    exang = factor(exang, labels = c('no', 'yes')),
    thal = ifelse(thal == 0, NA, thal),
    thal = factor(thal, labels = c('normal', 'fixed_defect', 'reversible_defect')),
    slope = factor(slope, labels = c('positive', 'flat', 'negative'))
  ) %>%
  rename(
    fasting_blood_sugar = fbs,
    chest_pain_type = cp,
    resting_bp = trestbps,
    cholesterol = chol,
    resting_ecg = restecg,
    max_heartrate = thalach,
    exer_angina = exang,
    n_vessels = ca,
    defect = thal,
    old_peak = oldpeak,
    heart_disease = target
  )

glimpse(heart_disease)
tidyext::describe_all(heart_disease)

usethis::use_data(heart_disease, overwrite = TRUE)

# age
#
# age in years
# sex
#
# (1 = male; 0 = female)
# cp
#
# chest pain type
# trestbps
#
# resting blood pressure (in mm Hg on admission to the hospital)
# chol
#
# serum cholestoral in mg/dl
# fbs
#
# (fasting blood sugar > 120 mg/dl) (1 = true; 0 = false)
# restecg
#
# resting electrocardiographic results
# thalach
#
# maximum heart rate achieved
# exang
#
# exercise induced angina (1 = yes; 0 = no)
# oldpeak
#
# ST depression induced by exercise relative to rest
# slope
#
# the slope of the peak exercise ST segment
# ca
#
# number of major vessels (0-3) colored by flourosopy
# thal
#
# 3 = normal; 6 = fixed defect; 7 = reversable defect
# target
#
# 1 or 0


# Complete attribute documentation: 1 id: patient identification number 2 ccf:
# social security number (I replaced this with a dummy value of 0) 3 age: age in
# years 4 sex: sex (1 = male; 0 = female) 5 painloc: chest pain location (1 =
# substernal; 0 = otherwise) 6 painexer (1 = provoked by exertion; 0 =
# otherwise) 7 relrest (1 = relieved after rest; 0 = otherwise) 8 pncaden (sum
# of 5, 6, and 7) 9 cp: chest pain type -- Value 1: typical angina -- Value 2:
# atypical angina -- Value 3: non-anginal pain -- Value 4: asymptomatic 10
# trestbps: resting blood pressure (in mm Hg on admission to the hospital) 11
# htn 12 chol: serum cholestoral in mg/dl 13 smoke: I believe this is 1 = yes; 0
# = no (is or is not a smoker) 14 cigs (cigarettes per day) 15 years (number of
# years as a smoker) 16 fbs: (fasting blood sugar > 120 mg/dl) (1 = true; 0 =
# false) 17 dm (1 = history of diabetes; 0 = no such history) 18 famhist: family
# history of coronary artery disease (1 = yes; 0 = no) 19 restecg: resting
# electrocardiographic results -- Value 0: normal -- Value 1: having ST-T wave
# abnormality (T wave inversions and/or ST elevation or depression of > 0.05 mV)
# -- Value 2: showing probable or definite left ventricular hypertrophy by
# Estes' criteria 20 ekgmo (month of exercise ECG reading) 21 ekgday(day of
# exercise ECG reading) 22 ekgyr (year of exercise ECG reading) 23 dig
# (digitalis used furing exercise ECG: 1 = yes; 0 = no) 24 prop (Beta blocker
# used during exercise ECG: 1 = yes; 0 = no) 25 nitr (nitrates used during
# exercise ECG: 1 = yes; 0 = no) 26 pro (calcium channel blocker used during
# exercise ECG: 1 = yes; 0 = no) 27 diuretic (diuretic used used during exercise
# ECG: 1 = yes; 0 = no) 28 proto: exercise protocol 1 = Bruce 2 = Kottus 3 =
# McHenry 4 = fast Balke 5 = Balke 6 = Noughton 7 = bike 150 kpa min/min (Not
# sure if "kpa min/min" is what was written!) 8 = bike 125 kpa min/min 9 = bike
# 100 kpa min/min 10 = bike 75 kpa min/min 11 = bike 50 kpa min/min 12 = arm
# ergometer 29 thaldur: duration of exercise test in minutes 30 thaltime: time
# when ST measure depression was noted 31 met: mets achieved 32 thalach: maximum
# heart rate achieved 33 thalrest: resting heart rate 34 tpeakbps: peak exercise
# blood pressure (first of 2 parts) 35 tpeakbpd: peak exercise blood pressure
# (second of 2 parts) 36 dummy 37 trestbpd: resting blood pressure 38 exang:
# exercise induced angina (1 = yes; 0 = no) 39 xhypo: (1 = yes; 0 = no) 40
# oldpeak = ST depression induced by exercise relative to rest 41 slope: the
# slope of the peak exercise ST segment -- Value 1: upsloping -- Value 2: flat
# -- Value 3: downsloping 42 rldv5: height at rest 43 rldv5e: height at peak
# exercise 44 ca: number of major vessels (0-3) colored by flourosopy 45
# restckm: irrelevant 46 exerckm: irrelevant 47 restef: rest raidonuclid (sp?)
# ejection fraction 48 restwm: rest wall (sp?) motion abnormality 0 = none 1 =
# mild or moderate 2 = moderate or severe 3 = akinesis or dyskmem (sp?) 49
# exeref: exercise radinalid (sp?) ejection fraction 50 exerwm: exercise wall
# (sp?) motion 51 thal: 3 = normal; 6 = fixed defect; 7 = reversable defect 52
# thalsev: not used 53 thalpul: not used 54 earlobe: not used 55 cmo: month of
# cardiac cath (sp?) (perhaps "call") 56 cday: day of cardiac cath (sp?) 57 cyr:
# year of cardiac cath (sp?) 58 num: diagnosis of heart disease (angiographic
# disease status) -- Value 0: < 50% diameter narrowing -- Value 1: > 50%
# diameter narrowing (in any major vessel: attributes 59 through 68 are vessels)
# 59 lmt 60 ladprox 61 laddist 62 diag 63 cxmain 64 ramus 65 om1 66 om2 67
# rcaprox 68 rcadist 69 lvx1: not used 70 lvx2: not used 71 lvx3: not used 72
# lvx4: not used 73 lvf: not used 74 cathef: not used 75 junk: not used 76 name:
# last name of patient (I replaced this with the dummy string "name")