Regresión Logística - Heart Disease

Teoría

La regresión logística es un modelo estadístico de clasificación binaria, que estima la probabilidad de que ocurra un evento (valor 1) frente a que no ocurra (valor 0), en función de variables independientes.

Instalar paquetes y llamar librerías

# Cargr la base de datos
library(readr)
heart <- read_csv("~/Conexión de interfaces/Conexión de interfaces/heart.csv")

## Rows: 1025 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (14): age, sex, cp, trestbps, chol, fbs, restecg, thalach, exang, oldpea...
## 
## 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.

# install.packages("caret")
library(caret)

## Loading required package: ggplot2
## Loading required package: lattice

# install.packages("tidyverse")
library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ stringr   1.5.1
## ✔ forcats   1.0.0     ✔ tibble    3.3.0
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
## ✔ purrr     1.1.0     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ✖ purrr::lift()   masks caret::lift()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Crear la base de datos

df <- heart

Entender la base de datos

summary(df)

##       age             sex               cp            trestbps    
##  Min.   :29.00   Min.   :0.0000   Min.   :0.0000   Min.   : 94.0  
##  1st Qu.:48.00   1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:120.0  
##  Median :56.00   Median :1.0000   Median :1.0000   Median :130.0  
##  Mean   :54.43   Mean   :0.6956   Mean   :0.9424   Mean   :131.6  
##  3rd Qu.:61.00   3rd Qu.:1.0000   3rd Qu.:2.0000   3rd Qu.:140.0  
##  Max.   :77.00   Max.   :1.0000   Max.   :3.0000   Max.   :200.0  
##       chol          fbs            restecg          thalach     
##  Min.   :126   Min.   :0.0000   Min.   :0.0000   Min.   : 71.0  
##  1st Qu.:211   1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:132.0  
##  Median :240   Median :0.0000   Median :1.0000   Median :152.0  
##  Mean   :246   Mean   :0.1493   Mean   :0.5298   Mean   :149.1  
##  3rd Qu.:275   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:166.0  
##  Max.   :564   Max.   :1.0000   Max.   :2.0000   Max.   :202.0  
##      exang           oldpeak          slope             ca        
##  Min.   :0.0000   Min.   :0.000   Min.   :0.000   Min.   :0.0000  
##  1st Qu.:0.0000   1st Qu.:0.000   1st Qu.:1.000   1st Qu.:0.0000  
##  Median :0.0000   Median :0.800   Median :1.000   Median :0.0000  
##  Mean   :0.3366   Mean   :1.072   Mean   :1.385   Mean   :0.7541  
##  3rd Qu.:1.0000   3rd Qu.:1.800   3rd Qu.:2.000   3rd Qu.:1.0000  
##  Max.   :1.0000   Max.   :6.200   Max.   :2.000   Max.   :4.0000  
##       thal           target      
##  Min.   :0.000   Min.   :0.0000  
##  1st Qu.:2.000   1st Qu.:0.0000  
##  Median :2.000   Median :1.0000  
##  Mean   :2.324   Mean   :0.5132  
##  3rd Qu.:3.000   3rd Qu.:1.0000  
##  Max.   :3.000   Max.   :1.0000

str(df)

## spc_tbl_ [1,025 × 14] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
##  $ age     : num [1:1025] 52 53 70 61 62 58 58 55 46 54 ...
##  $ sex     : num [1:1025] 1 1 1 1 0 0 1 1 1 1 ...
##  $ cp      : num [1:1025] 0 0 0 0 0 0 0 0 0 0 ...
##  $ trestbps: num [1:1025] 125 140 145 148 138 100 114 160 120 122 ...
##  $ chol    : num [1:1025] 212 203 174 203 294 248 318 289 249 286 ...
##  $ fbs     : num [1:1025] 0 1 0 0 1 0 0 0 0 0 ...
##  $ restecg : num [1:1025] 1 0 1 1 1 0 2 0 0 0 ...
##  $ thalach : num [1:1025] 168 155 125 161 106 122 140 145 144 116 ...
##  $ exang   : num [1:1025] 0 1 1 0 0 0 0 1 0 1 ...
##  $ oldpeak : num [1:1025] 1 3.1 2.6 0 1.9 1 4.4 0.8 0.8 3.2 ...
##  $ slope   : num [1:1025] 2 0 0 2 1 1 0 1 2 1 ...
##  $ ca      : num [1:1025] 2 0 0 1 3 0 3 1 0 2 ...
##  $ thal    : num [1:1025] 3 3 3 3 2 2 1 3 3 2 ...
##  $ target  : num [1:1025] 0 0 0 0 0 1 0 0 0 0 ...
##  - attr(*, "spec")=
##   .. cols(
##   ..   age = col_double(),
##   ..   sex = col_double(),
##   ..   cp = col_double(),
##   ..   trestbps = col_double(),
##   ..   chol = col_double(),
##   ..   fbs = col_double(),
##   ..   restecg = col_double(),
##   ..   thalach = col_double(),
##   ..   exang = col_double(),
##   ..   oldpeak = col_double(),
##   ..   slope = col_double(),
##   ..   ca = col_double(),
##   ..   thal = col_double(),
##   ..   target = col_double()
##   .. )
##  - attr(*, "problems")=<externalptr>

df <- df[, c("target", "age", "sex", "cp", "trestbps", "chol",
             "fbs", "restecg", "thalach", "exang", "oldpeak",
             "slope", "ca", "thal")]
df <- na.omit(df)

# Variables categóricas a factor
df$target  <- as.factor(df$target)
df$sex     <- as.factor(df$sex)
df$cp      <- as.factor(df$cp)
df$fbs     <- as.factor(df$fbs)
df$restecg <- as.factor(df$restecg)
df$exang   <- as.factor(df$exang)
df$slope   <- as.factor(df$slope)
df$ca      <- as.factor(df$ca)
df$thal    <- as.factor(df$thal)

Crear el modelo

modelo <- glm(target ~ ., data = df, family = binomial)
summary(modelo)

## 
## Call:
## glm(formula = target ~ ., family = binomial, data = df)
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -0.081901   2.028691  -0.040 0.967797    
## age          0.026846   0.013950   1.924 0.054297 .  
## sex1        -1.992347   0.314204  -6.341 2.28e-10 ***
## cp1          0.886380   0.308803   2.870 0.004100 ** 
## cp2          2.006394   0.286281   7.008 2.41e-12 ***
## cp3          2.409722   0.391965   6.148 7.86e-10 ***
## trestbps    -0.024979   0.006537  -3.821 0.000133 ***
## chol        -0.005462   0.002307  -2.367 0.017914 *  
## fbs1         0.380096   0.319620   1.189 0.234356    
## restecg1     0.397268   0.217975   1.823 0.068374 .  
## restecg2    -0.800417   1.536998  -0.521 0.602530    
## thalach      0.021692   0.006525   3.324 0.000886 ***
## exang1      -0.750331   0.248746  -3.016 0.002557 ** 
## oldpeak     -0.403411   0.132156  -3.053 0.002269 ** 
## slope1      -0.595618   0.472076  -1.262 0.207057    
## slope2       0.799689   0.504500   1.585 0.112941    
## ca1         -2.334076   0.286781  -8.139 3.99e-16 ***
## ca2         -3.597039   0.444870  -8.086 6.19e-16 ***
## ca3         -2.288131   0.532138  -4.300 1.71e-05 ***
## ca4          1.565677   0.930256   1.683 0.092363 .  
## thal1        2.796813   1.466219   1.908 0.056456 .  
## thal2        2.404646   1.421542   1.692 0.090727 .  
## thal3        0.991243   1.423972   0.696 0.486359    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1420.24  on 1024  degrees of freedom
## Residual deviance:  606.82  on 1002  degrees of freedom
## AIC: 652.82
## 
## Number of Fisher Scoring iterations: 6

Probar el modelo

# Tomar 2 registros 
prueba <- df[sample(nrow(df), 2), ]
prueba$target <- NULL   

probabilidad <- predict(modelo, newdata = prueba, type = "response")
cbind(prueba, probabilidad_target1 = probabilidad)

##   age sex cp trestbps chol fbs restecg thalach exang oldpeak slope ca thal
## 1  71   0  0      112  149   0       1     125     0     1.6     1  0    2
## 2  63   0  2      135  252   0       0     172     0     0.0     2  0    2
##   probabilidad_target1
## 1            0.9230850
## 2            0.9969894

Conclusiones

• Sexo (sex=1) baja la probabilidad de target=1, con un coeficiente de -1.99.

• Dolor de pecho (cp) tiene un gran peso, ya que comparado con cp=0, cp=1 aumenta un 0.89, cp=2 un 2.01 y cp=3 un 2.41 aumentan la probabilidad de target=1.

• Presión en reposo (trestbps) y colesterol (chol) tienen efecto negativo, con coeficientes de -0.025 y -0.005 respectivamente.

En las pruebas realizadas se muestra la probabilidad de target1 en 2 registros aleatorios de la base de datos