Arbol de decisión
Santiago Macias
2023-09-19
1. Importar la base de datos
2. Entender la base de datos
## pclass survived name sex
## Min. :1.000 Min. :0.000 Length:1310 Length:1310
## 1st Qu.:2.000 1st Qu.:0.000 Class :character Class :character
## Median :3.000 Median :0.000 Mode :character Mode :character
## Mean :2.295 Mean :0.382
## 3rd Qu.:3.000 3rd Qu.:1.000
## Max. :3.000 Max. :1.000
## NA's :1 NA's :1
## age sibsp parch ticket
## Min. : 0.1667 Min. :0.0000 Min. :0.000 Length:1310
## 1st Qu.:21.0000 1st Qu.:0.0000 1st Qu.:0.000 Class :character
## Median :28.0000 Median :0.0000 Median :0.000 Mode :character
## Mean :29.8811 Mean :0.4989 Mean :0.385
## 3rd Qu.:39.0000 3rd Qu.:1.0000 3rd Qu.:0.000
## Max. :80.0000 Max. :8.0000 Max. :9.000
## NA's :264 NA's :1 NA's :1
## fare cabin embarked boat
## Min. : 0.000 Length:1310 Length:1310 Length:1310
## 1st Qu.: 7.896 Class :character Class :character Class :character
## Median : 14.454 Mode :character Mode :character Mode :character
## Mean : 33.295
## 3rd Qu.: 31.275
## Max. :512.329
## NA's :2
## body home.dest
## Min. : 1.0 Length:1310
## 1st Qu.: 72.0 Class :character
## Median :155.0 Mode :character
## Mean :160.8
## 3rd Qu.:256.0
## Max. :328.0
## NA's :1189## 'data.frame': 1310 obs. of 14 variables:
## $ pclass : int 1 1 1 1 1 1 1 1 1 1 ...
## $ survived : int 1 1 0 0 0 1 1 0 1 0 ...
## $ name : chr "Allen, Miss. Elisabeth Walton" "Allison, Master. Hudson Trevor" "Allison, Miss. Helen Loraine" "Allison, Mr. Hudson Joshua Creighton" ...
## $ sex : chr "female" "male" "female" "male" ...
## $ age : num 29 0.917 2 30 25 ...
## $ sibsp : int 0 1 1 1 1 0 1 0 2 0 ...
## $ parch : int 0 2 2 2 2 0 0 0 0 0 ...
## $ ticket : chr "24160" "113781" "113781" "113781" ...
## $ fare : num 211 152 152 152 152 ...
## $ cabin : chr "B5" "C22 C26" "C22 C26" "C22 C26" ...
## $ embarked : chr "S" "S" "S" "S" ...
## $ boat : chr "2" "11" "" "" ...
## $ body : int NA NA NA 135 NA NA NA NA NA 22 ...
## $ home.dest: chr "St Louis, MO" "Montreal, PQ / Chesterville, ON" "Montreal, PQ / Chesterville, ON" "Montreal, PQ / Chesterville, ON" ...##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union#count(titanic, name, sort = TRUE)
#count(titanic, sex, sort = TRUE)
#count(titanic, ticket, sort = TRUE)
#count(titanic, cabin, sort = TRUE)
#count(titanic, embarked, sort = TRUE)
#count(titanic, boat, sort = TRUE)
#count(titanic, home.dest, sort = TRUE)Observaciones 1. Tenemos 2 registros de nombres repetidos 2. Hay NAs
3. Limpieza de la base de datos
# Cambiar de nombre a la variable pclass
colnames(titanic)[1] <- "class"
#Extraer las variables de interés
Titanic <- titanic [,c("class","age","sex","survived")]
#¿Cuántos NA tengo en la base de datos?
sum(is.na(Titanic))## [1] 266## class age sex survived
## 1 264 0 1#Eliminar renglon en blanco
Titanic <- Titanic [-1310,]
#Convertir las variablea categóricas en factores
Titanic$class <- as.factor(Titanic$class)
Titanic$sex <- as.factor(Titanic$sex)
Titanic$survived <- as.factor(ifelse(Titanic$survived==0, "Murió", "Sobrevivió"))
str(Titanic)## 'data.frame': 1309 obs. of 4 variables:
## $ class : Factor w/ 3 levels "1","2","3": 1 1 1 1 1 1 1 1 1 1 ...
## $ age : num 29 0.917 2 30 25 ...
## $ sex : Factor w/ 2 levels "female","male": 1 2 1 2 1 2 1 2 1 2 ...
## $ survived: Factor w/ 2 levels "Murió","Sobrevivió": 2 2 1 1 1 2 2 1 2 1 ...## class age sex survived
## 0 263 0 0#Eliminar NA
Titanic <- na.omit(Titanic)
#¿Cuántos tengo por variable?
sapply(Titanic, function(x) sum(is.na(x)))## class age sex survived
## 0 0 0 04. crear el arbol de decisión
## n= 1046
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 1046 427 Murió (0.59177820 0.40822180)
## 2) sex=male 658 135 Murió (0.79483283 0.20516717)
## 4) age>=9.5 615 110 Murió (0.82113821 0.17886179) *
## 5) age< 9.5 43 18 Sobrevivió (0.41860465 0.58139535)
## 10) class=3 29 11 Murió (0.62068966 0.37931034) *
## 11) class=1,2 14 0 Sobrevivió (0.00000000 1.00000000) *
## 3) sex=female 388 96 Sobrevivió (0.24742268 0.75257732)
## 6) class=3 152 72 Murió (0.52631579 0.47368421)
## 12) age>=1.5 145 66 Murió (0.54482759 0.45517241) *
## 13) age< 1.5 7 1 Sobrevivió (0.14285714 0.85714286) *
## 7) class=1,2 236 16 Sobrevivió (0.06779661 0.93220339) *
CANCER DE MAMA
1. Importar la base de datos
2. Entender la base de datos
## diagnosis radius_mean texture_mean perimeter_mean
## Length:569 Min. : 6.981 Min. : 9.71 Min. : 43.79
## Class :character 1st Qu.:11.700 1st Qu.:16.17 1st Qu.: 75.17
## Mode :character Median :13.370 Median :18.84 Median : 86.24
## Mean :14.127 Mean :19.29 Mean : 91.97
## 3rd Qu.:15.780 3rd Qu.:21.80 3rd Qu.:104.10
## Max. :28.110 Max. :39.28 Max. :188.50
## area_mean smoothness_mean compactness_mean concavity_mean
## Min. : 143.5 Min. :0.05263 Min. :0.01938 Min. :0.00000
## 1st Qu.: 420.3 1st Qu.:0.08637 1st Qu.:0.06492 1st Qu.:0.02956
## Median : 551.1 Median :0.09587 Median :0.09263 Median :0.06154
## Mean : 654.9 Mean :0.09636 Mean :0.10434 Mean :0.08880
## 3rd Qu.: 782.7 3rd Qu.:0.10530 3rd Qu.:0.13040 3rd Qu.:0.13070
## Max. :2501.0 Max. :0.16340 Max. :0.34540 Max. :0.42680
## concave.points_mean symmetry_mean fractal_dimension_mean radius_se
## Min. :0.00000 Min. :0.1060 Min. :0.04996 Min. :0.1115
## 1st Qu.:0.02031 1st Qu.:0.1619 1st Qu.:0.05770 1st Qu.:0.2324
## Median :0.03350 Median :0.1792 Median :0.06154 Median :0.3242
## Mean :0.04892 Mean :0.1812 Mean :0.06280 Mean :0.4052
## 3rd Qu.:0.07400 3rd Qu.:0.1957 3rd Qu.:0.06612 3rd Qu.:0.4789
## Max. :0.20120 Max. :0.3040 Max. :0.09744 Max. :2.8730
## texture_se perimeter_se area_se smoothness_se
## Min. :0.3602 Min. : 0.757 Min. : 6.802 Min. :0.001713
## 1st Qu.:0.8339 1st Qu.: 1.606 1st Qu.: 17.850 1st Qu.:0.005169
## Median :1.1080 Median : 2.287 Median : 24.530 Median :0.006380
## Mean :1.2169 Mean : 2.866 Mean : 40.337 Mean :0.007041
## 3rd Qu.:1.4740 3rd Qu.: 3.357 3rd Qu.: 45.190 3rd Qu.:0.008146
## Max. :4.8850 Max. :21.980 Max. :542.200 Max. :0.031130
## compactness_se concavity_se concave.points_se symmetry_se
## Min. :0.002252 Min. :0.00000 Min. :0.000000 Min. :0.007882
## 1st Qu.:0.013080 1st Qu.:0.01509 1st Qu.:0.007638 1st Qu.:0.015160
## Median :0.020450 Median :0.02589 Median :0.010930 Median :0.018730
## Mean :0.025478 Mean :0.03189 Mean :0.011796 Mean :0.020542
## 3rd Qu.:0.032450 3rd Qu.:0.04205 3rd Qu.:0.014710 3rd Qu.:0.023480
## Max. :0.135400 Max. :0.39600 Max. :0.052790 Max. :0.078950
## fractal_dimension_se radius_worst texture_worst perimeter_worst
## Min. :0.0008948 Min. : 7.93 Min. :12.02 Min. : 50.41
## 1st Qu.:0.0022480 1st Qu.:13.01 1st Qu.:21.08 1st Qu.: 84.11
## Median :0.0031870 Median :14.97 Median :25.41 Median : 97.66
## Mean :0.0037949 Mean :16.27 Mean :25.68 Mean :107.26
## 3rd Qu.:0.0045580 3rd Qu.:18.79 3rd Qu.:29.72 3rd Qu.:125.40
## Max. :0.0298400 Max. :36.04 Max. :49.54 Max. :251.20
## area_worst smoothness_worst compactness_worst concavity_worst
## Min. : 185.2 Min. :0.07117 Min. :0.02729 Min. :0.0000
## 1st Qu.: 515.3 1st Qu.:0.11660 1st Qu.:0.14720 1st Qu.:0.1145
## Median : 686.5 Median :0.13130 Median :0.21190 Median :0.2267
## Mean : 880.6 Mean :0.13237 Mean :0.25427 Mean :0.2722
## 3rd Qu.:1084.0 3rd Qu.:0.14600 3rd Qu.:0.33910 3rd Qu.:0.3829
## Max. :4254.0 Max. :0.22260 Max. :1.05800 Max. :1.2520
## concave.points_worst symmetry_worst fractal_dimension_worst
## Min. :0.00000 Min. :0.1565 Min. :0.05504
## 1st Qu.:0.06493 1st Qu.:0.2504 1st Qu.:0.07146
## Median :0.09993 Median :0.2822 Median :0.08004
## Mean :0.11461 Mean :0.2901 Mean :0.08395
## 3rd Qu.:0.16140 3rd Qu.:0.3179 3rd Qu.:0.09208
## Max. :0.29100 Max. :0.6638 Max. :0.20750## 'data.frame': 569 obs. of 31 variables:
## $ diagnosis : chr "M" "M" "M" "M" ...
## $ radius_mean : num 18 20.6 19.7 11.4 20.3 ...
## $ texture_mean : num 10.4 17.8 21.2 20.4 14.3 ...
## $ perimeter_mean : num 122.8 132.9 130 77.6 135.1 ...
## $ area_mean : num 1001 1326 1203 386 1297 ...
## $ smoothness_mean : num 0.1184 0.0847 0.1096 0.1425 0.1003 ...
## $ compactness_mean : num 0.2776 0.0786 0.1599 0.2839 0.1328 ...
## $ concavity_mean : num 0.3001 0.0869 0.1974 0.2414 0.198 ...
## $ concave.points_mean : num 0.1471 0.0702 0.1279 0.1052 0.1043 ...
## $ symmetry_mean : num 0.242 0.181 0.207 0.26 0.181 ...
## $ fractal_dimension_mean : num 0.0787 0.0567 0.06 0.0974 0.0588 ...
## $ radius_se : num 1.095 0.543 0.746 0.496 0.757 ...
## $ texture_se : num 0.905 0.734 0.787 1.156 0.781 ...
## $ perimeter_se : num 8.59 3.4 4.58 3.44 5.44 ...
## $ area_se : num 153.4 74.1 94 27.2 94.4 ...
## $ smoothness_se : num 0.0064 0.00522 0.00615 0.00911 0.01149 ...
## $ compactness_se : num 0.049 0.0131 0.0401 0.0746 0.0246 ...
## $ concavity_se : num 0.0537 0.0186 0.0383 0.0566 0.0569 ...
## $ concave.points_se : num 0.0159 0.0134 0.0206 0.0187 0.0188 ...
## $ symmetry_se : num 0.03 0.0139 0.0225 0.0596 0.0176 ...
## $ fractal_dimension_se : num 0.00619 0.00353 0.00457 0.00921 0.00511 ...
## $ radius_worst : num 25.4 25 23.6 14.9 22.5 ...
## $ texture_worst : num 17.3 23.4 25.5 26.5 16.7 ...
## $ perimeter_worst : num 184.6 158.8 152.5 98.9 152.2 ...
## $ area_worst : num 2019 1956 1709 568 1575 ...
## $ smoothness_worst : num 0.162 0.124 0.144 0.21 0.137 ...
## $ compactness_worst : num 0.666 0.187 0.424 0.866 0.205 ...
## $ concavity_worst : num 0.712 0.242 0.45 0.687 0.4 ...
## $ concave.points_worst : num 0.265 0.186 0.243 0.258 0.163 ...
## $ symmetry_worst : num 0.46 0.275 0.361 0.664 0.236 ...
## $ fractal_dimension_worst: num 0.1189 0.089 0.0876 0.173 0.0768 ...## diagnosis n
## 1 B 357
## 2 M 2123. crear el arbol de decisión
library(rpart)
library(rpart.plot)
arbol <- rpart(formula = diagnosis ~ ., data = cancer_de_mama)
arbol## n= 569
##
## node), split, n, loss, yval, (yprob)
## * denotes terminal node
##
## 1) root 569 212 B (0.62741652 0.37258348)
## 2) radius_worst< 16.795 379 33 B (0.91292876 0.08707124)
## 4) concave.points_worst< 0.1358 333 5 B (0.98498498 0.01501502) *
## 5) concave.points_worst>=0.1358 46 18 M (0.39130435 0.60869565)
## 10) texture_worst< 25.67 19 4 B (0.78947368 0.21052632) *
## 11) texture_worst>=25.67 27 3 M (0.11111111 0.88888889) *
## 3) radius_worst>=16.795 190 11 M (0.05789474 0.94210526) *
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