Multiple Imputation with MICE
data <- read.csv(file = "~/Dropbox/DKE/Machine Learning/Master Assignment/Chronic_Kidney_Disease/chronic_kidney_disease_full.csv")
attach(data)
# Data Preprocessing
# Sort dataframe by numerical
# and categorical cols so writing
# imputation code will be easier
### Data preproc
data$al <- as.factor(data$al)
data$su <- as.factor(data$su)
nums <- sapply(data, is.numeric)
cat <- sapply(data, is.factor)
data_num <- data[,nums]
data_cat <- data[,cat]
rm(nums, cat)
data <- cbind(data_num, data_cat)require(mice)
require(VIM)
require(lattice)aggr_plot <- aggr(data[-c(25)],combination=T, sortVars=TRUE, labels=names(data), cex.axis=.9, gap=1, ylab=c("Histogram of missing data","Pattern"))
##
## Variables sorted by number of missings:
## Variable Count
## rbc 0.3800
## rbcc 0.3275
## wbcc 0.2650
## pot 0.2200
## sod 0.2175
## pcv 0.1775
## pc 0.1625
## hemo 0.1300
## su 0.1225
## sg 0.1175
## al 0.1150
## bgr 0.1100
## bu 0.0475
## sc 0.0425
## bp 0.0300
## age 0.0225
## pcc 0.0100
## ba 0.0100
## htn 0.0050
## dm 0.0050
## cad 0.0050
## appet 0.0025
## pe 0.0025
## ane 0.0025# Number of rows without any missing value
nrow(data[complete.cases(data),])/nrow(data)## [1] 0.395marginplot(data[c("hemo","sc")])
Bottom Bar-plots are supposed to be quite similiar if data is MCAR.
Impute
##
## iter imp variable
## 1 1 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 2 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 3 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 4 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 5 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 6 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 7 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 8 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 9 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 10 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 11 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 12 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 13 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 14 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 15 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 16 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 17 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 18 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 19 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 1 20 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 1 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 2 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 3 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 4 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 5 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 6 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 7 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 8 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 9 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 10 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 11 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 12 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 13 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 14 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 15 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 16 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 17 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 18 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 19 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 2 20 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 1 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 2 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 3 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 4 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 5 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 6 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 7 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 8 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 9 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 10 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 11 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 12 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 13 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 14 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 15 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 16 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 17 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 18 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 19 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 3 20 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 1 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 2 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 3 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 4 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 5 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 6 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 7 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 8 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 9 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 10 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 11 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 12 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 13 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 14 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 15 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 16 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 17 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 18 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 19 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 4 20 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 1 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 2 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 3 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 4 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 5 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 6 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 7 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 8 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 9 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 10 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 11 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 12 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 13 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 14 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 15 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 16 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 17 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 18 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 19 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe ane
## 5 20 age bp sg bgr bu sc sod pot hemo pcv wbcc rbcc al su rbc pc pcc ba htn dm cad appet pe aneCompare density plot of imputed datasets to dataset with missing values
lattice::densityplot(data_imputed)