data("faithful")
head(faithful)
## eruptions waiting
## 1 3.600 79
## 2 1.800 54
## 3 3.333 74
## 4 2.283 62
## 5 4.533 85
## 6 2.883 55
eruption.lm<-lm(eruptions~waiting,data=faithful)
summary(eruption.lm)
##
## Call:
## lm(formula = eruptions ~ waiting, data = faithful)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.29917 -0.37689 0.03508 0.34909 1.19329
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.874016 0.160143 -11.70 <2e-16 ***
## waiting 0.075628 0.002219 34.09 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.4965 on 270 degrees of freedom
## Multiple R-squared: 0.8115, Adjusted R-squared: 0.8108
## F-statistic: 1162 on 1 and 270 DF, p-value: < 2.2e-16
plot(eruptions~waiting,data = faithful)
abline(eruption.lm,col="red")
plot(eruption.lm)
newdata<-data.frame(waiting=75)
predict(eruption.lm,newdata)
## 1
## 3.79808
data("stackloss")
head(stackloss)
## Air.Flow Water.Temp Acid.Conc. stack.loss
## 1 80 27 89 42
## 2 80 27 88 37
## 3 75 25 90 37
## 4 62 24 87 28
## 5 62 22 87 18
## 6 62 23 87 18
stackloss.lm<-lm(stack.loss~Air.Flow+Water.Temp+Acid.Conc.,data = stackloss)
summary(stackloss.lm)
##
## Call:
## lm(formula = stack.loss ~ Air.Flow + Water.Temp + Acid.Conc.,
## data = stackloss)
##
## Residuals:
## Min 1Q Median 3Q Max
## -7.2377 -1.7117 -0.4551 2.3614 5.6978
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -39.9197 11.8960 -3.356 0.00375 **
## Air.Flow 0.7156 0.1349 5.307 5.8e-05 ***
## Water.Temp 1.2953 0.3680 3.520 0.00263 **
## Acid.Conc. -0.1521 0.1563 -0.973 0.34405
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 3.243 on 17 degrees of freedom
## Multiple R-squared: 0.9136, Adjusted R-squared: 0.8983
## F-statistic: 59.9 on 3 and 17 DF, p-value: 3.016e-09
par(mfrow=c(2,3))
termplot(stackloss.lm)
plot(stackloss.lm)
newdata<-data.frame(Air.Flow=72,Water.Temp=20,Acid.Conc.=85)
predict(stackloss.lm,newdata)
## 1
## 24.58173
#install.packages("missForest")
#install.packages("mice")
#install.packages("VIM")
library(missForest)
## Loading required package: randomForest
## randomForest 4.6-12
## Type rfNews() to see new features/changes/bug fixes.
## Loading required package: foreach
## Loading required package: itertools
## Loading required package: iterators
data<-iris
#Genrerate 10% of missing values at random
iris.mis<-prodNA(iris,noNA = .1)
#check the missing values
View(iris.mis)
summary(iris.mis)
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100
## 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.550 1st Qu.:0.300
## Median :5.800 Median :3.000 Median :4.200 Median :1.300
## Mean :5.827 Mean :3.077 Mean :3.693 Mean :1.182
## 3rd Qu.:6.400 3rd Qu.:3.400 3rd Qu.:5.100 3rd Qu.:1.800
## Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500
## NA's :13 NA's :19 NA's :15 NA's :12
## Species
## setosa :45
## versicolor:43
## virginica :46
## NA's :16
##
##
##
iris.mis<-subset(iris.mis,select = -c(Species))
summary(iris.mis)
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100
## 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.550 1st Qu.:0.300
## Median :5.800 Median :3.000 Median :4.200 Median :1.300
## Mean :5.827 Mean :3.077 Mean :3.693 Mean :1.182
## 3rd Qu.:6.400 3rd Qu.:3.400 3rd Qu.:5.100 3rd Qu.:1.800
## Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500
## NA's :13 NA's :19 NA's :15 NA's :12
library(mice)
## Loading required package: Rcpp
## mice 2.25 2015-11-09
md.pattern(iris.mis)
## Petal.Width Sepal.Length Petal.Length Sepal.Width
## 100 1 1 1 1 0
## 9 1 0 1 1 1
## 16 1 1 1 0 1
## 9 1 1 0 1 1
## 7 0 1 1 1 1
## 3 1 0 0 1 2
## 1 1 1 0 0 2
## 1 0 0 1 1 2
## 2 0 1 1 0 2
## 2 0 1 0 1 2
## 12 13 15 19 59
library(VIM)
## Loading required package: colorspace
## Loading required package: grid
## Loading required package: data.table
## VIM is ready to use.
## Since version 4.0.0 the GUI is in its own package VIMGUI.
##
## Please use the package to use the new (and old) GUI.
## Suggestions and bug-reports can be submitted at: https://github.com/alexkowa/VIM/issues
##
## Attaching package: 'VIM'
## The following object is masked from 'package:datasets':
##
## sleep
mice_plot<-aggr(iris.mis,
col=c("navyblue","yellow"),
number=T,
sortVars=T,
labels=names(iris.mis),
cex.axis=.7,
gaps=3,
ylab=c("Missing data","Pattern"))
##
## Variables sorted by number of missings:
## Variable Count
## Sepal.Width 0.12666667
## Petal.Length 0.10000000
## Sepal.Length 0.08666667
## Petal.Width 0.08000000
imputed_data<-mice(iris.mis,m=5,maxit=50,
method='pmm',seed=500)
##
## iter imp variable
## 1 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 2 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 2 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 2 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 2 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 2 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 3 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 3 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 3 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 3 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 3 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 4 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 4 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 4 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 4 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 4 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 5 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 5 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 5 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 5 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 5 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 6 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 6 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 6 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 6 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 6 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 7 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 7 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 7 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 7 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 7 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 8 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 8 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 8 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 8 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 8 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 9 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 9 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 9 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 9 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 9 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 10 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 10 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 10 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 10 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 10 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 11 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 11 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 11 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 11 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 11 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 12 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 12 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 12 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 12 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 12 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 14 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 14 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 14 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 14 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 14 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 15 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 15 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 15 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 15 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 15 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 16 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 16 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 16 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 16 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 16 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 17 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 17 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 17 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 17 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 17 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 18 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 18 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 18 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 18 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 18 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 19 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 19 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 19 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 19 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 19 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 20 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 20 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 20 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 20 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 20 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 21 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 21 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 21 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 21 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 21 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 22 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 22 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 22 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 22 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 22 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 23 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 23 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 23 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 23 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 23 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 24 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 24 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 24 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 24 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 24 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 25 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 25 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 25 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 25 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 25 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 26 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 26 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 26 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 26 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 26 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 27 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 27 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 27 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 27 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 27 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 28 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 28 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 28 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 28 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 28 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 29 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 29 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 29 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 29 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 29 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 30 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 30 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 30 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 30 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 30 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 31 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 31 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 31 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 31 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 31 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 32 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 32 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 32 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 32 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 32 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 33 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 33 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 33 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 33 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 33 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 34 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 34 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 34 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 34 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 34 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 35 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 35 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 35 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 35 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 35 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 36 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 36 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 36 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 36 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 36 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 37 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 37 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 37 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 37 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 37 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 38 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 38 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 38 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 38 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 38 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 39 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 39 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 39 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 39 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 39 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 40 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 40 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 40 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 40 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 40 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 41 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 41 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 41 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 41 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 41 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 42 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 42 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 42 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 42 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 42 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 43 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 43 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 43 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 43 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 43 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 44 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 44 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 44 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 44 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 44 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 45 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 45 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 45 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 45 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 45 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 46 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 46 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 46 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 46 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 46 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 47 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 47 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 47 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 47 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 47 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 48 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 48 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 48 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 48 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 48 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 49 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 49 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 49 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 49 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 49 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 50 1 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 50 2 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 50 3 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 50 4 Sepal.Length Sepal.Width Petal.Length Petal.Width
## 50 5 Sepal.Length Sepal.Width Petal.Length Petal.Width
summary(imputed_data)
## Multiply imputed data set
## Call:
## mice(data = iris.mis, m = 5, method = "pmm", maxit = 50, seed = 500)
## Number of multiple imputations: 5
## Missing cells per column:
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## 13 19 15 12
## Imputation methods:
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## "pmm" "pmm" "pmm" "pmm"
## VisitSequence:
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 2 3 4
## PredictorMatrix:
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## Sepal.Length 0 1 1 1
## Sepal.Width 1 0 1 1
## Petal.Length 1 1 0 1
## Petal.Width 1 1 1 0
## Random generator seed value: 500
imputed_data$imp$Sepal.Width
## 1 2 3 4 5
## 4 3.1 3.2 2.9 2.9 3.3
## 7 3.2 3.3 3.2 3.3 3.4
## 23 3.4 4.1 3.4 3.4 3.5
## 37 3.8 3.9 4.2 3.8 3.9
## 51 3.1 3.8 3.0 3.0 3.8
## 58 3.1 3.0 2.7 3.0 2.8
## 63 2.9 3.0 3.4 2.4 2.5
## 67 3.0 2.7 2.7 2.0 3.0
## 70 2.9 2.8 2.9 3.0 3.0
## 71 2.8 3.0 2.7 3.0 2.3
## 75 3.0 3.2 3.1 2.9 3.3
## 80 2.9 3.0 2.2 3.2 3.2
## 87 3.3 3.1 3.1 3.4 2.3
## 93 2.9 3.0 3.4 2.8 2.6
## 115 3.0 3.3 3.8 3.2 3.0
## 123 2.8 3.0 2.7 3.0 3.0
## 124 2.5 2.9 3.0 3.0 3.4
## 133 2.2 2.7 2.8 2.8 3.0
## 142 2.9 2.8 3.1 3.8 2.8
completedData<-complete(imputed_data,2)
completedData
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## 1 4.8 3.5 1.4 0.2
## 2 4.9 3.0 1.4 0.2
## 3 4.7 3.2 1.3 0.2
## 4 4.6 3.2 1.5 0.2
## 5 5.0 3.6 1.4 0.2
## 6 5.4 3.9 1.7 0.4
## 7 4.6 3.3 1.5 0.3
## 8 5.0 3.4 1.5 0.2
## 9 4.4 2.9 1.4 0.2
## 10 4.9 3.1 1.5 0.1
## 11 5.4 3.7 1.5 0.2
## 12 4.8 3.4 1.6 0.2
## 13 4.8 3.0 1.4 0.1
## 14 4.3 3.0 1.1 0.1
## 15 5.8 4.0 1.2 0.3
## 16 5.4 4.4 1.5 0.4
## 17 5.4 3.9 1.3 0.4
## 18 5.1 3.5 1.4 0.3
## 19 5.7 3.8 1.7 0.3
## 20 5.1 3.8 1.5 0.3
## 21 5.4 3.4 1.7 0.2
## 22 5.1 3.7 1.5 0.4
## 23 4.6 4.1 1.0 0.2
## 24 5.1 3.3 1.7 0.5
## 25 4.8 3.4 1.9 0.2
## 26 5.0 3.0 1.6 0.2
## 27 5.0 3.4 1.6 0.4
## 28 5.2 3.5 1.5 0.2
## 29 5.2 3.4 1.4 0.2
## 30 4.7 3.2 1.6 0.5
## 31 4.8 3.1 1.6 0.2
## 32 5.4 3.4 1.5 0.4
## 33 5.2 4.1 1.5 0.1
## 34 5.5 4.2 1.4 0.2
## 35 4.9 3.1 1.5 0.2
## 36 5.0 3.2 1.2 0.2
## 37 5.5 3.9 1.3 0.2
## 38 4.9 3.6 1.4 0.1
## 39 4.4 3.0 1.3 0.2
## 40 5.1 3.4 1.5 0.2
## 41 5.1 3.5 1.3 0.3
## 42 4.5 2.3 1.3 0.3
## 43 4.4 3.2 1.3 0.2
## 44 5.0 3.5 1.6 0.6
## 45 5.1 3.8 1.9 0.4
## 46 4.8 3.0 1.4 0.3
## 47 5.1 3.8 1.6 0.2
## 48 4.6 3.2 1.4 0.2
## 49 5.3 3.7 1.5 0.2
## 50 5.0 3.3 1.4 0.2
## 51 7.0 3.8 4.7 1.4
## 52 6.7 3.2 4.7 1.5
## 53 6.9 3.1 4.9 1.5
## 54 5.5 2.3 4.0 1.3
## 55 6.5 2.8 4.6 1.5
## 56 5.7 2.8 4.5 1.3
## 57 6.3 3.3 4.6 1.6
## 58 4.9 3.0 3.3 1.0
## 59 6.6 2.9 4.6 1.3
## 60 5.2 2.7 4.1 1.4
## 61 5.0 2.0 3.5 1.0
## 62 5.9 3.0 4.2 1.5
## 63 6.0 3.0 4.0 1.0
## 64 6.1 2.9 4.7 1.4
## 65 5.6 2.9 3.6 1.3
## 66 6.7 3.1 4.4 1.4
## 67 5.6 2.7 4.5 1.5
## 68 5.7 2.7 4.1 1.0
## 69 6.2 2.2 4.5 1.5
## 70 5.6 2.8 3.9 1.1
## 71 5.9 3.0 4.8 1.8
## 72 6.1 2.8 4.5 1.3
## 73 6.3 2.5 4.9 1.5
## 74 6.1 2.8 4.7 1.2
## 75 6.4 3.2 4.3 1.3
## 76 6.6 3.0 4.4 1.4
## 77 6.8 2.8 4.8 1.5
## 78 6.7 3.0 4.5 1.3
## 79 6.0 2.9 4.5 1.5
## 80 5.7 3.0 3.5 1.0
## 81 4.9 2.4 3.8 1.3
## 82 5.5 2.4 3.7 1.0
## 83 5.8 2.7 3.9 1.2
## 84 6.3 2.7 5.1 1.6
## 85 5.4 3.0 4.5 1.5
## 86 6.0 3.4 4.5 1.6
## 87 6.7 3.1 4.7 1.5
## 88 6.3 2.3 4.4 1.3
## 89 5.6 3.0 4.1 1.3
## 90 5.5 2.5 4.0 1.3
## 91 5.5 2.6 4.4 1.2
## 92 6.1 3.0 4.6 1.4
## 93 5.8 3.0 4.0 1.2
## 94 5.0 2.3 3.3 1.0
## 95 5.6 2.7 4.2 1.3
## 96 5.7 3.0 4.2 1.2
## 97 5.7 2.9 4.2 1.3
## 98 6.2 2.9 4.5 1.3
## 99 5.1 2.5 3.0 1.1
## 100 5.7 2.8 4.1 1.3
## 101 6.8 3.3 6.0 2.5
## 102 5.8 2.7 5.1 1.9
## 103 7.1 3.0 5.9 2.1
## 104 6.3 2.9 5.6 1.8
## 105 6.5 3.0 5.8 2.2
## 106 7.6 3.0 6.7 2.1
## 107 4.9 2.5 4.5 1.4
## 108 6.1 2.9 4.9 1.8
## 109 6.7 2.5 5.8 1.8
## 110 7.2 3.6 6.1 2.5
## 111 6.5 3.2 5.1 2.0
## 112 6.4 2.7 5.3 1.9
## 113 6.8 3.0 5.5 2.1
## 114 5.7 2.5 5.1 2.0
## 115 5.8 3.3 5.1 2.4
## 116 6.4 3.2 5.3 2.3
## 117 6.9 3.0 5.5 1.8
## 118 7.7 3.8 6.7 2.2
## 119 7.7 2.6 6.9 2.3
## 120 6.0 2.2 5.0 1.5
## 121 6.9 3.2 5.7 2.3
## 122 5.6 2.8 4.9 2.0
## 123 7.7 3.0 6.7 2.0
## 124 6.3 2.9 4.9 1.8
## 125 6.7 3.3 5.7 2.1
## 126 7.2 3.2 6.0 2.1
## 127 6.2 2.8 4.8 1.8
## 128 6.1 3.0 4.9 1.8
## 129 6.4 2.8 5.6 2.1
## 130 7.2 3.0 5.8 1.6
## 131 7.1 2.8 6.1 1.9
## 132 7.9 3.8 6.1 1.9
## 133 6.4 2.7 5.6 2.4
## 134 6.3 2.8 5.1 1.5
## 135 6.1 2.6 5.6 1.4
## 136 7.7 3.0 6.1 2.3
## 137 6.3 3.4 5.6 2.4
## 138 6.4 3.1 5.5 1.8
## 139 6.0 3.0 4.8 1.8
## 140 6.9 3.1 5.4 2.1
## 141 6.7 3.1 5.6 2.4
## 142 6.9 2.8 5.1 1.8
## 143 5.8 2.7 5.1 1.9
## 144 6.8 3.2 5.9 2.3
## 145 6.7 3.3 5.7 2.5
## 146 6.7 3.0 5.7 2.3
## 147 6.3 2.5 5.0 1.9
## 148 6.5 3.0 5.2 2.0
## 149 6.5 3.4 5.4 2.3
## 150 5.9 3.0 5.1 1.8
summary(completedData)
## Sepal.Length Sepal.Width Petal.Length Petal.Width
## Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100
## 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300
## Median :5.800 Median :3.000 Median :4.400 Median :1.300
## Mean :5.837 Mean :3.086 Mean :3.755 Mean :1.199
## 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800
## Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500
###checking missing values in completed data
##we can observe no missing values....
mice_plot<-aggr(completedData,
col=c("navyblue","yellow"),
number=T,
sortVars=T,
labels=names(iris.mis),
cex.axis=.7,
gaps=3,
ylab=c("Missing data","Pattern"))
##
## Variables sorted by number of missings:
## Variable Count
## Sepal.Length 0
## Sepal.Width 0
## Petal.Length 0
## Petal.Width 0
iris_wo_Species<-data[-5]
iriswospecies.lm<-lm(Sepal.Width~Sepal.Length+Petal.Length+Petal.Width,data=iris_wo_Species)
newdata<-data.frame(Sepal.Length=5.3,Petal.Length=1.8,Petal.Width=0.4)
predict(iriswospecies.lm,newdata)
## 1
## 3.428893
##3.428893
completedData.lm<-lm(Sepal.Width~Sepal.Length+Petal.Length+Petal.Width,data = completedData)
predict(completedData.lm,newdata)
## 1
## 3.475087
##3.397943