test (1).ipynb

Kernel: R (R-Project)

Workshop Code

#this notebook will demonstrate how to run the analysis on this dataset

#install.packages("corrplot")
library("corrplot")
#read the dataset
data <- read.delim("./data 2.csv", #the file you are trying to read
                   header=T, #does the file include a header row?
                   sep=',' #what is the delimiter?
                  )

#remove the NA column
data <- subset(data, #the dataset you are trying to subset
               select=-X #what you are trying to subset. By placing a a negative infront of the variable name, the variable will be excluded
              )

#change the label to factor
data$diagnosis <- as.factor(data$diagnosis)


#assess correlation
options(repr.plot.width = 8, repr.plot.height = 6)

corrplot <- cor(data[,3:ncol(data)])
corrplot(corrplot, # add comment
         order = "hclust", # add comment
         tl.cex = 1, #add comment
         addrect = 8 #add comment
        ) 

# plotting the tree
library("party")
x <- ctree(data$diagnosis ~ .,
           data=data
          )
#change the size of the plot
options(repr.plot.width = 10, repr.plot.height = 8)

plot(x,
     labels=FALSE,
     terminal_panel=node_barplot(x,
                                 beside=FALSE,
                                 col="black",
                                 fill=c("coral4", "chartreuse4"),
                                 id=FALSE
                                )
    )

Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich

#modelling