Stat 622/422 (Dr. Baron)                                          Advanced Biostatistics

 

First steps in R. Variables, summary, folders, data sets

 

# Vectors and simple operations

> x <- c(1,3,5,6)              # Create a vector (c means concatenate)

> x = c(1,3,5,6)              # Another way to define a vector

> x

[1] 1 3 5 6

 

> x[2]                         # Get the 2nd element of vector x

[1] 3

 

> x[2:4]                      # Get all elements of x from the 2nd to the 4th

[1] 3 5 6

 

> x = rnorm(10000,2,100)       # Generate a vector of 10,000 Normal random variables

                               # with mean 2 and st. deviation 100

 

# Basic statistics

 

> mean(x)

[1] 2.379067

> sd(x)

[1] 100.0676

 

# Arithmetic operations

> x = c(1,3,5,7,0,-1)

> x

[1]  1  3  5  7  0 -1

> x^2

[1]  1  9 25 49  0  1

> sin(x)

[1]  0.8414710  0.1411200 -0.9589243  0.6569866  0.0000000  -0.8414710

> log(x)

[1] 0.000000 1.098612 1.609438 1.945910     -Inf      NaN

Warning message:

In log(x) : NaNs produced

 

 

# Define a matrix A based on a vector x

 

> A = matrix(x,2,3)

> A

     [,1] [,2] [,3]

[1,]    1    5    0

[2,]    3    7   -1

 

 

# READING DATA FROM EXTERNAL FILES

 

# To point to the right folder, go "File" -> "Change dir..." or use the setwd command 

# Which folder is R pointed to right now?
> getwd()
[1] "C:/Users/baron/Documents"
 
# Let's change the folder to the one where we have data. Notice slashes.
 

> setwd("C:/Users/baron/Advanced Biostatistics/data")

 

# Use read.csv(“file.csv”) to read CSV viles, read.table("file.txt") to read text files

# Rda and Rdata files should be opened with load("file.rda")

 

> load("Heart.rda")

 

# Or, load data from a public domain

 

>  Heart = read.csv("http://fs2.american.edu/baron/www/622/R/Heart.csv")

 

# Find out what variables are in the set

 

> dim(Heart)

[1] 303  15

 

> names (Heart)

[1] "X"         "Age"       "Sex"       "ChestPain" "RestBP"    "Chol"    

 [7] "Fbs"       "RestECG"   "MaxHR"     "ExAng"     "Oldpeak"   "Slope"   

[13] "Ca"        "Thal"      "AHD"     

 

> summary (Heart)

       X              Age             Sex          ChestPain       

 Min.   :  1.0   Min.   :29.00   Min.   :0.0000   Length:303       

 1st Qu.: 76.5   1st Qu.:48.00   1st Qu.:0.0000   Class :character 

 Median :152.0   Median :56.00   Median :1.0000   Mode  :character 

 Mean   :152.0   Mean   :54.44   Mean   :0.6799                    

 3rd Qu.:227.5   3rd Qu.:61.00   3rd Qu.:1.0000                    

 Max.   :303.0   Max.   :77.00   Max.   :1.0000                    

                                                                   

     RestBP           Chol            Fbs            RestECG     

 Min.   : 94.0   Min.   :126.0   Min.   :0.0000   Min.   :0.0000 

 1st Qu.:120.0   1st Qu.:211.0   1st Qu.:0.0000   1st Qu.:0.0000 

 Median :130.0   Median :241.0   Median :0.0000   Median :1.0000 

 Mean   :131.7   Mean   :246.7   Mean   :0.1485   Mean   :0.9901 

 3rd Qu.:140.0   3rd Qu.:275.0   3rd Qu.:0.0000   3rd Qu.:2.0000 

 Max.   :200.0   Max.   :564.0   Max.   :1.0000   Max.   :2.0000 

                                                                 

     MaxHR           ExAng           Oldpeak         Slope             Ca       

 Min.   : 71.0   Min.   :0.0000   Min.   :0.00   Min.   :1.000   Min.   :0.0000 

 1st Qu.:133.5   1st Qu.:0.0000   1st Qu.:0.00   1st Qu.:1.000   1st Qu.:0.0000 

 Median :153.0   Median :0.0000   Median :0.80   Median :2.000   Median :0.0000 

 Mean   :149.6   Mean   :0.3267   Mean   :1.04   Mean   :1.601   Mean   :0.6722 

 3rd Qu.:166.0   3rd Qu.:1.0000   3rd Qu.:1.60   3rd Qu.:2.000   3rd Qu.:1.0000 

 Max.   :202.0   Max.   :1.0000   Max.   :6.20   Max.   :3.000   Max.   :3.0000 

                                                                 NA's   :4      

     Thal               AHD          

 Length:303         Length:303       

 Class :character   Class :character 

 Mode  :character   Mode  :character

# Look at the data as a spreadsheet

> fix(Heart)

 

# Refer to the particular variable in this dataset with $ sign...

 

> Heart$Age

  [1] 63 67 67 37 41 56 62 57 63 53 57 56 56 44 52 57 48 54 48 49 64 58 58

     < truncated >

 

# or attach it the dataset that you plan to work with...

 

> attach(Heart)

 

# Descriptive statistics: mean and the 5-number summary

 

> mean(Heart$Chol)

[1] 246.6931

 

> summary(Chol)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.

  126.0   211.0   241.0   246.7   275.0   564.0

 

 

# PLOTS.

# Before you do anything with the data, look at them.

 

> plot(Age,Chol)

 

A graph with numbers and dots AI-generated content may be incorrect.

 

 

# Axis labels, graph title, color

 

> plot(Age, Chol, xlab="Patient’s Age", ylab="Level of Cholesterol", main="Plot of Cholesterol", col="blue", lwd=3)

 

A graph of a patient's age AI-generated content may be incorrect.

 

 

# SCATTERPLOT MATRIX #
# Use it to plot more than 2 variables. 
# First, partition the graphing window into a matrix
 
> par(mfrow=c(4,4))
 
# Then fill each non-diagonal space with the corresponding scatterplot
 
> pairs(~Age+RestBP+Chol+MaxHR)

 

A screenshot of a computer screen AI-generated content may be incorrect.

 

# Saving a graph in a file

> pdf("filename.pdf")

> plot(Chol, RestBP, col="blue")

 

> dev.off()

windows

      2

 

# Finish and quit R

> q()