Thanks for the reply!
Here is a file that I am trying to render. This is not the only file that is having this issue. If I render another .Rmd file, the same issue pops up.
I also tried to uninstall and reinstall the R, though without any success. Can you please guide?
output:
html_document: default
word_document: default

title: "R Notation" 
author: "Siddharth" 
date: "r Sys.Date() " 
output: 
html_document: default 
knitr::opts_chunk$set(echo = TRUE)
Load the Data Frame
To demonstrate the R notation, we will use deck.csv file, which contains 52 observations representing full deck of cards. Let's load the data set:
getwd()
setwd("E:/Training Modules/introduction to R/R Notation")
getwd()
card_deck < read.table("deck.csv",sep=',',header=TRUE, stringsAsFactors = FALSE)
Check first few rows of data set
head(card_deck)
Positive Integers
R treats positive integers just as ij notation in linear algebra: r
deck[i,j]`, will return the value of the deck that is in ith row and jth column
card_deck[1,1]
To extract more than one value use vector of positive integers
card_deck[1,c(1,2,3)]
R's notation system is not limited to data frames. You can use the same syntax to select values in any R object.
vec < c(1,2,3,4,5,6)
vec[1:3]
Negative Integers
R will return every index except the elements in the negative index.
card_deck[(2:52), 1:3]
R will return an error if you try to pair negative integer with positive integer in same index
card_deck[c(1,1),1]
Zero
What would happen if you used zero as an index?
card_deck[0,0]
Blank Spaces
Useful for extracting entire row or column from a data frame
card_deck[1,]
Logical Values
If you use a vector of TRUE and FALSE as index, R will match each TRUE and FALSE to a row/column in data frame
card_deck[1, c(TRUE, TRUE, FALSE)]
card_deck[c(FALSE,FALSE,TRUE),1:2]
Names
If the columns have names, then you can extract the columns of data frame using its name
card_deck[ , "suit"]
Dollar Sign and Double Brackets
$ symbol is used to extract values from data frame and lists. To select column from data frame, write the data frame's name and column name separated by $.
card_deck$value
mean(card_deck$value)
median(card_deck$value)
subsetting a list, $ notation, single bracket and double brakcet
lst < list(number=c(1,2),logical=c(TRUE,FALSE),strings=c("a","b","c"))
lst
Subsetting list  Using single bracket.
for single bracket subsetting, the result is smaller list within a list. This can cause problem, because many R functions do not work with the list. For. e.g. sum(list[1])
will throw an error
lst[1]
sum(list[1])
$ notation in the list
The above issue can be addressed by using $ notation. When $ notation is used, R will return selected values, with no list structure attached around them:
lst$number
sum(lst$number)
Subsetting list  Using double bracket.
If the elements in the list do not have names, you can use two brackets to subset the list. This is similar to using dollar notation for subsetting the list.
lst[[1]]
sum(lst[[1]])
Atomic vector used in example
myvec < c(1,4,56,21,14)
myvec
myvec[2]
Data frame used in example
my_dataframe < data.frame(person=c("Siddharth","Aarya","Meghana","Omkar","Atharva"),
age=c(42,40,17,14,1),
sex=factor(c("M","F","F","M","M")))
my_dataframe
my_dataframe[1,c(TRUE,TRUE,FALSE)]
List used in example
my_list < list(my_matrix=matrix(data=1:4,nrow=2,ncol=2),logical=c(T,F,T,T),strings="hello",numbers=c(10:14))
my_list
my_list[1]
thanks
Siddharth