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Workshop 1 - Introduction to R

09 Dec 2014

Basic syntax revision
Q1-1.Complete the following table, by assigning the following entries
(numbers etc) to the corresponding object names and determining the object class
for each.
NameEntrySyntaxClass
A100hint
BBighint
VAR1100 & 105 & 110hint
VAR25 + 6hint
VAR3150 to 250hint

  1. Print out the contents of the vector you called 'a'
    . Notice that the output appears on the line under the syntax that you entered, and that the output is proceeded by a [1]. This indicates that the value returned (100) is the first entry in the vector
  2. Print out the contents of the vector called 'b'. Again notice that the output is proceeded by [1].
  3. Print out the contents of the vector called 'var1'.
  4. Print out the contents of the vector called 'var2'. Notice that the output contains the product of the statement rather than the statement itself.
  5. Print out the contents of the vector called 'var3'. Notice that the output contains 100 entries (150 to 250) and that it spans multiple lines on the screen. Each new line begins with a number in square brackets [] to indicate the index of the entry that immediately follows.

Variables - vectors

Q1-2. Generate the following numeric vectors (variables)
  1. The numbers 1, 4, 7 & 9 (call the object y)
  2. The numbers 10 to 25 (call the object y1)

  3. The sequency of numbers 2, 4, 6, 8...20 (call the object y2)

Q1-3. Generate the following character vectors (factorial/categorical variables)
  1. A factor that lists the sex of individuals as 6 females followed by 6 males

  2. A factor called TEMPERATURE that lists 10 cases of 'High', 10 'Medium & 10 'Low'
  3. A factor called TEMPERATURE that lists 'High', 'Medium & 'Low' alternating 10 times
  4. A factor called TEMPERATURE that lists 10 cases of 'High', 8 cases of 'Medium' and 11 cases of 'Low'

Q1-4. Print out the contents of the 'TEMPERATURE' factor. A list of factor levels will be printed on the screen. This will take up multiple lines, each of which will start with a number in square brackets [ ] to indicate the index number of the entry immediately to the right. At the end, the output also indicates what the names of the factor levels are. These are listed in alphebetical order.

  R object classes

Assigning entries is basically the act of defining a new object name and specifying what that object contains (its value). For example if we wanted to store the number 10.513 as John Howards IQ, we instruct R to create a new object called (say IQ) and assign the value 10.513 to it. That is, we instruct R that IQ equals 10.513.
In R, the assignment operator is <- instead of =.

> name <- value

So to assign IQ the value of 10.513 in R 
> IQ <- 10.513

End of instructions

  R object classes

Object classes define how information in stored and displayed. The basic storage unit in R is called a vector. A vector is an array of one or more entries of the same class. The common classes include
  1. numeric - stores a number eg 1, 2.345 etc
  2. character - stores alphanumeric characters eg 'a', 'fish', 'color1'
  3. logical - stores either TRUE or FALSE
So the entries (1, 2, 3 & 4) might make up a numeric vector, whereas the entries ('Big', 'Small' & 'Tiny') would make up a character vector. To determine the class type of an object, use the following syntax (where bold font is used to represent the object whose class is to be determined).

> class(name)

End of instructions

  Print contents

In R, print means to output (list) the contents of an object. By default, the contents are output to the screen (the default output device). It is also possible to redirect output to a file or printer if necessary. The contents of a file are 'printed' by completing the 'print()' function or by just entering the name of the object. Consider the following; 
> numbers <- c(1, 4, 6, 7, 4, 345, 36, 78)
> numbers

[1]   1   4   6   7   4 345  36  78
The first line of this syntax generates and populates the numeric vector called 'numbers'. The second line uses the print function to tell R to list the contents of the 'numbers' object - the output of which appears on the third line. The forth and fifth line illustrate that the same outcome can be achieved by simply entering the name of the object.

End of instructions

  R vectors - variables

In biology, a variable is a collection of observations of the same type. For example, a variable might consist of the observed weights of individuals within a sample of 10 bush rats. Each item (or element) in the variable is of the same type (a weight) and will have been measured comparably (same techniques and units). Biological variables are therefore best represented in R by vectors.

End of instructions

  R Factors

There are a number of ways in which this can be done. One way is to use the 'factor' (makes a list into a factor) function in conjunction with the 'c' (concatenation) function.

> name <- factor(c(list of characters/words))

Another way is to use the 'gl' function (which generates factors according to specified patterns of their levels)

> name <- gl(number of levels, number of replicates, length of data set, lab=c(list of level names)))

Hence, consider the following alternative solutions; 
> sex <- factor(c('Female', 'Female', 'Female', 'Female', 'Female', 'Female', 'Male', 'Male', 'Male', 'Male', 'Male', 'Male'))
> #OR
> sex <- factor(c(rep('Female',6),rep('Male',6)))
> #OR
> sex <- gl(2,6,12,lab=c('Female','Male'))

The second option uses the 'rep()' function which in this case is used to repeat the level name (eg 'Female') 6 times.

End of instructions