1. R basics workshop J. Sebastián Tello Iván Jiménez
Center for Conservation and Sustainable Development
Missouri Botanical Garden

2. 3 fundamental concepts:
Function
Argument
Object

3. 2. Functions and Arguments

4. Jump three times forward
Writing in R is like writing in English
Jump three times forward
Modifiers
Action

5. Generate a sequence from 5 to 20 with values spaced by 0.5
Writing in R is like writing in English
Generate a sequence from 5 to 20 with values spaced by 0.5
Action
Modifiers

6. Generate a sequence from 5 to 20 with values spaced by 0.5
Writing in R is like writing in English
Action
Modifiers
Generate a sequence from 5 to 20 with values spaced by 0.5
Function
seq(from=5, to=20, by=0.5)
Arguments

7. Basic anatomy of an R command
Open
parenthesis
Close
parenthesis
Equal sign
Comma
seq(from = 5, to = 20, by = 0.5)
Other
arguments
Function
Argument
name
Argument
value

8. Basic anatomy of an R command
seq(from=5, to=20, by=0.5)
Function
Arguments
A function in R defines an action to take, and is similar to a verb in English
Functions apply to arguments, which define on what and how a function will work
Arguments are usually given within parenthesis after the function

9. Basic anatomy of an R command
1. Arguments almost always have names (e.g., "from ", "to", etc.)
seq(from=5, to=20, by=0.5)
2. Names can be eliminated if arguments are given in predetermined order
seq(5, 20, 0.5)
seq(0.5, 5, 20)
3. Arguments can be reordered if you use names
seq(by=0.5, to=20, from=5)

10. Basic anatomy of an R command
seq(from=5, to=20, by=0.5)
seq(to=10)
4. Frequently, functions have arguments with predetermined values
Predetermined arguments do not need to be specified
You can find predetermined values in the help page
?seq

11. Basic anatomy of an R command
5. You can use functions to give values to an argument (functions within functions)
c(19, 4, 2, 6, 2)
mean(x=c(19, 4, 2, 6, 2))
mean(x=19, 4, 2, 6, 2)
rnorm(n=50, mean=0, sd=1)
rnorm(n=50, mean=3, sd=1)
boxplot(x=list(rnorm(n=50, mean=0, sd=1), rnorm(n=50, mean=3, sd=1)))

12. Basic anatomy of an R command
Writing an R command is like writing a command in English
rep(x="R", times=10)
Repeat “R” 10 times
sum(19, 4, 2, 6, 2)
Sum 19, 4, 2, 6 and 2
paste("R", "Basics", "Workshop")
Paste the words “R”, “Basics” and “Worshop”

13. Basic anatomy of an R command
Some functions can be replaced by operators (more on operators later):
E.g. the operator + must be used between values
sum(19, 4)
Sum 19 and 4
19 + 4
Sum 19 and 4

14. Getting Help 1. Access help file for the function - RTFM
2. Make a search in or Google
3. Ask a friend
4. Ask a question in an on-line discussion forum -
5. Have a look at the internal code of the function

15. Getting Help 1. Access help file for the function by using ? or help()
?lm
help(lm)
Critical components of the help pages:
Usage – How to use the function
Arguments – Description of arguments
Details – Details on how the function works
Value – Description of the output
See Also – Other related functions
Examples – Examples on how to use the function

16. Getting Help
2. Make a search in

17. Getting Help 3. Ask a friend (that knows more than you do)
Iván Jiménez, Ph.D.
Associate Scientist
Center for Conservation and Sustainable Development
office phone: + 1 (314)
fax: + 1 (314)

18. Getting Help
4. Ask a question in an on-line r-project.org/mail.html

19. Getting Help 5. Have a look at the internal code of the function
The name of the function without parenthesis produces the R code behind the function; e.g.: lm
Some functions are not written in R and cannot be accessed this way; e.g.:
seq

20. Predetermined arguments
Summary: functions and arguments
seq(to=20, by=0.5)
Function
Arguments
Output
Predetermined arguments

21. Exercise 2
Functions and arguments