Week1: R studio, vector and function

Welcome to the first course! During the following 2 hrs, you will learn data type of vectors, function and %>%.

Note

1. set up Rstudio, Github, and name space
2. vector and 3 basic data types: (“chr”,“numeric”,“Date”)
3. functions, documentation and data type check
4. meaning of %>% and .

1 Set up your working directory

1.1 preparation

1. Please make sure you have installed R & Rstudio.

2. Open Rstudio, File -> New Project -> Wheat_BSC_project, click create a git repository
3. download the data from HU-box, save it in data.
4. create Week1.R and save it in folder src.
5. Open github desktop

6. comment&commit & push

7. Press Ctrl+ Shift +Nto open new script.
8. Save it as Week1.R Copy code from this website to your script and press run.

‘folder structure’

1.2 Concept of datatype & name space:

1. Don’t overwrite variable names in name space (what already exists in system).

   • eg., var,mean,aov, etc.

Warning

avoid something that will show in the drop down menu of auto-completion.

2. Separate long variable names with _.

   • eg., thermal_time,mean_yield, etc.

3. Don’t start variable names with number.

	Bad	Better
	3years	three_years
	1225measurement	measurement_1225
	13genotypes	genotypes_13

Structure of a vector

Variable = variable names + object

2 Data type is everything

variable
# assignment str"v" to name "variable"
## "" and unquote str and variable 
variable <- "v"
Variable <- 1

variable +1
Variable +1 

2.1 Always check your data type first!

# str??
str
?str
str(variable)
str(Variable)
# data type coersion
str(NA)
str(c(NA,1))
str(c(NA,"a"))
str(c(NA,TRUE))
str(c(1,"a"))

2.2 Date

as.Date("2023-04-17")
as.Date("2023-04-17",format="%Y-%m-%d")
# is ther any error?
as.Date("20230417")
as.Date("17042023")
# additive properties of Date 
as.Date("2023-04-17")-7
as.Date("2023-04-17")+2

3 Function: something ends with ()

How function works?

# example: fun(object)
c(1,2,3)
seq(1,3,1)

mean(c(1,2,3))
str(TRUE)

3.1 r packages : collection of functions

Check this great package tidyverse!

• Note that windows user may need to first download the Rtools that match your R version.

You can check your R version by typing version() in your R console.

install.packages(dplyr)
install.packages("dplyr")
library(dplyr)

3.2 separate individual function from nested functions with %>%

Pipe (%>%) is available in r-package either dplyr or magrittr.

Please use %>% to avoid embedded functions.

.stands for the result from the left side of the pipe.

For long line code, press enter after each %>%.

Select all the codes by ctrl A.

Indent the selected codes by ctrl I.

Concepts of using pipe

# syntax of using pipe
library(dplyr)

fun1(object)
# .= object
object %>% fun1(.)
# . could be also skipped
object %>% fun1()

# . = fun1(object)
object %>% fun1() %>% .
object %>% fun1(.) %>% .

#embedded functions
fun2(fun1(object))
# .=fun2(fun1(object))
object %>% 
  fun1() %>% 
  fun2() %>% .

Examples of using pipe

# how many ways of creating a sequence?
c(1,2,3)
seq(1,3,1)

# embedded function : fun2(fun1())
length(c(1,2,3))
# use pipe, "." is the result of previous step
c(1,2,3) %>% length(.)

# replicate element as vector
rep(1,3)
# remove duplicates
rep(1,3) %>% unique()
# cumulative sum 
rep(1,3) %>% cumsum()

# is there any difference?
paste(c("a","1"),collapse = "")
paste0(c("a","1"))
paste0("a","1")

challenge

We introduced data type Date in Section 2.2, It actually behave like numeric sequence. You have Vector of type date, length is 1, value is “2023-04-17”.

date_element <- as.Date('2023-04-17')

1. How to create date vector of length 5?

[1] "2023-04-17" "2023-04-18" "2023-04-19" "2023-04-20" "2023-04-21"

2. Could you do the average of this vector?

challenge

Use str() to check the data type of variable in your environment.

You have two vectors,

vec1<-c("a","b")
vec2<-c("1","2")

How to use paste and repto create sequence of char vector shown below?

[1] "a1" "a2" "b1" "b2"

[1] "a1" "b1" "a2" "b2"

Check the arguments of rep to get more hints.

?rep

e.g.,

• rep(c("a","b"),each=2)

• rep(c("a","b"),times=2)

3.3 write your first function

format: function_name(argument1, argument2) {code} example:

plusone <- function(x){
  x+1
}
# is function data type sensitive?
plusone(variable)
plusone(Variable) 

function with good documentation example:

function_name  <-function(input){
  # input: datatype, length, meaning.
  # output: datatype, length, meaning.
  # action1: intermediate_variable <- input %>% fun1()
  # action2: output <-intermediate_variable%>% fun2()
  ...
  return(output)
}

challenge

write a function with documentation: input vec is a numeric vector with length 3, return str of average value of vec ± standard deviation of vec.

Visualize the step in your function by first writing your the possible steps in text!