# Essential R
### What you need to get started
#### Eric Nord
##### Assistant Professor of Biology, Greenville College
##### Fulbright Scholar, Lilongwe University of Agriculture and Natural Resources, Malawi
## Chapter 1: Basics

### I: The Terminal ----
2 + 4 # this was 2+3
4*5
6^2
3+5*2
(3+5)*2
a = 5
a
a*2
a
a=a*2

# must *assign* to change a value
# = and <- and ->
# objects in R exist in your *workspace*
# console vs editor
# Editor - multiple files open - R script file contains R code and 
#   comments - not output unless pasted behind comments - easily run code 
#   from the editor - easy to save
# Open an new script file and type "# editor demo". Now press 
#   Ctrl+Enter, and R will run that command (since it is a comment, it 
#   will just be writen to the console). Now type "a*4" and press Ctrl+Enter.  
#   console not easily be saved - contains the output from your R code - 
#   up arrow to retrieve previous commands

### II: Working with Vectors ----
sms=c(0,1,2,0,0,0,1)
sms + 5
sms * 5
sms/2
sort(sms)
sum(sms)
sum(5,6,7)

### III. Subsetting Vectors - the magic "[]" ----
sms[3]
sms[2:4]
sms[-3]
sms[-(2:3)]
sms[-c(2,3,7)]
5:9

# logical extraction
sms>0
sms[sms>0]
# FALSE=0 and TRUE=1. 
sum(sms>0)

which(sms>0)
sms[which(sms>0)]
mean(sms[which(sms>0)])

sms

sms[1]=1
sms

a=sms; a[which(a==0)]<-1; a # note == vs =

1:50 # note the [1], etc.

x=c("a","b","c","d","e","f","g","h","i")
y=21:30
z=c(2,4,6)

x[y] # NA b/c no 21-30th elements
x[y-20] # only one NA b/c no 10th element
x[z]
x[rev(z)] # try rev(z)
y[z]
z[y]
y[x] # NA b/c the "ath" element of y doesn't make sense
y*z
# note warning -- recycling!

### IV. Other Useful Functions ----
# sd() # standard deviation
# median() # median
# max()# maximum
# min()# minimum
# range() #maximum and minimum
# length() # number of elements of a vector
# cummin() # cumulative min (or max cummax())
# diff() # differences between successive elements of a vector

# note + rather than output or >  
# auto matching in Rstudio
# :


### V. Exercises. ----

# 1) Enter the following data in R and call it P1:  
# 23,45,67,46,57,23,83,59,12,64  
# What is the maximum value? What is the minimum value? What is the mean value?
# 
# 2) Oh no! The next to last (9th) value was mistyped - it should be 42. 
#    Change it, and see how the mean has changed.   How many values are 
#    greater than 40? What is the mean of values over 40?
# Hint: how do you see the 9th element of the vector `P1`?
# 
# 3) Using the data from problem 1 find:  
# a) the sum of P1  
# b) the mean (using the sum and length(P1))
# c) the log(base10) - use log(base=10)  
# d) the difference between each element of P1 and the mean of P1
# 
# 4) If we  have two vectors, a=11:20 and b=c(2,4,6,8) describe (without 
#    running the code) the outcome of the following (check yourself by 
#    running the code):  
# a) a*2  
# b) a[b]  
# c) b[a]  
# d) c(a,b)  
# e) a+b