###Basic R Code

# this is a comment - R ignores it!
# I highly encourage you to use comments in your code as code is much like a foreign language
# If you go back to code several months after you've written it, it won't make much sense
# unless you have lots of comments 



### Basic Math

3+5 # add 3 and 5
2*3
4^2
exp(1.5) ### calculate e to the 1.5 power
x=exp(1.5) ### make 'x' equal to exp(1.5), doesn't report anything
x ### tell us what x is
y=log(x) ### make y equal to natural log of x
y ### tell us what y is


#### How to repeat commands
x=exp(1.5 #this code won't work as it is incomplete. R will give a '+' on the next line
)
### to complete the code, just type ')' or escape to get out. 
### you can scroll through old commands using up and down arrows

#### How to use the help files

help(exp) # brings up the help file for the 'exp' function
??'exponentiate' # searches for functions that include the words 'exponentiate'.


###Vectors

x=c(4,5,6) ### 'c' tells R you are making a list of values; also called a 'vector'
x ### tell us what x is
x[2] ### tell us what the 2nd value of x is

exp(x) ### calculate exp to the power of each value in x; return a list of scalars


###Functions – what they are and how they are used
###a function is any command that takes arguments (in parentheses) and returns results based on a calculation
y=log(15) # gives us the natural log of '15'
y=log(15, base=10) #gives us the log base 10 of '15'
y=log(15,10) ### calculates the log base-10 of '15'; careful not specifying arguments....



###Matrices

year=c(1800,1850,1900,1950,2000) ### create a vector called 'year' with 5 values
carbon=c(8,54,534,1630,6611) ###create a vector called 'carbon' with 5 values
### A matrix is a block of numbers with multiple rows and columns
datum=data.frame(Year=year,Carbon=carbon) #create a matrix with two columns (year and carbon) and 5 rows
datum #### show us the matrix 'datum'
datum[2] ### show just the second column of 'datum'
datum$carbon ### show just second column of 'datum' - the one named 'carbon'



###Easy summaries/analysis of data

summary(datum) ###give mean and quartile of datum
head(datum) ###checks that data was imported properly
names(datum) ### gives you attributes of data or other objects


### Making simple plots in R

plot(datum) ###note that x-axis will be first variable in matrix
plot(Carbon~Year) ###This line of code wont work. 'Carbon' doesn't exist outside the datum data.frame
plot(Carbon~Year,data=datum) #One way of doing plots (Y~X)
plot(x=datum$Year,y=datum$Carbon) #Another way of doing plots (X,Y)
plot(Carbon~Year,data=datum,type=’l’) #### plot a line graph - note that 'l' is an small L


###Cleaning up R

### Clear console by 'Edit', 'Clear Console'
### Does not eliminate the objects you created

ls() ### list all of the objects in memory
rm() ### remove objects in memory

### 'Misc', 'Remove all objects' to clear memory



### Packages

###'Packages', 'Install Package(s)' installs library of code

library(nlme) ### loads the package 'nlme'; note package must be installed. 


### Code to load data into R

datum=read.csv(file.choose()) ### loads a csv file (that must be found in an explorer window) and calls it 'datum'