###Code for Lab 0

# 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(1,2,3) ### '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....



###Make your own functions

expTest=function(zed){   ###create a function to calculate e to the power of x - bracket starts the calculations
	###arguments in parentheses are arguments that must be specified when calling the function
	###in this case, first argument will be assigned to 'x'; note that x only exists in function
	y=2.718282^zed   ###run a calculation using the argument x
	return(y) #### return the answer of the calculation
} ###bracket ends the calculations

expTest(1.5) ###run the expTest function
zed ### proof that zed only exists in the function


###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) ###gives column names plus first 6 rows of data
names(datum) ### gives just the column names

### 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


###Saving in R


###'File', 'Save Workspace' saves the objects in memory

###'File', 'Save History' saves the commands your ran, but not the objects

###'File', 'Save to File' saves all text in the console: commands you ran and the output
### Doesn't save objects


###Packages

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

library(MASS) ### loads the package 'MASS'



###Loading data into R

datum=read.csv(file.choose()) ### loads a data-file that you select and creates object 'datum'
### can call data anything you want, but don't call 'data' - function already exists
#### Note that data must be in a comma-delimited format
### avoid funny characters in column headers or text entries