## A very first R tutorial!
## "Let's start in the very beginning, the very best place to start"
## By Liz Mandeville, April 2024 (lmandevi@nmu.edu)

## This is an R script
## Lines that start with "#" or "##" are comments and aren't interpreted as code

## There are R extras called "packages" - we are going to install a couple of packages that are useful
install.packages("palmerpenguins") #this is a dataset
install.packages("ggplot2")

## You install packages only once, but every time you need them you need to load them with library()
library(palmerpenguins)
library(ggplot2)

## We will work a lot with this dataset today
data(package='palmerpenguins')
View(penguins)

## but, usually we bring in data like this, and this is historically one of the things R newbies find hardest
## First: tell R where the file is
setwd("~/northernmichigan/teaching/fishecol_BI467_w24/code_n_data/")
## Then, bring it in! Give it a good name to refer to
fish <- read.csv("length_weight_example.csv")

## You refer to one column like this:
penguins$species
fish$length

## Take a mean (average)
mean(penguins$body_mass_g) ## uh oh!
mean(penguins$body_mass_g, na.rm=TRUE)

## plotting code - this is base R
plot(penguins$flipper_length_mm,penguins$body_mass_g)

## Can color-code, but it's messy
plot(penguins$flipper_length_mm, penguins$body_mass_g, type="n")
  points(penguins$flipper_length_mm[penguins$species=="Adelie"],penguins$body_mass_g[penguins$species=="Adelie"], col="deeppink")
  points(penguins$flipper_length_mm[penguins$species=="Gentoo"],penguins$body_mass_g[penguins$species=="Gentoo"], col="seagreen")
  points(penguins$flipper_length_mm[penguins$species=="Chinstrap"],penguins$body_mass_g[penguins$species=="Chinstrap"], col="purple")

## Most people prefer ggplot!
ggplot(penguins, aes(x=flipper_length_mm, y=body_mass_g, color=species)) +
  geom_point()

## If we still have time, try replacing a variable and plotting something different! Or try to make these same plots with the fish dataset