Homework_12

The purpose of these figures is to examine the length frequencies of smelt and alewife in main lake and by North, Central, and South Main Lake for lake trout diet data.

#Loading libraries
library(readr)
library(readxl)
library(foreign)
library(dplyr)
library(magrittr)
library(lubridate)
library(reshape2)
library(ggplot2)
library(gridExtra)
library(tidyverse)
library(knitr)
library(kableExtra)
library(ggeasy)

#Import data

#Setting working directory
setwd("~/UVM/NonFF/MattLKTData")
getwd()

## [1] "C:/Users/shelb/OneDrive/Documents/UVM/NonFF/MattLKTData"

#Import individual fish csv
Individual_fish <- read.csv("IndividualFish.csv")


#Import sample csv
Sample <- read.csv("Sample.csv")


#Import site csv
Site <- read.csv("Sites.csv")

#Mushing data into useable formats

#Join sites and sample by site
Sample.0 <- Sample %>%
  left_join(., Site, by = "site")

#Selecting relevant categories
Sample.1 <- Sample.0 %>%
  select(sampleID, gear, gear_spec, site, basin, minor_basin, goodsample, date_start,month, year, duration_min, depth_start_m, depth_end_m, depth_mean_m)

#Merge sample.1 with Individual_fish
Fish_sampled.0 <- Sample.1 %>%
  left_join(., Individual_fish, by = "sampleID") %>%
  select(sampleID, site, basin, minor_basin, gear, gear_spec, spec_code, tl_mm, wt_g, goodsample, year, month, date_start,duration_min, depth_start_m, depth_end_m, depth_mean_m)

#Order basins
Fish_sampled.0$minor_basin = factor(Fish_sampled.0$minor_basin, levels = c("North Main Lake", "Central Main Lake", "South Main Lake"), ordered = TRUE)

#Filter by gear, basin, year, and species
Fish_sampled.1 <- Fish_sampled.0 %>%
  filter(gear == "BOT") %>%
  #filter((year == "2019") | (year == "2020") | (year == "2021"))%>%
  filter(gear_spec == "3 in 1") %>%
  filter(!goodsample == "N" ) %>%
  filter(!spec_code == "") %>%
  filter(basin == "Main Lake") %>%
  filter(!site == "Burlington Bay Cross-Contour") %>%
  filter((spec_code == "ALW")|(spec_code == "RSM")) %>%
  filter((depth_mean_m <= 60 ) | (depth_start_m <=60 & depth_end_m <=60))

#Figures

#Length frequency for ALW and RSM for N,C,S main lake for all years
LenFreqAllYr <- ggplot(data = Fish_sampled.1, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2016-2021")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreqAllYr
LenFreqAllYr

#Filter by gear, basin, 2016, and species
Fish_sampled.2016 <- Fish_sampled.1 %>%
  filter(year == "2016")
  

#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2016
LenFreq2016 <- ggplot(data = Fish_sampled.2016, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2016")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2016
LenFreq2016

#Filter by gear, basin, 2017, and species
Fish_sampled.2017 <- Fish_sampled.1 %>%
  filter(year == "2017")

#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2017
LenFreq2017 <- ggplot(data = Fish_sampled.2017, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2017")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2017
LenFreq2017

#Filter by gear, basin, 2018, and species
Fish_sampled.2018 <- Fish_sampled.1 %>%
  filter(year == "2018")


#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2018
LenFreq2018 <- ggplot(data = Fish_sampled.2018, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2018")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2018
LenFreq2018

#Filter by gear, basin, 2019, and species
Fish_sampled.2019 <- Fish_sampled.1 %>%
  filter(year == "2019")

#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2019
LenFreq2019 <- ggplot(data = Fish_sampled.2019, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2019")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2019
LenFreq2019

#Filter by gear, basin, 2020, and species
Fish_sampled.2020 <- Fish_sampled.1 %>%
  filter(year == "2020")

#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2020
LenFreq2020 <- ggplot(data = Fish_sampled.2020, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2020")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2020
LenFreq2020

#Filter by gear, basin, 2021, and species
Fish_sampled.2021 <- Fish_sampled.1 %>%
  filter(year == "2021")


#Length frequency for ALW and RSM for N,C,S main lake for ONLY 2021
LenFreq2021 <- ggplot(data = Fish_sampled.2021, aes(x= tl_mm))+
  geom_histogram(binwidth = 5, boundary = 0, closed = "left", fill = "darkslategray3", color= "black")+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2021")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()

#View LenFreq2021
LenFreq2021

# ALW and RSM Length Frequency 2019-2021 by N,C,S Main Lake
Fish_sampled.2 <- Fish_sampled.1

Fish_sampled.2$year = factor(Fish_sampled.2$year)

AllTheThings <- ggplot(data = Fish_sampled.2, aes(x= tl_mm))+
  geom_histogram(aes(fill = year),binwidth = 5, boundary = 0, closed = "left", color= "black", position = "stack")+
  scale_fill_manual(values= c("darkorchid4", "mediumorchid", "orchid2", "darkblue", "mediumblue", "lightblue"))+
  scale_y_continuous(name = "Number of Fish", expand = expansion(mult = c(0, 0.05)))+
  scale_x_continuous(name = "Total Length (mm)") +
  ggtitle("ALW and RSM Length Frequency 2016-2021")+
  theme_bw() +
  facet_grid(rows = vars(minor_basin),cols=vars(spec_code), scales = "free_y")+
  easy_center_title()
AllTheThings