In sophiasternberg/fcess:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(fcess)
library(tidyverse)

# View initial data
head(fce_bullshark)

# Detach Year, Month, and Day from the Date variable
fce_bullshark <- fce_bullshark %>% mutate(Year = format(Date, "%Y"),
                                          Month = format(Date, "%m"),
                                          Day = format(Date, "%d"))
fce_bullshark

# Group the counts of Bull Sharks by Year
counts <- fce_bullshark %>% 
  group_by(Year) %>% 
  summarise(bycount = sum(Bull_Shark_Count))

# Plot Bull Shark Count Overtime
ggplot(data = counts, aes(x = Year, y = bycount, fill = bycount)) +
  geom_bar(stat = "identity") +
  labs(x = "Year",
    y = "Number of Bull Sharks",
    title = "Bull Shark Counts Overtime") +
  geom_text(aes(label = bycount)) +
  theme(plot.title = element_text(hjust = 0.5))

# Group the counts of Bull Sharks by Sitename
sitecounts <- fce_bullshark %>% 
  group_by(SITENAME, Year) %>% 
  summarise(bycount = sum(Bull_Shark_Count), temp = mean(Temperature))
sitecounts

# Plot the site Bullshark counts from 2005 to 2009
ggplot(data = sitecounts, aes(x = Year, y = bycount, group = SITENAME, color = SITENAME)) +
  geom_line() +
  labs(x = "Year",
       y = "Bull Shark Count",
       title = "Bull Shark Counts by Site") +
  theme(plot.title = element_text(hjust = 0.5))

ggplot(data = fce_bullshark, aes(x = Date, y = Temperature)) +
  geom_line() +
  labs(x = "Date",
    y = "Temperature",
    title = "Temperature Overtime") +
  theme(plot.title = element_text(hjust = 0.5))

# Plot the site Bullshark counts from 2005 to 2009
ggplot(data = sitecounts, aes(x = Year, y = temp, group = SITENAME, color = SITENAME)) +
  geom_line() +
  labs(x = "Year",
       y = "Temperature (Cº)",
       title = "Yearly Mean Temperatures by Site") +
  theme(plot.title = element_text(hjust = 0.5))

# boxplot by salinity by site
ggplot(data = fce_bullshark, aes(x = reorder(SITENAME, Salinity, FUN = median), 
                                 y = Salinity, 
                                 color =SITENAME)) +
  geom_boxplot() +
  labs(x = "Site Name",
       y = "Salinity", 
       title = "Salinity by Site") +
  theme(plot.title = element_text(hjust = 0.5))

ggplot(data = fce_bullshark, aes(x = Date, y = Salinity)) +
  geom_line() +
  labs(x = "Date",
    y = "Salinity",
    title = "Salinity Overtime") +
  theme(plot.title = element_text(hjust = 0.5))

year06 <- as.tibble(fce_bullshark)
year06 <- filter(fce_bullshark, Date >= as.Date("2006-01-01"), Date <= as.Date("2006-12-31"))

ggplot(data = year06, aes(x = Date, y = Bull_Shark_Count)) +
      geom_bar(stat = "identity", fill = "dodgerblue") +
      labs(title = "Total Bull Shark Count",
           x = "Date", 
           y = "Number of Bull Sharks") +
  theme(plot.title = element_text(hjust = 0.5))

year09 <- as.tibble(fce_bullshark)
year09 <- filter(fce_bullshark, Date >= as.Date("2009-01-01"), Date <= as.Date("2009-12-31"))

ggplot(data = year09, aes(x = Date, y = Bull_Shark_Count)) +
      geom_bar(stat = "identity", fill = "dodgerblue") +
      labs(title = "Total Bull Shark Count",
           x = "Date", 
           y = "Number of Bull Sharks") +
  theme(plot.title = element_text(hjust = 0.5))

Citation

Heithaus, M. and P. Matich. 2014. Bull shark catches, water temperatures, salinities, and dissolved oxygen levels in the Shark River Slough, Everglades National Park (FCE) , from May 2005 to May 2009 ver 3. Environmental Data Initiative. https://doi.org/10.6073/pasta/04a8792fed9ceed4237bd3273a97e8f8 (Accessed 2021-04-19).