install.packages(“tidyverse”)
install.packages(“lubridate”)
install.packages(“sf”)
install.packages(“units”)

# Tidyverse and other support libraries
library(tidyverse)
library(lubridate)
library(sf)
library(units)

# Load stoichUtilities
library(stoichUtilities)

# Load the STOICH data (assumed to be in a directory named "data" inside the home directory)
stoichData <- stoichUtilities::loadSTOICH(dataPath=file.path(path.expand("~"), "data"))

# Filter the STOICH data
stoichFiltered <- stoichUtilities::filterSTOICH(dataTables=stoichData, var="State", val="FL", condition="Equal")

# Match organism stoichiometry data with water chemsitry data for samples that weren't taken at the exact same time
stoichPaired <- stoichUtilities::locateDataPairsSTOICH(stoichData, timeDiff=2, timeUnits="weeks", distance=5, pairMethod="Min Time", ignoreExisting=TRUE)

# Join all the tables into one large wide table
stoichTable <- stoichUtilities::joinSTOICH(stoichPaired)

# Install the Leaflet package if it isn't installed.
install.packages("leaflet")

# Load the leaflet library.
library(leaflet)

# Split out the GPS data.
gpsGroups <- stoichTable %>% 
  select(c("Latitude", "Longitude")) %>% 
  drop_na(Latitude, Longitude) %>% 
  # Round the GPS coordinates so small differences in location are lumped together.
  mutate(across(everything(), round, 2)) %>% 
  group_by(Latitude, Longitude) %>% 
  # Summarise to get the number of entries for each location in the database.
  summarise(nSamples=n(), .groups="keep") %>%
  # Convert the numbers to characters for use in popups
  mutate(nSamples = paste("Samples: ", nSamples, sep=""), .keep="all")

# Start building the map.
leaflet() %>% 
  # Select the background style.
  addProviderTiles(providers$OpenTopoMap) %>%
  # Add markers for all the sites and group them based on zoom level.
  addMarkers(data = gpsGroups, lng = ~Longitude, lat = ~Latitude, label=~nSamples, clusterOptions = markerClusterOptions())

help(loadSTOICH)