Functions for the Mississippi Sound Estuary Program • mseptools

The goal of mseptools is to provide R functions helpful to the Mississippi Sound Estuary Program and other MSEP-area researchers.

Installation

You can install mseptools from GitHub with the following code:

# install.packages("devtools")
devtools::install_github("cmep-ms/mseptools")

Example

Get Data

This is a basic example of downloading a week’s worth of salinity data from all USGS stations in the Mississippi Sound:

library(mseptools)
dat <- get_mssnd_data(startDate = "2025-01-01", endDate = "2025-01-08")
head(dat$data)
head(dat$daily)
head(dat$siteInfo)

Plot

This graph uses plotly, which makes the graphics interactive. In addition to hovering over parts of the graph to see the exact values, you can click on a legend entry to remove (or re-show) a station; double-click to show only that station. There is a slider bar below so you can narrow the date range.

plot_mssnd_salinity(dat)

Map the stations

This function uses leaflet to show the USGS monitoring stations on a map.

map_mssnd_usgs(dat$siteInfo)

Color palette

plot_mssnd_salinity() takes a named vector of colors; leaflet does not. A common palette can be created and used in both functions as follows:

stns <- sort(dat$siteInfo$clean_nm)

# static color palette
colors_static <- as.character(khroma::color("roma")(length(stns)))
names(colors_static) <- stns

# color function
color_function <- leaflet::colorFactor(palette = colors_static,
                                       domain = names(colors_static))

# plot and map with these palettes
plot_mssnd_salinity(dat, colors = colors_static)
map_mssnd_usgs(dat$siteInfo, color_function = color_function)