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SWMPrExtension (version 2.2.5.1)

Functions for Analyzing and Plotting Estuary Monitoring Data

Description

Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System . This package builds on the functionality of the 'SWMPr' package , which is used to retrieve and organize the data. The combined set of tools address common challenges associated with continuous time series data for environmental decision making, and are intended for use in annual reporting activities. References: Beck, Marcus W. (2016) Rudis, Bob (2014) . United States Environmental Protection Agency (2015) .

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Version

Install

install.packages('SWMPrExtension')

Monthly Downloads

299

Version

2.2.5.1

License

CC0

Maintainer

Matt Dornback

Last Published

January 11th, 2024

Functions in SWMPrExtension (2.2.5.1)

load_shp_file

Load and format shapefile for reserve level map
raw_boxplot

Boxplots of raw data by user-defined season for a target year
res_local_map

Local Reserve Map
national_sk_map

Reserve National Map with Seasonal Kendall Results
res_national_map

Reserve National Map
res_custom_sk_map

Local Reserve Map With Seasonal Kendall Results for Custom Stations
set_date_break_labs

Set reasonable date breaks labels
seasonal_dot

Seasonal Dot Plot
res_sk_map

Local Reserve Map With Seasonal Kendall Results
threshold_summary

Summary Plots for Threshold Identification
threshold_criteria_plot

Water Quality Threshold Plot For Parameters With Criteria
historical_range

Historical Monthly/Seasonal Range Timeseries
get_reserve

Identify NERRS reserve from metadata
import_local_nut

Import local CDMO data
reserve_locs

NERRS Sampling Location Data Frame
lm_p_labs

P-Value labels for Plotting
sampling_stations_backup

A Backup of Detailed NERRS site data
threshold_percentile_plot

Threshold Percentile Plot
summarise_handoff_files

Summarise Hand-off Files from Reserve Level Reports
remove_inf_and_nan

Replace Inf/-Inf/NaN values
seasonal_barplot

Cumulative Bar Plot
geographic_unique_stations

Return a vector of geographically unique NERR Stations
historical_daily_range

Historical Daily Range Timeseries
sk_seasonal

Seasonal Kendall Analysis for Seasonal Data
sampling_stations

Detailed NERRS site data
title_labeler

Generate Plot Title Based on NERR Site ID
std_param_check

Standard Parameter Check
seasonal_boxplot

Seasonal boxplots
y_labeler

Generate y-axis Label Based on SWMP Parameter Abbreviation
update_sampling_stations

Update reserve sampling stations
sk_tidy

Tidy Seasonal Kendall Results
set_date_breaks_minor

threshold_identification

Tabulate Threshold Exceedances
set_date_breaks

Set reasonable date breaks
us_4269

US State Map
y_count_labeler

Generate y-axis Label Based on SWMP Parameter Abbreviation
create_sk_flextable_list

Create a List of Flextable Objects
cbm_spatial

Spatial Data from Chesapeake Bay - Maryland
create_sk_national_ft_results

Create a Flextable Object of Seasonal Kendall Results
create_sk_national_ft_reserves

Create a Flextable Object of Reserve Names
annual_range

Annual Range Timeseries
assign_season

Assign seasons to SWMP sampling data
base_map

Create background map
generate_results_table

Filter Reformatted Seasonal Kendall Results
get_sites

Identify NERRS reserve stations from metadata
get_site_coordinates

Identify NERRS sampling locations from metadata
generate_station_table

Filter Reformatted Seasonal Kendall Results
get_site_code

Return NERRS reserve site code based on data in the data file
get_shp_name

Identify shapefile for NERRS reserve
ft_col_names

Convert Parameter Abbreviations
elksmwq

Water Quality Data from Elkhorn Slough - South Marsh Station
elk_spatial

Spatial Data from Elkhorn Slough
elknmnut

Nutrient Data from Elkhorn Slough - North Marsh Station
counties_4269

US County Map
res_custom_map

Local Reserve Map for Custom Stations