Package: SWMPrExtension 2.2.4.2

Matt Dornback

SWMPrExtension: Functions for Analyzing and Plotting Estuary Monitoring Data

Tools for performing routine analysis and plotting tasks with environmental data from the System Wide Monitoring Program of the National Estuarine Research Reserve System <https://cdmo.baruch.sc.edu/>. This package builds on the functionality of the 'SWMPr' package <https://cran.r-project.org/package=SWMPr>, 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) <ISSN 2073-4859><https://journal.r-project.org/archive/2016-1/beck.pdf> Rudis, Bob (2014) <https://rud.is/b/2014/11/16/moving-the-earth-well-alaska-hawaii-with-r/>. United States Environmental Protection Agency (2015) <https://cfpub.epa.gov/si/si_public_record_Report.cfm?Lab=OWOW&dirEntryId=327030>. United States Environmental Protection Agency (2012) <https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.646.1973&rep=rep1&type=pdf>.

Authors:Julie Padilla [aut, ctb], Marcus Beck [ctb], Kimberly Cressman [ctb], Dave Eslinger [aut, ctb], Kirk Waters [ctb], Bob Rudis [ctb], Davis Vaughan [ctb], Matt Dornback [aut, cre]

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SWMPrExtension.pdf |SWMPrExtension.html✨
SWMPrExtension/json (API)
NEWS

# Install 'SWMPrExtension' in R:

install.packages('SWMPrExtension', repos = c('https://noaa-ocm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/noaa-ocm/swmprextension/issues

Datasets:

cbm_spatial - Spatial Data from Chesapeake Bay - Maryland
counties_4269 - US County Map
elk_spatial - Spatial Data from Elkhorn Slough
elknmnut - Nutrient Data from Elkhorn Slough - North Marsh Station
elksmwq - Water Quality Data from Elkhorn Slough - South Marsh Station
sampling_stations - Detailed NERRS site data
sampling_stations_backup - A Backup of Detailed NERRS site data
us_4269 - US State Map

On CRAN:

47 exports 12 stars 1.88 score 130 dependencies 42 scripts 476 downloads

Last updated 1 years agofrom:681e1a6d59. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 13 2024
R-4.5-win	ERROR	Sep 13 2024
R-4.5-linux	ERROR	Sep 13 2024
R-4.4-win	ERROR	Sep 13 2024
R-4.4-mac	ERROR	Sep 13 2024
R-4.3-win	ERROR	Sep 13 2024
R-4.3-mac	ERROR	Sep 13 2024

Exports:annual_range assign_season base_map create_sk_flextable_list create_sk_national_ft_reserves create_sk_national_ft_results ft_col_names generate_results_table generate_station_table geographic_unique_stations get_reserve get_shp_name get_site_code get_site_coordinates get_sites historical_daily_range historical_range import_local_nut lm_p_labs load_shp_file national_sk_map raw_boxplot remove_inf_and_nan res_custom_map res_custom_sk_map res_local_map res_national_map res_sk_map reserve_locs seasonal_barplot seasonal_boxplot seasonal_dot set_date_break_labs set_date_breaks set_date_breaks_minor sk_seasonal sk_tidy std_param_check summarise_handoff_files threshold_criteria_plot threshold_identification threshold_percentile_plot threshold_summary title_labeler update_sampling_stations y_count_labeler y_labeler

Dependencies:askpass backports base64enc bit bit64 broom bslib cachem class classInt cli clipr cluster colorspace cpp11 crayon curl data.table DBI deldir digest dplyr e1071 EnvStats evaluate fansi farver fastmap flextable fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggfun ggimage ggplot2 ggplotify ggthemes glue gridExtra gridGraphics gsw gtable hexbin highr hms htmltools httr interp isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lattice latticeExtra lifecycle lubridate magick magrittr mapproj maps MASS Matrix memoise mgcv mime munsell nlme nortest oce officer openair openssl pillar pkgconfig plyr png prettyunits progress proxy purrr R6 ragg rappdirs RColorBrewer Rcpp RcppEigen readr reshape2 rlang rmarkdown s2 sass scales sf stringi stringr suncalc SWMPr sys systemfonts textshaping tibble tictoc tidyr tidyselect timechange tinytex tzdb units utf8 uuid vctrs viridisLite vroom withr wk xfun XML xml2 yaml yulab.utils zip zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annual Range Timeseries	annual_range annual_range.swmpr
Assign seasons to SWMP sampling data	assign_season
Create background map	base_map
Spatial Data from Chesapeake Bay - Maryland	cbm_spatial
US County Map	counties_4269
Create a List of Flextable Objects	create_sk_flextable_list
Create a Flextable Object of Reserve Names	create_sk_national_ft_reserves
Create a Flextable Object of Seasonal Kendall Results	create_sk_national_ft_results
Spatial Data from Elkhorn Slough	elk_spatial
Nutrient Data from Elkhorn Slough - North Marsh Station	elknmnut
Water Quality Data from Elkhorn Slough - South Marsh Station	elksmwq
Convert Parameter Abbreviations	ft_col_names
Filter Reformatted Seasonal Kendall Results	generate_results_table
Filter Reformatted Seasonal Kendall Results	generate_station_table
Return a vector of geographically unique NERR Stations	geographic_unique_stations
Identify NERRS reserve from metadata	get_reserve
Identify shapefile for NERRS reserve	get_shp_name
Return NERRS reserve site code based on data in the data file	get_site_code
Identify NERRS sampling locations from metadata	get_site_coordinates
Identify NERRS reserve stations from metadata	get_sites
Historical Daily Range Timeseries	historical_daily_range historical_daily_range.swmpr
Historical Monthly/Seasonal Range Timeseries	historical_range historical_range.swmpr
Import local CDMO data	import_local_nut
P-Value labels for Plotting	lm_p_labs
Load and format shapefile for reserve level map	load_shp_file
Reserve National Map with Seasonal Kendall Results	national_sk_map
Boxplots of raw data by user-defined season for a target year	raw_boxplot raw_boxplot.swmpr
Replace Inf/-Inf/NaN values	remove_inf_and_nan
Local Reserve Map for Custom Stations	res_custom_map
Local Reserve Map With Seasonal Kendall Results for Custom Stations	res_custom_sk_map
Local Reserve Map	res_local_map
Reserve National Map	res_national_map
Local Reserve Map With Seasonal Kendall Results	res_sk_map
NERRS Sampling Location Data Frame	reserve_locs
Detailed NERRS site data	sampling_stations
A Backup of Detailed NERRS site data	sampling_stations_backup
Cumulative Bar Plot	seasonal_barplot seasonal_barplot.swmpr
Seasonal boxplots	seasonal_boxplot seasonal_boxplot.swmpr
Seasonal Dot Plot	seasonal_dot seasonal_dot.swmpr
Set reasonable date breaks labels	set_date_break_labs
Set reasonable date breaks	set_date_breaks
Select reasonable minor breaks for 'scale_x_datetime'	set_date_breaks_minor
Seasonal Kendall Analysis for Seasonal Data	sk_seasonal sk_seasonal.swmpr
Tidy Seasonal Kendall Results	sk_tidy
Standard Parameter Check	std_param_check
Summarise Hand-off Files from Reserve Level Reports	summarise_handoff_files
Water Quality Threshold Plot For Parameters With Criteria	threshold_criteria_plot threshold_criteria_plot.swmpr
Tabulate Threshold Exceedances	threshold_identification threshold_identification.swmpr
Threshold Percentile Plot	threshold_percentile_plot threshold_percentile_plot.swmpr
Summary Plots for Threshold Identification	threshold_summary threshold_summary.swmpr
Generate Plot Title Based on NERR Site ID	title_labeler
Update reserve sampling stations	update_sampling_stations
US State Map	us_4269
Generate y-axis Label Based on SWMP Parameter Abbreviation	y_count_labeler
Generate y-axis Label Based on SWMP Parameter Abbreviation	y_labeler