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]

SWMPrExtension_2.2.4.2.tar.gz
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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'))

Peer review:

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

Datasets:

On CRAN:

5.10 score 12 stars 42 scripts 450 downloads 47 exports 130 dependencies

Last updated 2 years agofrom:681e1a6d59. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winERRORNov 12 2024
R-4.5-linuxERRORNov 12 2024
R-4.4-winERRORNov 12 2024
R-4.4-macERRORNov 12 2024
R-4.3-winERRORNov 12 2024
R-4.3-macERRORNov 12 2024

Exports:annual_rangeassign_seasonbase_mapcreate_sk_flextable_listcreate_sk_national_ft_reservescreate_sk_national_ft_resultsft_col_namesgenerate_results_tablegenerate_station_tablegeographic_unique_stationsget_reserveget_shp_nameget_site_codeget_site_coordinatesget_siteshistorical_daily_rangehistorical_rangeimport_local_nutlm_p_labsload_shp_filenational_sk_mapraw_boxplotremove_inf_and_nanres_custom_mapres_custom_sk_mapres_local_mapres_national_mapres_sk_mapreserve_locsseasonal_barplotseasonal_boxplotseasonal_dotset_date_break_labsset_date_breaksset_date_breaks_minorsk_seasonalsk_tidystd_param_checksummarise_handoff_filesthreshold_criteria_plotthreshold_identificationthreshold_percentile_plotthreshold_summarytitle_labelerupdate_sampling_stationsy_count_labelery_labeler

Dependencies:askpassbackportsbase64encbitbit64broombslibcachemclassclassIntclicliprclustercolorspacecpp11crayoncurldata.tableDBIdeldirdigestdplyre1071EnvStatsevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggfunggimageggplot2ggplotifyggthemesgluegridExtragridGraphicsgswgtablehexbinhighrhmshtmltoolshttrinterpisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglatticelatticeExtralifecyclelubridatemagickmagrittrmapprojmapsMASSMatrixmemoisemgcvmimemunsellnlmenortestoceofficeropenairopensslpillarpkgconfigplyrpngprettyunitsprogressproxypurrrR6raggrappdirsRColorBrewerRcppRcppEigenreadrreshape2rlangrmarkdowns2sassscalessfstringistringrsuncalcSWMPrsyssystemfontstextshapingtibbletictoctidyrtidyselecttimechangetinytextzdbunitsutf8uuidvctrsviridisLitevroomwithrwkxfunXMLxml2yamlyulab.utilszipzoo

Readme and manuals

Help Manual

Help pageTopics
Annual Range Timeseriesannual_range annual_range.swmpr
Assign seasons to SWMP sampling dataassign_season
Create background mapbase_map
Spatial Data from Chesapeake Bay - Marylandcbm_spatial
US County Mapcounties_4269
Create a List of Flextable Objectscreate_sk_flextable_list
Create a Flextable Object of Reserve Namescreate_sk_national_ft_reserves
Create a Flextable Object of Seasonal Kendall Resultscreate_sk_national_ft_results
Spatial Data from Elkhorn Sloughelk_spatial
Nutrient Data from Elkhorn Slough - North Marsh Stationelknmnut
Water Quality Data from Elkhorn Slough - South Marsh Stationelksmwq
Convert Parameter Abbreviationsft_col_names
Filter Reformatted Seasonal Kendall Resultsgenerate_results_table
Filter Reformatted Seasonal Kendall Resultsgenerate_station_table
Return a vector of geographically unique NERR Stationsgeographic_unique_stations
Identify NERRS reserve from metadataget_reserve
Identify shapefile for NERRS reserveget_shp_name
Return NERRS reserve site code based on data in the data fileget_site_code
Identify NERRS sampling locations from metadataget_site_coordinates
Identify NERRS reserve stations from metadataget_sites
Historical Daily Range Timeserieshistorical_daily_range historical_daily_range.swmpr
Historical Monthly/Seasonal Range Timeserieshistorical_range historical_range.swmpr
Import local CDMO dataimport_local_nut
P-Value labels for Plottinglm_p_labs
Load and format shapefile for reserve level mapload_shp_file
Reserve National Map with Seasonal Kendall Resultsnational_sk_map
Boxplots of raw data by user-defined season for a target yearraw_boxplot raw_boxplot.swmpr
Replace Inf/-Inf/NaN valuesremove_inf_and_nan
Local Reserve Map for Custom Stationsres_custom_map
Local Reserve Map With Seasonal Kendall Results for Custom Stationsres_custom_sk_map
Local Reserve Mapres_local_map
Reserve National Mapres_national_map
Local Reserve Map With Seasonal Kendall Resultsres_sk_map
NERRS Sampling Location Data Framereserve_locs
Detailed NERRS site datasampling_stations
A Backup of Detailed NERRS site datasampling_stations_backup
Cumulative Bar Plotseasonal_barplot seasonal_barplot.swmpr
Seasonal boxplotsseasonal_boxplot seasonal_boxplot.swmpr
Seasonal Dot Plotseasonal_dot seasonal_dot.swmpr
Set reasonable date breaks labelsset_date_break_labs
Set reasonable date breaksset_date_breaks
Select reasonable minor breaks for 'scale_x_datetime'set_date_breaks_minor
Seasonal Kendall Analysis for Seasonal Datask_seasonal sk_seasonal.swmpr
Tidy Seasonal Kendall Resultssk_tidy
Standard Parameter Checkstd_param_check
Summarise Hand-off Files from Reserve Level Reportssummarise_handoff_files
Water Quality Threshold Plot For Parameters With Criteriathreshold_criteria_plot threshold_criteria_plot.swmpr
Tabulate Threshold Exceedancesthreshold_identification threshold_identification.swmpr
Threshold Percentile Plotthreshold_percentile_plot threshold_percentile_plot.swmpr
Summary Plots for Threshold Identificationthreshold_summary threshold_summary.swmpr
Generate Plot Title Based on NERR Site IDtitle_labeler
Update reserve sampling stationsupdate_sampling_stations
US State Mapus_4269
Generate y-axis Label Based on SWMP Parameter Abbreviationy_count_labeler
Generate y-axis Label Based on SWMP Parameter Abbreviationy_labeler