waterNETN

This package contains functions that import database views from the water data package Access database and/or CSVs in the NETN water data package and provides functions to query, summarize, and visualize NETN water data. The R package can be installed using pak::pkg_install('doi-nps/waterNETN'). Previous archived versions of this R package can be found at www.github.com/katemmiller/waterNETN

This package includes the following functions:

• importData: Import views from data package MS Access database or as a zip file of csvs.
• exportData: Export views as CSVs to prepare for data package.
• prepFMtoAccess: preps water data exported from the FileMaker app for import into the MS Access backend database. Note: Not sure if this function is fully functional (depends on whether database is set up to import a CSV).


• getSites: queries location information common across lakes and streams.
• getSitesLake: queries location information specific to lakes.
• getSitesStream: queries location information specific to streams.
• getEvents: queries visit-level data for NETN water monitoring.


• getChemistry: queries NETN water chemistry data that were measured in the lab.
• getDischarge: queries NETN water discharge data for stream sites.
• getLightPen: queries light penetration data for lake monitoring.
• getSecchi: queries Secchi depth data for lake monitoring.
• getSondeInSitu: queries water data collected with by a Sonde in the field.
• getStreamObs: queries stream observation data.
• getWaterLevel: queries water level data.
plotLakeProfile: plots metrics collected in lake profiles.
• plotPrecipDischarge: plots precipitation vs. stream discharge. The package doi-nps/climateNETN must be installed for this function.
• plotScatterPlot: plots a scatterplot of 2 water quality or quantity metrics.
• plotTrend: plots a water metric over time and includes option to add loess smoother.
• plotWaterBands: plots current year of water in comparison to the distribution of water data collected in specified previous years.


• sumEvents: Summarize the number of samples collected at each site by year, month, parameter, and whether measurement was real or censored.
• theme_WQ: custom ggplot2 theme for plotting NETN water data.

The docs/ folder includes multiple files that are useful for automated reporting and the tutorial website:

• index.Rmd and its output index.html are the files that generate the waterNETN tutorial website.
• QC_NETN_report.RMD performs automated QC checks on the data. Note that the WC_NETN_compile.R and QC_NETN_report_functions.R are sourced in the RMD.
• header_manual.html generates th NPS banner for both RMD headers.
• www/ folder contains the css and images sourced in the RMDs.