Using waterNETN R pkg.

Using the waterNETN R package

Getting started

Installation

Step 1. Install R, RStudio, and RTools in Company Portal

Step 2. Install pak package in R:

install.packages('pak')

Step 3. Install waterNETN from github

Note that whenever the waterNETN package is updated, you can rerun this code to install the latest version.

library(pak)
pkg_install("doi-nps/waterNETN")

Step 4. Load waterNETN R package

library(waterNETN)

Step 5. Import data

Note that R is not able to connect to files on Sharepoint or MS Teams (b/c Teams also stores all files on Sharepoint). That means you need to store data package files on your local machine or on a server (e.g. NETN Z drive). The default option for importing data will add the data package views (i.e., flatfiles) to an environment called VIEWS_WQ to your Environment work space (i.e. Environment tab in top right panel). If you would rather import each individual view into your R session, specify with the new_env argument (e.g., importData(new_env = F)).

Option 1. Import data via .csv files. The file path should be where csvs are on your machine or server.

importData(type = 'csv',
           filepath = "./data/records-2313941") # update filepath to your computer

Option 2. Import data via zip file of csvs. The filepath should be the location and name of the zip file.

importData(type = 'zip', 
           filepath = "./data/records-2313941.zip")

Option 3. Import data via data package database file on your computer

importData(type = 'dbfile',
           filepath = "./data/NETN_h3Ov4_DataPackage_202331115.accdb")

Option 4. Import data via data package database DSN (Data Source Name) on your computer. Note that this is the default setting. As long as you have a named DSN called “NETNWQ_DP” that links to the data package database, and that database links to the latest NETN WQ backend database, the code below will run. See Setting up DSN tab for how to set up DSN.

importData() # easiest but must have DSN set up
importData(type = 'DSN', odbc = "NETNWQ_DP") # equivalent to line above

Step 6. (Optional) Export data package to zip

You can export all of the csvs to a zip file with the day’s date stamped on the file name. This allows you to import the tables from the database, then export the csvs as one zip file.

importData() # easiest bust must have DSN set up
exportData(filepath = "./data", zip = TRUE) 

Step 7. Play with the data

The functions in the waterNETN package are designed to work with the views, and are the best way to interact with the data to query by park, site, site type, year, parameter, etc. However, if you want to view the raw data, and you imported the data into the VIEWS_WQ environment, you can access them with the code below:

# See list of the views
names(VIEWS_WQ)

# View one of the views
View(VIEWS_WQ$Chemistry_Data)

# Assign a view to a data frame named chem in R. Interact with chem the way you would work with any normal data frame in R. 
chem <- VIEWS_WQ$Chemistry_Data

If you want to use the print_head() function that shows output in the markdown, run the code below. This makes the results print cleaner in the markdown report. For your purposes, you can just run: head(dataframe).

print_head <- function(df){
  knitr::kable(df[1:6,]) |> #, table.attr = "style='width:60%;'") |> 
    kableExtra::kable_classic(full_width = F, font_size = 12, 
                              bootstrap_options = c("condensed"))
}

Getting help

Getting (and improving) help

The functions in waterNETN have help documentation like any R package. To view the help, you can go to the Packages tab and click on waterNETN (see below). That will show you all the functions in the package. Clicking on individual functions will take you to the help documentation for that function.

You can also see the help of a function by running, for example:

?importData

If waterNETN isn’t loaded yet, you’d run:

?waterNETN::importData

Each function’s help includes a Description, Usage (i.e. function arguments and their defaults), Argument options/definitions, and several examples showing how the function can be used.

This is where you come in! If you notice typos or can think of better descriptions, examples, error messages, etc., please send them my way! After we’re more comfortable with R packages and get versed on GitHub, you’ll be able to make those changes directly in the package. For now, you can just send me your suggestions and I’ll make the changes.

Finally, if you ever want to peak under the hood at the function, you can view it several ways.

1. Keep F2 key pressed and click on the function name in R. This trick works for many but not all functions in R.

2. View code in the GitHub doi-nps/waterNETN repo. The functions are in the R folder.

Setting up DSN

Setting up a DSN

1. Go to Windows Start Menu and search ODBC. Click on ODBC Data Sources (64-bit)

2. Click on Add, then select Microsoft Access Driver (*.mdb, *.accdb) then click Finish in next menu.



3. Enter NETNWQ_DP into the Data Source Name (red arrow), click on Select (red circle). In new window, click on C:/ (orange arrow) and find the path to your database. If it’s on the Z drive, then click on the Drives window and select correct Drive. Click on the data package database (yellow arrow). When complete, click OK. Finally, add the name of the database file to the Description (blue arrow), so it’s easier to check whether you’re using the latest version.



4. If updating an existing DSN, follow similar process, except click on the DSN in the first window and select Configure instead of Add.

Data Ingestion Step

Before FileMaker Go files are ingested into the MS Access database, use the prepFMtoAccess() function to scrub placeholder values from the exported .csv files. The function converts placeholder values that FileMaker uses to prevent null values to NAs when “No measurement” is selected for Datum Name and/or Discharge Method in the FileMaker Go application. Additionally, it converts certain placeholder values to NAs when “No water sample taken” is recorded in the application. The table below shows the FileMaker Go export placeholders that are converted to NAs for both Stream and Lake applications.

Table 1. Details of FileMaker ingestion script changes prior to MS Access import.

FileMaker app	FileMaker export column name	FileMaker export value	Ingestion script replacement value
Lake	Stage_GageReading	0	NA
Lake	Stage_Time	00:00:00	NA
Lake, Stream	WaterSample_QC_IBWExp	1/1/0001	NA
Lake, Stream	WaterSample_QC_Time	00:00:00	NA
Lake, Stream	WaterSample_Time	00:00:00	NA
Stream	Flow_AvgVel	0	NA
Stream	Flow_Discharge_calc	0	NA
Stream	Flow_Discharge_cfs	0	NA
Stream	Flow_TotalArea	0	NA
Stream	Flow_TotalWidth	0	NA
Stream	FlowTrackerTemp	0	NA
Stream	tbl_Stage::Stage_Reading_1	0	NA
Stream	tbl_Stage::Stage_Reading_2	0	NA
Stream	tbl_Stage::Stage_Time_1	00:00:00	NA
Stream	tbl_Stage::Stage_Time_2	00:00:00	NA

The prepFMtoAccess() function requires users to specify the path and file name, and currently works with xlsx files for import and csv for export. The function will determine whether the data is from a lake or stream based on column names. The function then exports a csv in the same filepath and with the same excel_name with ‘cleaned’ and the date added to the filename, and that is ready to be imported into MS Access. Note that function can only work with lake or stream data, not both in the same function call. Examples are below. Note that additional testing of the data and import in MS Access is necessary to ensure dates and GUIDs are importing properly. Depending on how the MS Access import works, the cleaned csv may need to be opened in Excel and saved as an xlsx. Better yet, the export from FileMaker is as a csv or txt file instead of xlsx.

Clean lake data and return cleaned data in global environment.

prepFMtoAccess(filepath = "../data", excel_name = "ACAD_WQ_Lakes_2025-06.xlsx", keep_file = T)

Clean stream data.

prepFMtoAccess(filepath = "../data", excel_name = "ACAD_WQ_Stream_2025-06.xlsx")

get Data functions

getSites()

getSites()

Query site-level data. This function combines columns in common between the Sites_Stream and Sites_Lake views. This is a good building block for other functions, but may be less helpful on its own. Though, one helpful use of this function is to get the site codes for a given park or site.

Get site info for ACAD streams

ACAD_streams <- getSites(park = 'ACAD', site_type = 'stream')
print_head(ACAD_streams)# top 6 rows

GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	Datum	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	IsPointCUI	site_type
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACABIN	Aunt Betty Pond Inlet	Stream	44.36502	-68.27243	NAD83	2.48	The inlet flows north from Gilmore Meadow into Aunt Betty Pond.	Beavers often present both US & DS of carriage road.	AA	FALSE	stream
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACBRKB	Breakneck Brook	Stream	44.41093	-68.25175	NAD83	3.72	The stream flows north from the Breakneck Ponds and into the ocean (Hulls Cove).	Exact sampling point can vary depending on streamflow/water level. Hits baseflow in dry years.	AA	FALSE	stream
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACBRWN	Browns Brook	Stream	44.33908	-68.30123	NAD83	1.18	The stream flows northwest from Parkman Mountain into the ocean (Somes Sound). Measure east (US) of culvert under Sargent Drive.	Very close to municipal sand/salt storage facility.	AA	FALSE	stream
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACCADS	Cadillac Stream	Stream	44.34480	-68.21700	NAD83	0.62	On right bank approximately 500 feet upstream of the crossing of Canon Brook Trail (500 ft upstream from confluence with Otter Creek and 0.5 miles southeast of Cadillac summit)	High-elevation stream flows south on the east face of Cadillac mountain into Canon Brook- Otter Creek. Former site of USGS stream gage 01022835 (1999- 2006).	AA	FALSE	stream
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACDKLI	Duck Pond Brook	Stream	44.33123	-68.37826	NAD83	0.48	The stream flows north from Duck Pond into Long Pond (MDI).	Can be near or at baseflow in dry years and difficult to measure streamflow.	AA	FALSE	stream
NETN	Northeast Temperate Network	ACAD	Acadia National Park	NA	NA	ACDUCK	Duck Brook	Stream	44.37760	-68.24509	NAD83	9.62	Sample site is located north of Rte. 233 crossing, approx. 200 ft. DS of culvert.	Duck Brook flows north from Eagle Lake into the ocean (Hulls Cove/Frenchman Bay). Established in 2009, replaces ACEGLO.	AA	FALSE	stream

Get site info for all sites in MABI

mabi <- getSites(park = "MABI")
print_head(mabi)# top 6 rows

	GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	Datum	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	IsPointCUI	site_type
1	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABISA	Pogue Brook	Stream	43.63493	-72.52937	NAD83	0.99	Only stream within the park, the outlet of The Pogue. One stream-sampling site was selected to represent Pogue Brook. This site was chosen because it is the most downstream location within park boundaries.	None	A(1)	FALSE	stream
2	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABIPA	The Pogue	Lake	43.63336	-72.54263	NAD83	0.57	The Pogue is a 14-acre pond at the headwaters of the Pogue Brook. Naturally a spring-fed boggy area, it was created in the 1880s with an earthen dam. Swimming, fishing, or wading is prohibited.	None	A(1)	FALSE	lake
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

List site codes and their full site name for SARA

sara_sites <- getSites(park = "SARA") |> select(SiteCode, SiteName)
print_head(sara_sites)# top 6 rows

	SiteCode	SiteName
1	SARASA	Kroma Kill
2	SARASC	Upper Mill Creek
3	SARASD	Mill Creek Confluence
NA	NA	NA
NA.1	NA	NA
NA.2	NA	NA

Get all fields of site info for Primrose Brook in MORR

prim <- getSites(site = "MORRSB", output = "verbose")
print_head(prim)# top 6 rows

	GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	Datum	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	IsPointCUI	site_type
1	NETN	Northeast Temperate Network	MORR	Morristown National Historical Park	NA	NA	MORRSB	Primrose Brook Confluence	Stream	40.76506	-74.52978	NAD83	2.79	The monitoring site is located downstream of the USGS staff gage (01378780) installed just below the confluence of East and West Primrose Brooks.	Primrose Brook, a tributary of the Passaic River, drains an area almost entirely contained within the Jockey Hollow Unit of Morristown NHP.	A	FALSE	stream
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.4	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

getSitesLake()

Query site-level data for lakes only. This returns lake-only columns in the Sites_Lake views

Get site info for ACAD lakes

ACAD_lakes <- getSitesLake(park = "ACAD")
print_head(ACAD_lakes)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	HUC12	ContribWshedArea_km2	Inlet	Outlet	MaxDepth_m	TrophicType	LegislativeClass	FishMgtType	SiteDescription	Notes
ACANTB	Aunt Bettys Pond	ACAD	NA	10500021502	2.77	unnamed	RICHARDSON BRK	2.1	EUTROPHIC	GPA	COLDWATER	Shallow, marshy pond with an area of 31.5 acres. Inlet: Aunt Betty Inlet. Outlet: Richardson Brook.	Pond is full of emergent vegetation by mid-summer. Deep hole is in NE corner, near outlet. Surrounded by ANP. Last surveyed by IFW in 1982. Closed to ice fishing.
ACBOWL	The Bowl	ACAD	NA	10500021501	0.21	NA	OTTER CREEK	9.0	MESOTROPHIC	GPA	NONE	High elevation, mesotrophic pond located between Cahamplaine Mtn. and The Beehive.	Located off the Beehive Trail. Fish survey conducted in 1995 BY J.R. Burgess. Not monitored by NETN- sampled annually for acid depositon effects by ACAD staff. Once served as water supply for Satterlee estate.
ACBRBK	Bear Brook Pond	ACAD	NA	10500021501	NA	BEAR BROOK	BEAR BROOK	3.9	MESOTROPHIC	GPA	NONE	Mesotrophic, unstratified pond with an area of 7.5 acres. Its inlet and outlet is Bear Brook.	Located on Park Loop Road near Jackson Lab. Site of ANP purple loosestrife monitoring/control plots. Active beaver in area. Fish survey in 1995 by J.R. Burgess. Also known as Beaver Dam Pond.
ACBUBL	Bubble Pond	ACAD	NA	10500021501	1.77	unnamed	BUBBLE BROOK	11.9	MESOTROPHIC	GPA	COLDWATER	Oligotrophic, stratified lake with an area of 33 acres. Part of the public water supply. Inlet: unnamed stream on southern end. Outlet: Bubble Brook.	Surrounded by ANP. Connects with Bar Harbor water supply. Last surveyed by IFW in 1942. Closed to ice fishing.
ACEAGL	Eagle Lake	ACAD	NA	10500021501	5.60	BUBBLE BROOK	DUCK BROOK	33.5	OLIGOTROPHIC	GPA	COLDWATER	Oligotrophic, stratified lake with an area of 465.8 acres. Part of the public water supply. Inlet: Bubble Brook. Outlet: Duck Brook.	LLS spawning area built in outlet in 55. 10 hp outboard limit. Last surveyed by IFW in 1990. Surrounded by ANP.
ACECHO	Echo Lake	ACAD	NA	10500021502	5.10	LURVEY SPRG BRK	DENNING BROOK	20.1	OLIGOTROPHIC	GPA	COLDWATER	Oligotrophic, stratified lake with an area of 236.8 acres. Inlet: Lurvey Spring Brook. Outlet: Denning Brook.	Partial boundary w/ANP. Last surveyed by IFW in 1988. Outboard hp restrictions. Reclaimed in 1956. Guarded ANP swim beach on south end.

Get all site info for the Pogue Pond

pogue <- getSitesLake(site = "MABIPA", output = 'verbose')
print_head(pogue)# top 6 rows

	GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	Datum	HUC12	ContribWshedArea_km2	Inlet	Outlet	MaxDepth_m	TrophicType	LegislativeClass	FishMgtType	SiteDescription	Notes	IsPointCUI
1	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABIPA	The Pogue	Lake	43.63336	-72.54263	NAD83	10801060206	0.57	NA	Pogue Brk	3.4	MESOTROPHIC	A(1)	COLDWATER	The Pogue is a 14-acre pond at the headwaters of the Pogue Brook. Naturally a spring-fed boggy area, it was created in the 1880s with an earthen dam. Swimming, fishing, or wading is prohibited.	None	FALSE
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.4	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

Get all site info for lakes in LNETN

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
lnetn_lks <- getSitesLake(park = lnetn)
print_head(lnetn_lks)# top 6 rows

	SiteCode	SiteName	UnitCode	SubUnitCode	HUC12	ContribWshedArea_km2	Inlet	Outlet	MaxDepth_m	TrophicType	LegislativeClass	FishMgtType	SiteDescription	Notes
1	MABIPA	The Pogue	MABI	NA	10801060206	0.57	NA	Pogue Brk	3.40	MESOTROPHIC	A(1)	COLDWATER	The Pogue is a 14-acre pond at the headwaters of the Pogue Brook. Naturally a spring-fed boggy area, it was created in the 1880s with an earthen dam. Swimming, fishing, or wading is prohibited.	None
2	SAGAPA	Blow-Me-Down Pond	SAGA	NA	10801060303	117.15	Blow-Me-Down Br	Blow-Me-Down Br	2.03	MESOTROPHIC	A	WARMWATER	Blow-Me-Down Pond, the result of the impoundment of Blow-Me-Down Brook, has been a water quality site measured by the park since 1997 (Historic site 5). Concerns for the site include siltation of the area behind the dam.	Listed as impaired for fish consumption (Hg) in 2012)
3	WEFAPA	Weir Pond	WEFA	NA	11000060202	0.36	NA	unnamed stream	2.09	MESOTROPHIC	AA	WARMWATER	J. A. Weir authorized workers to construct an earthen dam in 1896 to form the 3.28 acre pond. The pond has been used for artistic inspiration, recreational fishing, as a hiking destination, and as a source of ice until the 1940s.	Dam extends >200’ along the NE perimeter & varies in width from 8- 10’. A roughly circular section of land in the NE section was likely left unexcavated to form an island on which Weir built a summerhouse (gone by 1930s). AKA Nod Hill Pond (CT DEEP map).
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

getSitesStream()

Query site-level data for streams only. This returns stream-only columns in the Sites_Stream views

Get site info for ACAD streams

ACAD_str <- getSitesStream(park = "ACAD")
print_head(ACAD_str)# top 6 rows

SiteCode	UnitCode	SubUnitCode	USGS_StaNumb	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	FisheryType
ACABIN	ACAD	NA	1022869	2.48	The inlet flows north from Gilmore Meadow into Aunt Betty Pond.	Beavers often present both US & DS of carriage road.	AA	Warmwater
ACBRKB	ACAD	NA	1022825	3.72	The stream flows north from the Breakneck Ponds and into the ocean (Hulls Cove).	Exact sampling point can vary depending on streamflow/water level. Hits baseflow in dry years.	AA	Coldwater
ACBRWN	ACAD	NA	1022866	1.18	The stream flows northwest from Parkman Mountain into the ocean (Somes Sound). Measure east (US) of culvert under Sargent Drive.	Very close to municipal sand/salt storage facility.	AA	Coldwater
ACCADS	ACAD	NA	1022835	0.62	On right bank approximately 500 feet upstream of the crossing of Canon Brook Trail (500 ft upstream from confluence with Otter Creek and 0.5 miles southeast of Cadillac summit)	High-elevation stream flows south on the east face of Cadillac mountain into Canon Brook- Otter Creek. Former site of USGS stream gage 01022835 (1999- 2006).	AA	Coldwater
ACDKLI	ACAD	NA	10228755	0.48	The stream flows north from Duck Pond into Long Pond (MDI).	Can be near or at baseflow in dry years and difficult to measure streamflow.	AA	Coldwater
ACDUCK	ACAD	NA	1022827	9.62	Sample site is located north of Rte. 233 crossing, approx. 200 ft. DS of culvert.	Duck Brook flows north from Eagle Lake into the ocean (Hulls Cove/Frenchman Bay). Established in 2009, replaces ACEGLO.	AA	Coldwater

Get all site info for the Pogue Stream

poguestr <- getSitesStream(site = "MABISA", output = 'verbose')
print_head(poguestr)# top 6 rows

	GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	Datum	USGS_StaNumb	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	FisheryType	IsPointCUI
1	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABISA	Pogue Brook	Stream	43.63493	-72.52937	NAD83	NA	0.99	Only stream within the park, the outlet of The Pogue. One stream-sampling site was selected to represent Pogue Brook. This site was chosen because it is the most downstream location within park boundaries.	None	A(1)	Coldwater	FALSE
NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
NA.4	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA

Get all site info for streams in LNETN

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
lnetn_str <- getSitesStream(park = lnetn)
print_head(lnetn_str)# top 6 rows

SiteCode	UnitCode	SubUnitCode	USGS_StaNumb	ContribWshedArea_km2	SiteDescription	Notes	LegislativeClass	FisheryType
MABISA	MABI	NA	NA	0.99	Only stream within the park, the outlet of The Pogue. One stream-sampling site was selected to represent Pogue Brook. This site was chosen because it is the most downstream location within park boundaries.	None	A(1)	Coldwater
MIMASA	MIMA	NA	NA	406.56	The Mill Brook site is located upstream of Lowell Road between a small retail complex and a private residence.	The monitoring site is located outside park boundaries because the brook is intermittent where it flows through the Wayside Unit and becomes a wetland where it flows through the North Bridge Unit.	A	Coldwater
MIMASB	MIMA	NA	110057120	1.58	The Elm Brook site is within park boundaries at State Route 2A, 4.3 miles upstream from the confluence with the Shawsheen River. The sampling site represents water quality conditions in Elm Brook within the Battle Road Unit.	None	A	Coldwater
MIMASC	MIMA	NA	NA	860.72	The Concord River site is at the Old North Bridge, 0.49 miles downstream from the confluence of the Sudbury and Assabet Rivers. The site is intended to represent water quality conditions in the Concord River within the North Bridge Unit.	In situ WQ measurements are taken at 7 points (near both banks and at each of 5 bridge pylons, measured at half depth) on the bridge. Cumulative watershed area: 212,688.73 acres (860.72 km2)	A	Warmwater
MORRSB	MORR	NA	1378780	2.79	The monitoring site is located downstream of the USGS staff gage (01378780) installed just below the confluence of East and West Primrose Brooks.	Primrose Brook, a tributary of the Passaic River, drains an area almost entirely contained within the Jockey Hollow Unit of Morristown NHP.	A	Coldwater
MORRSD	MORR	NA	1378680	5.62	The Indian Grove Brook monitoring site is located near where the brook first enters the park, just downstream of the Hardscrabble Road bridge.	A tributary of the Passaic River, the brook meanders in and out of the western boundary of the New Jersey Brigade Encampment Unit. Upstream of the monitoring site, the watershed is characterized by a low-density suburban, but largely forested, landscape.	A	Coldwater

getEvents()

Query water data by park, site, site_type, year and month.

Get events for all sites in MABI from 2021-2023

mabi <- getEvents(park = "MABI", years = 2021:2023)
print_head(mabi)# top 6 rows

UnitCode	UnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	EventDate	EventCode	year	month	doy	Project
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-05-24	4178	2021	5	144	NETN_LS
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-06-22	4192	2021	6	173	NETN_LS
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-07-20	4239	2021	7	201	NETN_LS
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-08-25	4281	2021	8	237	NETN_LS
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-09-21	4315	2021	9	264	NETN_LS
MABI	Marsh-Billings-Rockefeller National Historical Park	MABIPA	The Pogue	Lake	43.63336	-72.54263	2021-10-22	4349	2021	10	295	NETN_LS

Get events for SARA sites sampled in 2019 and 2023

sara <- getEvents(park = "SARA", years = c(2019, 2023))
print_head(sara) # top 6 rows

UnitCode	UnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	EventDate	EventCode	year	month	doy	Project
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-05-16	3790	2019	5	136	NETN_LS
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-06-13	3852	2019	6	164	NETN_LS
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-07-16	3892	2019	7	197	NETN_LS
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-08-08	3920	2019	8	220	NETN_LS
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-09-11	3963	2019	9	254	NETN_LS
SARA	Saratoga National Historical Park	SARASA	Kroma Kill	Stream	43.00583	-73.6173	2019-10-09	4005	2019	10	282	NETN_LS

Get info for all ACAD lakes sampled in April

ACAD_lake <- getEvents(park = 'ACAD', site_type = 'lake', months = 4, event_type = 'all')
print_head(ACAD_lake) # top 6 rows

UnitCode	UnitName	SiteCode	SiteName	SiteType	SiteLatitude	SiteLongitude	EventDate	EventCode	year	month	doy	Project
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2006-04-12	4	2006	4	102	ACAD_ACID
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2008-04-24	380	2008	4	115	ACAD_ACID
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2009-04-23	1127	2009	4	113	ACAD_ACID
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2010-04-21	143	2010	4	111	ACAD_ACID
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2011-04-19	1515	2011	4	109	ACAD_ACID
ACAD	Acadia National Park	ACBUBL	Bubble Pond	Lake	44.34506	-68.23886	2012-04-30	1374	2012	4	121	ACAD_ACID

getChemistry()

This function allows you to query the Chemistry_Data view by park, site, site type, year, month, parameter, and sample type. The returned data frame is long (i.e. stacked) to facilitate data summary and plotting. Note that sample depth is not a filter in getChemistry() as it is with the Sonde In Situ data.

Get N parameters for all sites and non-QAQC events in MIMA.

Note that QC_type = "0" is the default for this function, which returns only non-QAQC events. Note also the use of named objects for the arguments. This allows you to set them at the top of a script, rather than having to type them out repeatedly. You can then change them in 1 place (i.e., update the year to 2024) and rerun the code.

n_params <- c("NH3", "NH3_mgL", "NO2", "NO2_mgL", "NO2+NO3", 
              "NO2+NO3_mgL", "NO3", "NO3_ueqL", "TN", "TN_mgL")
period <- 2006:2023
mima_n <- getChemistry(park = "MIMA", years = period, parameter = n_params)
print_head(mima_n) # top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
MIMASA	Mill Brook	MIMA	NA	2006-08-21	766	NETN_LS	2006	8	233	2006-08-21 12:45:00	ENV	G	12:45:00	0.2	TN_mgL	0.560	NA	mg/L	Detected and Quantified	FALSE	NWQL
MIMASA	Mill Brook	MIMA	NA	2006-08-21	766	NETN_LS	2006	8	233	2006-08-21 12:45:00	ENV	G	12:45:00	0.2	NO2+NO3_mgL	0.169	NA	mg/L	Detected and Quantified	FALSE	NWQL
MIMASA	Mill Brook	MIMA	NA	2006-08-21	766	NETN_LS	2006	8	233	2006-08-21 12:45:00	ENV	G	12:45:00	0.2	NO2_mgL	0.002	NA	mg/L	Detected and Quantified	FALSE	NWQL
MIMASA	Mill Brook	MIMA	NA	2006-08-21	766	NETN_LS	2006	8	233	2006-08-21 12:45:00	ENV	G	12:45:00	0.2	NH3_mgL	0.030	NA	mg/L	Detected and Quantified	FALSE	NWQL
MIMASA	Mill Brook	MIMA	NA	2007-05-07	770	NETN_LS	2007	5	127	2007-05-07 12:31:00	ENV	G	12:31:00	0.2	TN_mgL	0.840	NA	mg/L	Detected and Quantified	FALSE	NWQL
MIMASA	Mill Brook	MIMA	NA	2007-05-07	770	NETN_LS	2007	5	127	2007-05-07 12:31:00	ENV	G	12:31:00	0.2	NO2+NO3_mgL	0.338	NA	mg/L	Detected and Quantified	FALSE	NWQL

Get chemistry data for all sites and all parameters in MABI from 2021-2023

mabi <- getChemistry(park = "MABI", years = 2021:2023)
print_head(mabi)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	2021-05-24 10:42:33	ENV	G	10:42:33	0.5	TN_mgL	0.241	NA	mg/L	Detected and Quantified	FALSE	SWRL
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	2021-05-24 10:42:33	ENV	G	10:42:33	0.5	ChlA_ugL	2.800	NA	ug/L	Detected and Quantified	FALSE	SWRL
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	2021-05-24 10:42:33	ENV	G	10:42:33	0.5	TP_ugL	8.200	NA	ug/L	Detected and Quantified	FALSE	SWRL
MABIPA	The Pogue	MABI	NA	2021-06-22	4192	NETN_LS	2021	6	173	2021-06-22 16:17:35	ENV	G	16:17:35	0.5	ChlA_ugL	1.400	NA	ug/L	Detected and Quantified	FALSE	SWRL
MABIPA	The Pogue	MABI	NA	2021-06-22	4192	NETN_LS	2021	6	173	2021-06-22 16:17:35	ENV	G	16:17:35	0.5	TN_mgL	0.332	NA	mg/L	Detected and Quantified	FALSE	SWRL
MABIPA	The Pogue	MABI	NA	2021-06-22	4192	NETN_LS	2021	6	173	2021-06-22 16:17:35	ENV	G	16:17:35	0.5	TP_ugL	9.100	NA	ug/L	Detected and Quantified	FALSE	SWRL

Get lab pH for all sites in MIMA and SAIR. Note that by not specifying years, all years by default will be included in the output.

ma_parks <- getChemistry(park = c("SAIR", "MIMA"), parameter = "pH_Lab")
print_head(ma_parks)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
MIMASA	Mill Brook	MIMA	NA	2007-05-07	770	NETN_LS	2007	5	127	2007-05-07 12:31:00	ENV	G	12:31:00	0.2	pH_Lab	7.08	NA	pH std units	Detected and Quantified	FALSE	SECRL
MIMASA	Mill Brook	MIMA	NA	2007-08-13	773	NETN_LS	2007	8	225	2007-08-13 12:45:00	ENV	G	12:45:00	0.2	pH_Lab	7.15	NA	pH std units	Detected and Quantified	FALSE	SECRL
MIMASA	Mill Brook	MIMA	NA	2008-05-19	1115	NETN_LS	2008	5	140	NA	ENV	G	NA	0.2	pH_Lab	7.27	NA	pH std units	Detected and Quantified	FALSE	SECRL
MIMASA	Mill Brook	MIMA	NA	2008-08-20	776	NETN_LS	2008	8	233	NA	ENV	G	NA	0.2	pH_Lab	7.00	NA	pH std units	Detected and Quantified	FALSE	SECRL
MIMASA	Mill Brook	MIMA	NA	2009-05-08	1204	NETN_LS	2009	5	128	NA	ENV	G	NA	0.2	pH_Lab	6.88	NA	pH std units	Detected and Quantified	FALSE	SECRL
MIMASA	Mill Brook	MIMA	NA	2009-08-19	1232	NETN_LS	2009	8	231	NA	ENV	G	NA	0.2	pH_Lab	7.46	NA	pH std units	Detected and Quantified	FALSE	SECRL

Get chemistry for all ACAD lakes sampled in April for acidification.

ACAD_lake<- getChemistry(park = 'ACAD', site_type = 'lake', months = 4, event_type = 'all')
print_head(ACAD_lake)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	ANC_ueqL	46.40	NA	ueq/L	Detected and Quantified	FALSE	GMC
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	Cl_ueqL	127.60	NA	ueq/L	Detected and Quantified	FALSE	GMC
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	DOC_mgL	2.30	NA	mg/L	Detected and Quantified	FALSE	GMC
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	NO3_ueqL	1.30	NA	ueq/L	Detected and Quantified	FALSE	GMC
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	pH_Lab	6.42	NA	pH std units	Detected and Quantified	FALSE	GMC
ACBUBL	Bubble Pond	ACAD	NA	2006-04-12	4	ACAD_ACID	2006	4	102	NA	ENV	G	NA	0.2	SO4_ueqL	56.80	NA	ueq/L	Detected and Quantified	FALSE	GMC

Get ANC for lower NETN parks from May to Oct.

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
anc <- getChemistry(park = lnetn, parameter = "ANC_ueqL", months = 5:10)
print_head(anc)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
MABIPA	The Pogue	MABI	NA	2006-06-13	1330	NETN_LS	2006	6	164	2006-06-13 15:30:00	ENV	G	15:30:00	0.2	ANC_ueqL	1640.0	NA	ueq/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2006-08-23	1331	NETN_LS	2006	8	235	2006-08-23 10:45:00	ENV	G	10:45:00	0.2	ANC_ueqL	1660.0	NA	ueq/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2007-06-07	1058	NETN_LS	2007	6	158	2007-06-07 14:30:00	ENV	G	14:30:00	0.2	ANC_ueqL	1654.0	NA	ueq/L	Detected and Quantified	FALSE	SECRL
MABIPA	The Pogue	MABI	NA	2007-08-14	1060	NETN_LS	2007	8	226	2007-08-14 14:20:00	ENV	G	14:20:00	0.2	ANC_ueqL	1614.8	NA	ueq/L	Detected and Quantified	FALSE	SECRL
MABIPA	The Pogue	MABI	NA	2008-06-17	1101	NETN_LS	2008	6	169	NA	ENV	G	NA	0.2	ANC_ueqL	1496.0	NA	ueq/L	Detected and Quantified	FALSE	SECRL
MABIPA	The Pogue	MABI	NA	2008-08-22	1063	NETN_LS	2008	8	235	NA	ENV	G	NA	0.2	ANC_ueqL	1380.0	NA	ueq/L	Detected and Quantified	FALSE	SECRL

Get censored and non-censored NH3 data for LNETN all years. Note the Flag column indicates the measurement is censored by reporting the detection limit used.

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
nh3_cen <- getChemistry(park = lnetn, parameter = "NH3_mgL", include_censored = T)
print_head(nh3_cen)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
MABIPA	The Pogue	MABI	NA	2006-06-13	1330	NETN_LS	2006	6	164	2006-06-13 15:30:00	ENV	G	15:30:00	0.2	NH3_mgL	0.006	E, <MRL 0.01	mg/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2006-08-23	1331	NETN_LS	2006	8	235	2006-08-23 10:45:00	ENV	G	10:45:00	0.2	NH3_mgL	0.068	NA	mg/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2007-06-07	1058	NETN_LS	2007	6	158	2007-06-07 14:30:00	ENV	G	14:30:00	0.2	NH3_mgL	0.053	NA	mg/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2007-08-14	1060	NETN_LS	2007	8	226	2007-08-14 14:20:00	ENV	G	14:20:00	0.2	NH3_mgL	0.099	NA	mg/L	Detected and Quantified	FALSE	NWQL
MABIPA	The Pogue	MABI	NA	2008-06-17	1101	NETN_LS	2008	6	169	NA	ENV	G	NA	0.2	NH3_mgL	NA	<MRL 0.08	mg/L	Present Below Quantification Limit	FALSE	SECRL
MABIPA	The Pogue	MABI	NA	2008-08-22	1063	NETN_LS	2008	8	235	NA	ENV	G	NA	0.2	NH3_mgL	NA	<MRL 0.08	mg/L	Present Below Quantification Limit	FALSE	SECRL

getDischarge()

This function allows you to query the Discharge_Data view by park, site, site type, year, month, measurement method (e.g., flowtracker or pygmy), and measurement rating (e.g., E, G, F, P). Note that you can also return all columns or a reduced set of columns with the output argument. Default is output = ‘short’. This function is set up to work with site_type = ‘stream’, so you don’t have to specify that.

Get discharge for all sites in SARA from 2022-2024

sara <- getDischarge(park = "SARA", years = 2022:2024)
print_head(sara)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	ReachType	FlowStatus	DischargeMethod	TotalArea_sqft	AvgVel_fs	VelocityFlag	Discharge_cfs	DischargeFlag	MeasurementRating	Comments
SARASA	Kroma Kill	SARA	NA	2022-05-25	4422	NETN_LS	2022	5	145	Run	Stable	Flowtracker	9.48	0.25	NA	2.35	NA	F	From 5-9ft concentrated flow and swirling in center of channel; best site available given flow levels.
SARASA	Kroma Kill	SARA	NA	2022-06-14	4464	NETN_LS	2022	6	165	Run	Stable	Flowtracker	8.17	0.33	NA	2.69	NA	F	Control is the shale rock bed bars about 6ft downstream of tag line.
SARASA	Kroma Kill	SARA	NA	2022-07-19	4508	NETN_LS	2022	7	200	Chute	Stable	Flowtracker	1.19	0.44	NA	0.53	NA	P	Chute only spot with enough flow and depth to run flowtracker. Control is rockbed about 1 foot downstream.
SARASA	Kroma Kill	SARA	NA	2022-08-22	4540	NETN_LS	2022	8	234	Run	Rising	Flowtracker	7.19	0.04	NA	0.31	NA	F	Needed to move flowtracker measurement again, too shallow to repeat where taken at last visit. Water moving slow on
SARASA	Kroma Kill	SARA	NA	2022-09-15	4592	NETN_LS	2022	9	258	Run	Falling	Flowtracker	0.96	1.60	NA	1.54	NA	P	Control is opening of stream into pool about 3-4ft downstream of tagline. Velocity errors, flow over rocks must have interfered.
SARASA	Kroma Kill	SARA	NA	2022-10-20	4635	NETN_LS	2022	10	293	Run	Stable	Flowtracker	1.29	1.53	NA	1.98	NA	F	Struggled to find a better flow tracker spot. Control seems to be curves of stream.

Get discharge for ACAD streams in July 2023

acad_dis <- getDischarge(park = "ACAD", years = 2023, months = 7)
print_head(acad_dis)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	ReachType	FlowStatus	DischargeMethod	TotalArea_sqft	AvgVel_fs	VelocityFlag	Discharge_cfs	DischargeFlag	MeasurementRating	Comments
ACBRWN	Browns Brook	ACAD	NA	2023-07-05	4747	NETN_LS	2023	7	186	Run	Falling	Flowtracker	2.01	0.67	NA	1.35	NA	F	None
ACCADS	Cadillac Stream	ACAD	NA	2023-07-11	4754	NETN_LS	2023	7	192	NA	Stable	Rating curve estimate	NA	NA	NA	0.31	NA	NA	1.050+0.30=1.350 0.961+0.39=1.351
ACDKLI	Duck Pond Brook	ACAD	NA	2023-07-06	4751	NETN_LS	2023	7	187	Run	Stable	Flowtracker	2.88	0.13	NA	0.39	NA	F	None
ACDUCK	Duck Brook	ACAD	NA	2023-07-10	4753	NETN_LS	2023	7	191	Run	Stable	Flowtracker	5.52	1.16	NA	6.43	NA	F	None
ACHADB	Hadlock Brook	ACAD	NA	2023-07-12	4756	NETN_LS	2023	7	193	NA	Stable	Rating curve estimate	NA	NA	NA	0.17	NA	NA	RP1: 4.964-1.19= 3.774 RM2: 3.604+0.17=3.774 RM3: 3.218 0.56= 3.77
ACLKWO	Lake Wood Outlet	ACAD	NA	2023-07-06	4752	NETN_LS	2023	7	187	Run	Stable	Flowtracker	3.69	0.33	NA	1.22	NA	G	None

Get discharge measured with Flowtracker

flow <- getDischarge(method = c("Flowtracker"))
print_head(flow)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	ReachType	FlowStatus	DischargeMethod	TotalArea_sqft	AvgVel_fs	VelocityFlag	Discharge_cfs	DischargeFlag	MeasurementRating	Comments
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2014-05-13	2485	NETN_LS	2014	5	133	Run	NA	Flowtracker	6.29	0.12	NA	0.74	NA	NA	NA
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2014-06-05	2484	NETN_LS	2014	6	156	Run	NA	Flowtracker	5.68	0.05	NA	0.27	NA	NA	NA
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2014-07-14	2488	NETN_LS	2014	7	195	Run	NA	Flowtracker	5.61	0.04	NA	0.24	NA	NA	NA
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2014-08-14	2489	NETN_LS	2014	8	226	Run	NA	Flowtracker	8.08	0.17	NA	1.35	NA	NA	SNR’s differed btw beams
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2016-05-10	3137	NETN_LS	2016	5	131	Run	Rising	Flowtracker	5.72	0.31	NA	1.76	NA	NA	None.
ACABIN	Aunt Betty Pond Inlet	ACAD	NA	2016-06-06	3141	NETN_LS	2016	6	158	Run	Rising	Flowtracker	8.91	0.45	NA	3.98	NA	NA	None.

Get excellent rated measurements only for MIMA

exc <- getDischarge(park = "MIMA", rating = "E")
print_head(exc)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	ReachType	FlowStatus	DischargeMethod	TotalArea_sqft	AvgVel_fs	VelocityFlag	Discharge_cfs	DischargeFlag	MeasurementRating	Comments
MIMASA	Mill Brook	MIMA	NA	2018-05-04	3522	NETN_LS	2018	5	124	Run	Falling	Flowtracker	6.87	0.69	NA	4.70	NA	E	Even flow
MIMASA	Mill Brook	MIMA	NA	2021-07-06	4250	NETN_LS	2021	7	187	Run	Falling	Flowtracker	20.87	0.50	NA	10.43	NA	E	Hugh discharge due to recent rains
MIMASA	Mill Brook	MIMA	NA	2021-09-10	4329	NETN_LS	2021	9	253	Run	Stable	Flowtracker	18.64	0.49	NA	9.20	NA	E	Very high flow due to recent rain storms
MIMASA	Mill Brook	MIMA	NA	2022-10-19	4632	NETN_LS	2022	10	292	Run	Stable	Flowtracker	14.84	0.48	NA	7.09	NA	E	None
MIMASA	Mill Brook	MIMA	NA	2023-06-06	4717	NETN_LS	2023	6	157	Run	Falling	Flowtracker	19.45	0.67	NA	12.96	NA	E	No FlowTracker errors, had even, straight banks, decent amount of water.
MIMASA	Mill Brook	MIMA	NA	2023-07-05	4758	NETN_LS	2023	7	186	Run	Stable	Flowtracker	20.45	0.62	NA	12.77	NA	E	Great measurement. Only one error and 29 bins.

getLightPen()

This function allows you to query the Light_Penetration_Data view by park, site, site type, year, and month. Again output = ‘short’ is the default. If specify output = ‘verbose’, you’ll get all possible columns. This is only set up to work with site_type = ‘lake’, so you don’t have to specify that.

Get light penetration for the Pogue in MABI from 2021-2023.

 mabi <- getLightPen(site = "MABIPA", years = 2021:2023)
print_head(mabi)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	MeasurementTime	MeasurementDepth_m	LightDeck	LightUW	PenetrationRatio
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:17:51	0.10	2009.6	2198.80	1.09410
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:20:00	0.25	1861.2	1812.80	0.97403
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:20:49	0.50	1965.9	1424.30	0.72451
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:21:56	0.75	1906.9	1102.30	0.57807
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:22:29	1.00	1963.9	1081.30	0.55059
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	11:22:56	1.25	1941.3	963.28	0.49621

Get light penetration for all ACAD lakes sampled in August.

acad <- getLightPen(park = 'ACAD', months = 8)
print_head(acad) # top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	MeasurementTime	MeasurementDepth_m	LightDeck	LightUW	PenetrationRatio
ACANTB	Aunt Bettys Pond	ACAD	NA	2006-08-09	48	NETN_LS	2006	8	221	11:25:53	0.10	1708.7	1428.700	0.840030
ACANTB	Aunt Bettys Pond	ACAD	NA	2006-08-09	48	NETN_LS	2006	8	221	11:27:04	0.50	1747.9	533.940	0.305670
ACANTB	Aunt Bettys Pond	ACAD	NA	2006-08-09	48	NETN_LS	2006	8	221	11:28:15	1.00	1678.9	209.400	0.125140
ACANTB	Aunt Bettys Pond	ACAD	NA	2006-08-09	48	NETN_LS	2006	8	221	11:29:49	1.75	1728.1	60.852	0.035237
ACANTB	Aunt Bettys Pond	ACAD	NA	2009-08-25	730	NETN_LS	2009	8	237	14:53:26	0.10	1518.0	749.500	0.493740
ACANTB	Aunt Bettys Pond	ACAD	NA	2009-08-25	730	NETN_LS	2009	8	237	14:54:25	0.50	1519.4	116.960	0.076982

Get light penetration for the given ACAD sites related to the ACAD_ACID project.

acad_acid <- getChemistry(site = c("ACJORD", "ACEAGL", "ACBUBL"), event_type = "acid")
print_head(acad_acid) # top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	datetime	QCtype	SampleType	SampleTime	SampleDepth_m	Parameter	Value	ValueFlag	ValueUnit	ValueDetectionCondition	censored	LabCode
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	NO3_ueqL	NA	<MRL 1	ueq/L	Present Below Quantification Limit	FALSE	SECRL
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	ANC_ueqL	65.600	NA	ueq/L	Detected and Quantified	FALSE	SECRL
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	DOC_mgL	2.410	NA	mg/L	Detected and Quantified	FALSE	SECRL
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	pH_Lab	6.450	NA	pH std units	Detected and Quantified	FALSE	SECRL
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	SO4_ueqL	64.400	NA	ueq/L	Detected and Quantified	FALSE	SECRL
ACBUBL	Bubble Pond	ACAD	NA	2006-10-17	71	NETN+ACID	2006	10	290	NA	ENV	G	NA	0.2	TN_mgL	0.118	NA	mg/L	Detected and Quantified	FALSE	SECRL

getSecchi()

This function allows you to query Secchi data by park, site, site type, years, months and whether you want to return all observations, the first or the second. Default returns all observations with data. Note that this function is designed to only work with lakes, and doesn’t require site_type = “lake” to be specified.

Get Secchi depth the Pogue from 2021-2023, first observer only

mabi <- getSecchi(site = "MABIPA", years = 2021:2023, observer_type = "first")
print_head(mabi)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	Parameter	Value	SD_HitBottom	Observer
MABIPA	The Pogue	MABI	NA	2021-05-24	4178	NETN_LS	2021	5	144	SecchiDepth_m	2.80	TRUE	1
MABIPA	The Pogue	MABI	NA	2021-06-22	4192	NETN_LS	2021	6	173	SecchiDepth_m	3.00	TRUE	1
MABIPA	The Pogue	MABI	NA	2021-07-20	4239	NETN_LS	2021	7	201	SecchiDepth_m	2.90	TRUE	1
MABIPA	The Pogue	MABI	NA	2021-08-25	4281	NETN_LS	2021	8	237	SecchiDepth_m	3.01	TRUE	1
MABIPA	The Pogue	MABI	NA	2021-09-21	4315	NETN_LS	2021	9	264	SecchiDepth_m	3.05	TRUE	1
MABIPA	The Pogue	MABI	NA	2021-10-22	4349	NETN_LS	2021	10	295	SecchiDepth_m	2.85	TRUE	1

Get Secchi for all ACAD lakes sampled in July for all observers

ACAD_lake <- getSecchi(park = 'ACAD', months = 7)
print_head(ACAD_lake)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	Project	year	month	doy	Parameter	Value	SD_HitBottom	Observer
ACANTB	Aunt Bettys Pond	ACAD	NA	2006-07-13	38	NETN_LS	2006	7	194	SecchiDepth_m	1.95	TRUE	1
ACANTB	Aunt Bettys Pond	ACAD	NA	2009-07-23	1136	NETN_LS	2009	7	204	SecchiDepth_m	2.34	TRUE	1
ACANTB	Aunt Bettys Pond	ACAD	NA	2012-07-24	1389	NETN_LS	2012	7	206	SecchiDepth_m	2.44	FALSE	1
ACANTB	Aunt Bettys Pond	ACAD	NA	2015-07-30	2717	NETN_LS	2015	7	211	SecchiDepth_m	2.25	TRUE	1
ACANTB	Aunt Bettys Pond	ACAD	NA	2018-07-20	3617	NETN_LS	2018	7	201	SecchiDepth_m	2.05	TRUE	1
ACANTB	Aunt Bettys Pond	ACAD	NA	2021-07-19	4231	NETN_LS	2021	7	200	SecchiDepth_m	1.60	TRUE	1

Get the long version of Secchi depth for all LNETN parks from May to October

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
lnetn_secchi <- getSecchi(park = lnetn, months = 5:10, output = "verbose") 
print_head(lnetn_secchi)# top 6 rows

SiteCode	SiteType	EventDate	EventCode	Project	GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteName	Parameter	Value	SD_HitBottom	ObsInit	IsEventCUI	year	month	doy	Observer
MABIPA	Lake	2006-07-20	671	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	2.00	FALSE	NA	FALSE	2006	7	201	1
MABIPA	Lake	2010-05-25	292	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	2.75	TRUE	DF	FALSE	2010	5	145	1
MABIPA	Lake	2010-06-15	293	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	2.70	TRUE	NA	FALSE	2010	6	166	1
MABIPA	Lake	2010-07-08	291	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	2.30	TRUE	NA	FALSE	2010	7	189	1
MABIPA	Lake	2010-08-11	290	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	3.22	TRUE	NA	FALSE	2010	8	223	1
MABIPA	Lake	2010-09-08	294	NETN_LS	NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	The Pogue	SecchiDepth_m	2.40	TRUE	NA	FALSE	2010	9	251	1

getSondeInSitu()

This function allows you to query Sonde in situ data by park, site, site type, years, months, parameter, QC type, surface vs. all, etc. Default returns all non-QAQC observations with data. The Sonde_InSitu_Data view is large and can take a few seconds to run for most parks, sites, years, parameters, etc. Surface only measurements, defined as as the medium of all samples within 2m of the surface, are the default.

Get Sonde data for all sites and parameters in MABI from 2021-2023 for non-QAQC samples

mabi <- getSondeInSitu(park = "MABI", years = 2021:2023)
print_head(mabi)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	SiteType	Project	year	month	doy	datetime	QCtype	SampleDepth_m	Parameter	Value	ValueFlag	FlagComments
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	DO_mgL	8.660	NA	NA
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	DOsat_pct	97.400	NA	NA
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	SpCond_uScm	186.400	NA	NA
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	Temp_C	20.870	NA	NA
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	Temp_F	69.566	NA	NA
MABIPA	The Pogue	MABI	NA	2021-05-24	Lake	NETN_LS	2021	5	144	2021-05-24 12:00:00	0	0.97	Turbidity_FNU	0.390	NA	NA

get data for all DO parameters in MIMA from 2006-2023 for non-QAQC samples

params <- c("DOsat_pct", "DOsatLoc_pct", "DO_mgL")
period <- 2006:2023
mima_do <- getSondeInSitu(park = "MIMA", years = period, parameter = params)
print_head(mima_do)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	SiteType	Project	year	month	doy	datetime	QCtype	SampleDepth_m	Parameter	Value	ValueFlag	FlagComments
MIMASA	Mill Brook	MIMA	NA	2006-05-15	Stream	NETN_LS	2006	5	135	2006-05-15 12:00:00	0	0.13	DO_mgL	7.35	NA	NA
MIMASA	Mill Brook	MIMA	NA	2006-05-15	Stream	NETN_LS	2006	5	135	2006-05-15 12:00:00	0	0.13	DOsat_pct	64.90	NA	NA
MIMASA	Mill Brook	MIMA	NA	2006-06-12	Stream	NETN_LS	2006	6	163	2006-06-12 12:00:00	0	0.49	DO_mgL	6.38	NA	NA
MIMASA	Mill Brook	MIMA	NA	2006-06-12	Stream	NETN_LS	2006	6	163	2006-06-12 12:00:00	0	0.49	DOsat_pct	67.40	NA	NA
MIMASA	Mill Brook	MIMA	NA	2006-07-17	Stream	NETN_LS	2006	7	198	2006-07-17 12:00:00	0	0.23	DO_mgL	5.62	NA	NA
MIMASA	Mill Brook	MIMA	NA	2006-07-17	Stream	NETN_LS	2006	7	198	2006-07-17 12:00:00	0	0.23	DOsat_pct	64.00	NA	NA

Get Temp data for all sample depths in Jordan Pond in ACAD for non-QAQC samples

ACAD_lake <- getSondeInSitu(site = 'ACJORD', parameter = "Temp_C", 
                            sample_depth = "all")
print_head(ACAD_lake)

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	SiteType	Project	year	month	doy	datetime	QCtype	SampleDepth_m	Parameter	Value	ValueFlag	FlagComments
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	21.23	Temp_C	6.41	NA	NA
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	17.17	Temp_C	7.13	NA	NA
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	24.13	Temp_C	6.00	NA	NA
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	24.13	Temp_C	6.01	NA	NA
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	24.14	Temp_C	6.02	NA	NA
ACJORD	Jordan Pond	ACAD	NA	2006-05-23	Lake	NETN_LS	2006	5	143	2006-05-23 12:00:00	0	24.16	Temp_C	6.05	NA	NA

Get pH for lower NETN parks from May to Oct for QAQC and non-QAQC samples

lnetn_ph <- getSondeInSitu(park = "LNETN", param = "pH", months = 5:10, 
                           QC_type = 'all')
print_head(lnetn_ph)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	SiteType	Project	year	month	doy	datetime	QCtype	SampleDepth_m	Parameter	Value	ValueFlag	FlagComments
MABIPA	The Pogue	MABI	NA	2006-06-13	Lake	NETN_LS	2006	6	164	2006-06-13 12:00:00	0	0.990	pH	8.690	NA	NA
MABIPA	The Pogue	MABI	NA	2006-06-13	Lake	NETN_LS	2006	6	164	2006-06-13 12:00:00	999	0.000	pH	8.560	NA	NA
MABIPA	The Pogue	MABI	NA	2006-07-20	Lake	NETN_LS	2006	7	201	2006-07-20 12:00:00	0	0.990	pH	8.520	NA	NA
MABIPA	The Pogue	MABI	NA	2006-07-20	Lake	NETN_LS	2006	7	201	2006-07-20 12:00:00	999	-0.162	pH	8.325	NA	NA
MABIPA	The Pogue	MABI	NA	2006-08-23	Lake	NETN_LS	2006	8	235	2006-08-23 12:00:00	0	1.000	pH	8.160	NA	NA
MABIPA	The Pogue	MABI	NA	2006-08-23	Lake	NETN_LS	2006	8	235	2006-08-23 12:00:00	899	0.000	pH	7.930	NA	NA

getStreamObs()

This function allows you to query stream observation data by park, site, year and month

Get stream observations for Pogue Stream all years

mabi <- getStreamObs(park = "MABI")
print_head(mabi)# top 6 rows

SiteCode	UnitCode	SubUnitCode	EventDate	EventCode	year	month	doy	WaterClarity	WaterColor	WaterCondition	AlgaeSlimeExtent	AlgaeSlimeAmount	AlgaeSlimeColor	AlgaeFilExtent	AlgaeFilColor	AlgaeClumpsExtent	AlgaeClumpsColor	Algae_Notes
MABIPA	MABI	NA	2013-05-06	2424	2013	5	126	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None
MABIPA	MABI	NA	2013-06-04	2423	2013	6	155	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None
MABIPA	MABI	NA	2013-07-09	2421	2013	7	190	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None
MABISA	MABI	NA	2013-05-06	2136	2013	5	126	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None
MABISA	MABI	NA	2013-06-04	2135	2013	6	155	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None
MABISA	MABI	NA	2013-07-09	2139	2013	7	190	Clear	Colorless	None	None	Light Coating	Green	None	Green	None	NA	None

Get observations for all streams in ACAD May 2023

ACAD_streams <- getStreamObs(park = 'ACAD', years = 2023, months = 5)
print_head(ACAD_streams)# top 6 rows

SiteCode	UnitCode	SubUnitCode	EventDate	EventCode	year	month	doy	WaterClarity	WaterColor	WaterCondition	AlgaeSlimeExtent	AlgaeSlimeAmount	AlgaeSlimeColor	AlgaeFilExtent	AlgaeFilColor	AlgaeClumpsExtent	AlgaeClumpsColor	Algae_Notes
ACBRWN	ACAD	NA	2023-05-08	4669	2023	5	128	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None
ACCADS	ACAD	NA	2023-05-05	4666	2023	5	125	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None
ACDKLI	ACAD	NA	2023-05-04	4664	2023	5	124	Clear	Colorless	Foamy	None	NA	NA	None	NA	None	NA	None
ACDUCK	ACAD	NA	2023-05-09	4670	2023	5	129	Clear	Colorless	None	Occasional	Light Coating	Green	None	NA	None	NA	None
ACHADB	ACAD	NA	2023-05-05	4667	2023	5	125	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None
ACLKWO	ACAD	NA	2023-05-03	4663	2023	5	123	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None

Get the long versions of stream observations in LNETN parks from May to October

lnetn <- c("MABI", "MIMA", "MORR", "ROVA", "SAGA", "SAIR", "SARA", "WEFA")
lnetn_obs <- getStreamObs(park = lnetn, months = 5:10, output = "verbose")
print_head(lnetn_obs)# top 6 rows

GroupCode	GroupName	UnitCode	UnitName	SubUnitCode	SubUnitName	SiteCode	SiteName	SiteType	Project	EventDate	EventCode	WaterClarity	WaterColor	WaterCondition	AlgaeSlimeExtent	AlgaeSlimeAmount	AlgaeSlimeColor	AlgaeFilExtent	AlgaeFilColor	AlgaeClumpsExtent	AlgaeClumpsColor	Algae_Notes	IsEventCUI	year	month	doy
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABIPA	The Pogue	Lake	NETN_LS	2013-05-06	2424	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None	FALSE	2013	5	126
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABIPA	The Pogue	Lake	NETN_LS	2013-06-04	2423	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None	FALSE	2013	6	155
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABIPA	The Pogue	Lake	NETN_LS	2013-07-09	2421	NA	NA	None	NA	NA	NA	NA	NA	NA	NA	None	FALSE	2013	7	190
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABISA	Pogue Brook	Stream	NETN_LS	2013-05-06	2136	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None	FALSE	2013	5	126
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABISA	Pogue Brook	Stream	NETN_LS	2013-06-04	2135	Clear	Colorless	None	None	NA	NA	None	NA	None	NA	None	FALSE	2013	6	155
NETN	Northeast Temperate Network	MABI	Marsh-Billings-Rockefeller National Historical Park	NA	NA	MABISA	Pogue Brook	Stream	NETN_LS	2013-07-09	2139	Clear	Colorless	None	None	Light Coating	Green	None	Green	None	NA	None	FALSE	2013	7	190

getWaterLevel()

This function joins stage and water level data, and allows you to query by park, site, site_type, year, and month. Note that WL data start in 2013 in the view.

Get water level data for Bubble Pond.

bubl <- getWaterLevel(site = "ACBUBL", years = 2013:2023)
print_head(bubl)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	year	month	doy	DatumName	DatumType	DatumFunction	Active	TU.TD	StageMethod	DatumLatitude	DatumLongitude	DatumElevation_ft	DatumElevationFeet	GageReadingFeet	WaterLevel_Feet	WaterLevel_m
ACBUBL	Bubble Pond	ACAD	NA	2013-05-31	2128	2013	5	151	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.49	332.90	101.4679
ACBUBL	Bubble Pond	ACAD	NA	2013-06-24	2129	2013	6	175	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.77	332.62	101.3826
ACBUBL	Bubble Pond	ACAD	NA	2013-07-18	2130	2013	7	199	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.96	332.43	101.3247
ACBUBL	Bubble Pond	ACAD	NA	2013-08-28	2370	2013	8	240	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.96	332.43	101.3247
ACBUBL	Bubble Pond	ACAD	NA	2013-09-19	2389	2013	9	262	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.78	332.61	101.3795
ACBUBL	Bubble Pond	ACAD	NA	2013-10-24	2410	2013	10	297	SD1	Drilled hole	Stage Measurement	TRUE	TD	Ruler	44.34948	-68.24053	333.39	333.39	-0.78	332.61	101.3795

Get water level data for Weir Pond in August.

weir <- getWaterLevel(site = "WEFAPA", months = 8)
print_head(weir)# top 6 rows

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	year	month	doy	DatumName	DatumType	DatumFunction	Active	TU.TD	StageMethod	DatumLatitude	DatumLongitude	DatumElevation_ft	DatumElevationFeet	GageReadingFeet	WaterLevel_Feet	WaterLevel_m
WEFAPA	Weir Pond	WEFA	NA	2013-08-28	2226	2013	8	240	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-0.80	568.20	173.1874
WEFAPA	Weir Pond	WEFA	NA	2014-08-12	2668	2014	8	224	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-0.96	568.04	173.1386
WEFAPA	Weir Pond	WEFA	NA	2015-08-20	2827	2015	8	232	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-1.19	567.81	173.0685
WEFAPA	Weir Pond	WEFA	NA	2016-08-25	3161	2016	8	238	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-1.05	567.95	173.1112
WEFAPA	Weir Pond	WEFA	NA	2017-08-24	3403	2017	8	236	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-1.20	567.80	173.0654
WEFAPA	Weir Pond	WEFA	NA	2018-08-14	3664	2018	8	226	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	41.26022	-73.45142	569	569	-0.51	568.49	173.2758

Get water level data for ACAD lakes in July 2023.

acad_jul <- getWaterLevel(park = "ACAD", years = 2023, months = 7)
print_head(acad_jul)

SiteCode	SiteName	UnitCode	SubUnitCode	EventDate	EventCode	year	month	doy	DatumName	DatumType	DatumFunction	Active	TU.TD	StageMethod	DatumLatitude	DatumLongitude	DatumElevation_ft	DatumElevationFeet	GageReadingFeet	WaterLevel_Feet	WaterLevel_m
ACBRWN	Browns Brook	ACAD	NA	2023-07-05	4747	2023	7	186	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	44.33926	-68.30148	46.73	46.729	-0.37	46.359	14.13022
ACBRWN	Browns Brook	ACAD	NA	2023-07-05	4747	2023	7	186	SD1	Bolt	Stage Measurement	TRUE	TD	Ruler	44.33926	-68.30148	46.73	46.729	-0.38	46.349	14.12718
ACBUBL	Bubble Pond	ACAD	NA	2023-07-17	4734	2023	7	198	SD2	Bolt	Stage Measurement	TRUE	TU	Ruler	NA	NA	332.00	332.000	1.70	333.700	101.71176
ACCADS	Cadillac Stream	ACAD	NA	2023-07-11	4754	2023	7	192	RP2	Bolt	Stage Measurement	TRUE	TU	Ruler	44.34490	-68.21690	418.05	418.050	0.30	418.350	127.51308
ACCADS	Cadillac Stream	ACAD	NA	2023-07-11	4754	2023	7	192	RP2	Bolt	Stage Measurement	TRUE	TU	Ruler	44.34490	-68.21690	418.05	418.050	0.30	418.350	127.51308
ACCADS	Cadillac Stream	ACAD	NA	2023-07-11	4754	2023	7	192	RP3	Bolt	Stage Measurement	TRUE	TU	Ruler	44.34490	-68.21690	417.96	417.961	0.39	418.351	127.51338

Plotting Functions

plotWaterBands()

This function produces a plot that summarizes the range of historic data compared with current measurements. The function can handle chemistry, Sonde in situ, Secchi depth, Light Penetration, and Discharge data, although it functions best with sonde and chemistry data. Historic measurements are displayed as the min-max values ever previously recorded (outermost band), upper and lower 95% distribution and middle 50% distribution (inner quartiles) of values previously recorded (inner bands). The line represents the median value.

Currently you can only specify one parameter at a time. Values that exceed water quality thresholds (where they exist) are plotted as orange and will show an orange point in the legend. Values within WQ thresholds or for parameters without set thresholds are black. You can include threshold lines (default), or remove them, where they make the y axis range too big, via threshold = FALSE. If multiple sites are specified, they will be faceted.

You can now add gridlines to the plot via the gridlines argument, and Temp in F via “Temp_F” argument.

Plot pH in Jordan Pond for 2023 with gridlines on the y-axis

pjord_ph <- 
  plotWaterBands(site = "ACJORD", year_curr = 2023, years_historic = 2006:2022, 
    parameter = "pH", legend_position = 'right', gridlines = 'grid_y')

pjord_ph

Plot TN in Jordan Pond for 2023, including censored and gridlines on both x and y axes

pjord_tn <- 
  plotWaterBands(site = "ACJORD", year_curr = 2023, years_historic = 2006:2022,
    parameter = "TN_mgL", legend_position = 'right', include_censored = T, gridlines = "both")

pjord_tn

Same as above, but drop threshold lines and add gridlines on x-axis

pjord_tn2 <- 
plotWaterBands(site = "ACJORD", year_curr = 2023, years_historic = 2006:2022,
  parameter = "TN_mgL", legend_position = 'right', include_censored = T, threshold = F, gridlines = "grid_x")

pjord_tn2

Plot TN in Kroma Kill in SARA in 2023, with no gridlines (Default)

kroma <- 
plotWaterBands(site = "SARASA", year_curr = 2023, years_historic = 2006:2022, parameter = "TN",
               legend_position = 'right')

kroma

plotScatterPlot()

This function produces points or loess smoothed lines of 2 variables, filtered on park, site, year, month, and 2 parameters. Works with lab chemistry, Sonde in situ, discharge, secchi depth, water level, and light penetration ratio. If multiple sites are specified, they will be plotted on the same figure, unless facet_site = T. Note that if you specify a site and parameter combination that doesn’t exist (e.g., a stream site and a parameter only collected in lakes), the function will return an error message instead of an empty plot. Censored values are not permitted in this function.

Plot Temp vs DO for ROVA all years on same figure

rova_scat <- 
plotScatterPlot(park = "ROVA", parameters = c("DO_mgL", "Temp_C"),
  palette = 'viridis', facet_site = F, legend_position = "bottom")

rova_scat

Plot Secchi depth vs. surface DOC in Eagle Lake, Jordan Pond, Echo Lake, and Witch Hole Pond

secchi_doc <- 
plotScatterPlot(site = c("ACEAGL", "ACJORD", "ACWHOL", "ACECHO"), 
                parameters = c("SDepth_m", "DOC_mgL"),
                span = 0.9, facet_site = F, legend_position = 'bottom', 
                palette = c("red", "orange", "purple4", "blue"))
secchi_doc

Same as above, but points only

plotScatterPlot(site = c("ACEAGL", "ACJORD", "ACWHOL", "ACECHO"), 
                parameters = c("SDepth_m", "DOC_mgL"),
                span = 0.9, facet_site = F, legend_position = 'bottom', 
                layers = 'points')

Plot smoothed discharge vs. specific conductance for the Pogue Brook using span of 0.9, and green symbols.

mabi_dsc <- 
plotScatterPlot(site = "MABISA", parameters = c("SpCond_uScm", "Discharge_cfs"), 
                span = 0.9, palette = c("forestgreen"))
mabi_dsc

Plot smoothed discharge vs. specific conductance for SARA streams using span of 0.9.

sara_scd <- 
plotScatterPlot(park = "SARA", parameters = c("SpCond_uScm", "Discharge_cfs"), 
                span = 0.9, facet_site = F, legend_position = 'bottom', 
                palette = c("blue", "orange"))

sara_scd

Same as above, but faceted by site.

plotScatterPlot(park = "SARA", parameters = c("SpCond_uScm", "Discharge_cfs"), 
                span = 0.9, facet_site = T)

Plot TN vs discharge in SARA streams

sara_tnd <- 
plotScatterPlot(park = "SARA", parameters = c("TN_mgL", "Discharge_cfs"), 
                span = 0.9, facet_site = F)
sara_tnd

plotTrend()

This function produces a trend plot filtered on park, site, year, month, and parameter. It works with chemistry, Sonde in situ, Secchi depth, Light Penetration, and Discharge data. If multiple sites are specified, they will be plotted on the same figure. If multiple parameters are specified, they will be plotted on separate figures. If smooth = T, a loess smoothed line will connect through the data. If smooth = F and layers includes “lines”, then lines will connect the sample points, but will not connect across years, because of the break between October and May.

There are several arguments to customize plots.

• Choose whether to include only active sites (default) or all sites that have been monitored via active.
• Choose whether to add points, lines, or both (default) via layers argument.
• If lines are chosen as a layer, choose whether to plot a loess smoothed line (default) or a line that connects the sample points via smooth.
• Choose whether to plot any water quality thresholds that exist via threshold. Upper limits are dashed. Lower limits are dotted.
• Choose whether to add gridlines, either both, grid_y or grid_x. Default is none.
• Choose whether to plot surface (default) or all depth measurements via sample_depth.
• Choose whether to include censored values or not via include_censored.
• Choose color palette via palette. Default is ‘viridis’, but other options are magma (yellow, red, purple), plasma (brighter version of magma), turbo (rainbow), or specify a vector of colors manually. See the intro do viridis site for more info on built in color palettes.
• Choose position of legend via legend_position. If you don’t want to show the legend, legend_position = 'none'.
• Plot temperature in F via parameter = "Temp_F".
• Additional customizations are defined in the help documentation, accessable via ?plotTrend()

Single site; single parameter

Plot non-smoothed surface pH for Eagle Lake for all years with gridlines on y-axis.

eag_ph <- 
plotTrend(site = "ACEAGL", parameter = "pH", palette = 'mako', years = 2021:2023) + theme_WQ()

eag_ph

Plot smoothed surface pH for Eagle Lake for past 3 years using default span of 0.3 and by default not including the legend.

plotTrend(site = "ACEAGL", parameter = "pH", palette = 'dimgrey', years = 2021:2023)

Plot smoothed surface pH for Eagle Lake and Jordan Pond for all years, with turbo palette, and using span of 0.75.

eag_jord <- 
  plotTrend(site = c("ACEAGL", "ACJORD"), parameter = "pH", span = 0.75, 
            palette = "turbo", legend_position = 'bottom')
eag_jord

Plot smoothed Secchi Depth in Jordan Pond for all years, including the legend, different color palette, and using span of 0.75.

jord_sec <- 
plotTrend(site = "ACJORD", parameter = "SDepth_m", span = 0.75, palette = 'mako')

jord_sec

Plot unsmoothed SO4 in Witch Hole Pond for all years, including censored values.

whol_so4 <- 
plotTrend(site = "ACWHOL", parameter = "SO4_ueqL", 
          smooth = F, include_censored = TRUE, legend_position = 'bottom')

whol_so4

Plot unsmoothed line only for pH in Witch Hole Pond for all years.

whol_ph <- 
plotTrend(site = "ACWHOL", parameter = "pH", layers = "lines", 
          smooth = F, legend_position = 'none')
whol_ph

Multiple sites or params

Plot smoothed surface pH for active SARA streams over all years with 0.6 span.

p <- plotTrend(park = "SARA", site = c("SARASA", "SARASC", "SARASD"), 
               site_type = "stream", parameter = "pH", 
               legend_position = "right", span = 0.6)
p

Plot smoothed surface Specific Conductance for all MIMA streams over all years with 0.6 span.

mima_sc <- 
plotTrend(park = "MIMA", site_type = "stream", 
          parameter = "SpCond_uScm", legend_position = "right", span = 0.6, 
          palette = c("blue", "orange", "green3"))
mima_sc

Plot non-smoothed surface of multiple Sonde parameters for all MIMA streams over all years with 0.6 span. Note that here I used Temp_F.

params <- c("Temp_F", "SpCond_uScm", "DOsat_pct", "pH")
mima_sonde <- 
plotTrend(park = "MIMA", site_type = "stream", 
          parameter = params, legend_position = "right", span = 0.6)
mima_sonde

Plot smoothed surface Secchi Depth, Specific Conductance, pH, and DOC in Jordan Pond for all years, including the legend, different color palette, and using span of 0.75.

jord4 <- 
plotTrend(site = "ACJORD", parameter = c("SDepth_m", "SpCond_uScm", "pH", "DOC_mgL"), 
          span = 0.75, palette = 'mako')
jord4

Plot smoothed surface water depth in the Pogue for all years, including a different color palette, and using span of 0.75.

pogue_wl <- 
plotTrend(site = "MABIPA", parameter = "WaterLevel_Feet", span = 0.75, 
          palette = 'mako')
pogue_wl

Plot smoothed TN, TP and SO4 in all MORR sites for all years, including the legend, different color palette, and using span of 0.6. Thresholds, where they exist, plot by default.

morr <- 
plotTrend(park = "MORR", parameter = c("TN_mgL", "TP_ugL", "SO4_ueqL"), 
          span = 0.6, legend_position = 'bottom', palette = 'plasma')
morr

plotLakeProfile()

This function produces a heatmap in 1-m bins for ACAD and 0.25m bins for LNETN. You can filter on park, site, year, month, Sonde in situ parameter and either sample relative to the surface or relative to surface elevation. You can only specify one parameter at a time. If multiple sites or years are selected, plots will be faceted on those factors. Keep options limited for best plotting. Note also that you can either select ACAD or LNETN parks, because of the differences in binning.

The option to plot relative to surface elevation (eg depth_type = ‘elev’) corrects sample depth for elevation using water level data and datum elevation for that sampling event. The elevation-corrected option allows you to see how the water column is shifting over time, but currently only works for years >= 2013 in ACAD, as water levels prior to that are not in the current data package. Default setting is raw, where the raw sample depths are plotted instead of elevation.

Note that occasionally profiles skip a bin, which show up as white sections in the plots. Incomplete sampling in 2020 and 2021 also shows up as white sections. If you specify a lake x year x parameter combination that doesn’t exist (e.g., a year a lake isn’t sampled), the function will return an error message instead of an empty plot.

The width of the profiles take into account the number of days between sampling events. For the first and last months (typically May and October), the left/right side of the profiles are padded by 14 days. Otherwise, profile widths are centered on the sample day with the left side representing half the number of days between that visit and the previous visit and the right side representing half the number of days between that visit and the following visit. Black lines are the thermocline, as calculated by rLakeAnalyzer.

There are several arguments to customize plots.

• Choose whether to plot the theromocline as points on each profile via plot_thermocline = TRUE (default). The thermocline is calculated by rLakeAnalyzer, and is the depth/elevation at which the largest change in temperature occurs in the sampled water column. If no thermocline is detected, as defined by rLakeAnalyzer::thermo.depth(), nothing is plotted.
• Choose whether to include only active sites (default) or all sites that have been monitored via active.
• Add gridlines on the y, x or both axes.
• Choose palette. Current enabled themes are ‘viridis’ (yellow - green - blue), and built in continuous color patterns in RColorBrewer. If you prefer other palettes, I can add those too. The only thing I’m trying to avoid is creating the palette manually, since number 1-m bins varies by site and across years. More info on built in ggplot scales can be found here: https://ggplot2-book.org/scales-colour.
• Choose position of legend via legend_position. If you don’t want to show the legend, legend_position = 'none'.
• Include site name as plot title (title = TRUE). Only enabled when 1 site is selected. Otherwise site names will be in the facets.
• Plot temperature in F via parameter = "Temp_F".

Continuous RColorBrewer palettes are below. Note that there are only as many colors as shown.

RColorBrewer::display.brewer.all(type = 'div')

RColorBrewer::display.brewer.all(type = 'seq')

Simple plots

Plot temperature (in F) for Upper Hadlock for years 2013 - 2023 corrected by elevation with thermocline plotted as black lines, with gridlines on y.

uhad_f <- 
plotLakeProfile(site = "ACUHAD", parameter = "Temp_F", depth_type = 'elev', 
                years = 2013:2023, gridlines = "grid_y")
uhad_f

Plot temp (in C) using raw sample depth (default) for all LNETN lakes sampled in 2023.

lnetn_c <- 
plotLakeProfile(park = "LNETN", parameter = "Temp_C", years = 2023, palette = "Spectral")
lnetn_c

Plot temperature for Eagle Lake for years 2006 - 2023 with raw sample depth. Note that we can go back to 2006 because we’re using raw sample depth instead of elevation.

eag_c <- 
plotLakeProfile(site = "ACEAGL", parameter = "Temp_C", depth_type = 'raw', 
                years = 2006:2023)
eag_c

Same plot as above, but with no plot title or thermocline.

plotLakeProfile(site = "ACEAGL", parameter = "Temp_C", depth_type = 'raw', 
                years = 2006:2023, plot_title = FALSE, plot_thermocline = F)

Plot temperature for all ACAD lakes sampled in 2023 and raw sample depth.

lakes23 <- c("ACBUBL", "ACEAGL", "ACECHO", "ACJORD", "ACLONG", "ACROUN", 
             "ACSEAL", "ACUBRK", "ACUHAD", "ACWHOL")
plot_23C <- 
plotLakeProfile(park = "ACAD", site = lakes23, parameter = "Temp_C", 
                depth_type = 'raw', years = 2023)
plot_23C

Plot DO all ACAD lakes sampled in 2023 and raw sample depth, using reversed RdYlBu palette. Temperature thermocline is also included as black lines.

plot_23do <- 
plotLakeProfile(park = "ACAD", site = lakes23, 
                parameter = "DOsat_pct", depth_type = 'raw', years = 2023, 
                palette = 'RdYlBu', color_rev = TRUE)
plot_23do

Plot specific conductance for Seal Cove Pond from 2013 to 2023 and sample elevation. Uses spectral palette by default and adds site name as title by default. Thermocline is also plotted as default.

scove_sc <- 
plotLakeProfile(site = "ACSEAL", parameter = "SpCond_uScm", 
                depth_type = 'elev', years = 2013:2023)
scove_sc

Plot pH for Jordan Pond from 2013 to 2023 and sample elevation, using reversed spectral palette.

jord_ph <- 
plotLakeProfile(site = "ACJORD", parameter = "pH", 
                depth_type = 'elev', years = 2013:2023, 
                color_rev = TRUE)
jord_ph

Plot pH for all ACAD lakes sampled in 2022 and 2023 and raw sample depth, using reversed RdYlBu palette.

p223 <- 
plotLakeProfile(park = "ACAD", site = c("ACBUBL", "ACEAGL", "ACECHO", "ACJORD", "ACLONG", "ACSEAL", 
                                        "ACUHAD", "ACWHOL"), 
                parameter = "pH", depth_type = 'raw', years = 2022:2023, 
                palette = 'RdYlBu', color_rev = TRUE)
p223

Combining plots

Combine plots for temp, DO, pH, and conductance in Bubble Pond for 2023 using the cowplot package.

To minimize typing, I define the parameters I wanted at the beginning. This allows you to adjust the parameters once (i.e., change site), and run through the rest of the code without having to edit it. I also only included the plot title on the first figure, and turned it off for the rest.

The cowplot package must be installed to use this code. Install the package via install.packages('cowplot'). There are other packages to combine plots, including grid and gridExtra, and the function ggarrage() in ggpubr. I tend to start with cowplot, because it’s easy to use and has a great help page. If I really need to customize a plot (like custom spacing for each plot), then I use grid/gridExtra, which allows for more customization, but is a bit harder to work with.

library(cowplot)
sitecode = "ACBUBL"
sitename = getSites(site = sitecode)$SiteName
year = 2023
mon = 5:10
depth = 'elev'
ptitle = F

tplot <- plotLakeProfile(site = sitecode, parameter = "Temp_C", depth_type = depth,
                         years = year, months = mon, plot_title = ptitle)

doplot <- plotLakeProfile(site = sitecode, parameter = "DOsat_pct", depth_type = depth,
                          years = year, months = mon, color_rev = T, plot_title = ptitle)

pHplot <- plotLakeProfile(site = sitecode, parameter = "pH", depth_type = depth,
                          years = year, months = mon, palette = "RdYlBu", color_rev = T,
                          plot_title = ptitle)

cnplot <- plotLakeProfile(site = sitecode, parameter = "SpCond_uScm", depth_type = depth,
                         years = year, months = mon, palette = 'RdBu',
                         plot_title = ptitle)

# Default settings
plot_grid(tplot, doplot, pHplot, cnplot)

Same plot as above, but customize plot widths, so DO and SpCond have more space for legend, and add title above the grid.

In this case, we’re creating the plot grid with relative widths for each plot. Then we’re combining the title and the plot grid in another grid, setting the title height to be much smaller than the plot grid.

Note that sitename and year are defined in code chunk above.

title <- ggdraw() + draw_label(paste0(sitename, " (", year, ")"), size = 11, fontface = 'bold',
                               x = 0.05, hjust = 0, vjust = 0) 
pgrid <- plot_grid(tplot, doplot, pHplot, cnplot, rel_widths = c(0.9, 0.95, 0.85, 1)) # doesn't seem to be working 
plot_grid(title, pgrid, ncol = 1, rel_heights = c(0.1, 1))

plotPrecipDischarge()

This function produces a plot with dual y-axes, one for precipitation and one for discharge. The x-axis is date. This function only works for one stream monitoring site at a time. Note that ggplot tends to have a lot of warnings that are hard to suppress, particularly for this plot, which has a daily value for precipitation and only monthly values for discharge. You’re always going to get a message about that by using this function. Function currently only plots years where discharge is collected. Discharge is plotted as points and not lines, because discharge can change a lot between sampling events.

Note that the climateNETN package must be installed for this function to work, as it relies on downloading daily precipitation data. To install run pak::pkg_install("doi-nps/climateNETN")

Plot Discharge for Mill Brook in MIMA for past 3 years using default colors and gridlines on the y-axis and english units.

mima_disch <-
plotPrecipDischarge(site = c("MIMASA"), years = 2021:2023, gridlines = "grid_y", units = "eng")
mima_disch

Plot daily precipitation vs discharge for all ROVA sites in 2021, only accepting observations of”Excellent”, “Good”, or “Fair”.

rova_disch <- 
plotPrecipDischarge(park = "ROVA", years = 2021, rating = c("E", "G", "F"))
rova_disch

Plot Discharge for Aunt Betty Inlet and Kebo Stream for 2024 using different colors. Note that this can be slow because has to download precip. data from NADP. LNETN parks download from a faster web service.

bin_keb <- 
plotPrecipDischarge(site = c("ACABIN", "ACKEBO"), years = 2024, palette = c("cornflowerblue", "orange"))
bin_keb

Summary Functions

sumEvents()

Summarize number of samples collected per park, site, month, and parameter. Resulting data frame show number of samples collected for each month, and whether the value is real (month) or censored (month_cens).

Summarize all events for ACAD for all years and active sites

acad_ev <- sumEvents(park = "ACAD")
print_head(acad_ev)

UnitCode	SiteType	SiteName	param_type	Parameter	year_range	num_years	May	Jun	Jul	Aug	Sep	Oct	May_cens	Jun_cens	Jul_cens	Aug_cens	Sep_cens	Oct_cens
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	ANC_ueqL	2006 – 2024	7	0	4	0	4	0	0	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	ChlA_ugL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	DOC_mgL	2006 – 2024	7	3	5	3	5	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	TN_mgL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	TP_ugL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Light penetration	PenetrationRatio	2006 – 2024	7	27	38	34	31	35	35	0	0	0	0	0	0

Summarize only lake events for ACAD for all years

acad_lk <- sumEvents(park = "ACAD", site_type = "lake")
print_head(acad_lk)

UnitCode	SiteType	SiteName	param_type	Parameter	year_range	num_years	May	Jun	Jul	Aug	Sep	Oct	May_cens	Jun_cens	Jul_cens	Aug_cens	Sep_cens	Oct_cens
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	ANC_ueqL	2006 – 2024	7	0	4	0	4	0	0	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	ChlA_ugL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	DOC_mgL	2006 – 2024	7	3	5	3	5	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	TN_mgL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Lab chemistry	TP_ugL	2006 – 2024	7	3	7	3	7	3	3	0	0	0	0	0	0
ACAD	Lake	Aunt Bettys Pond	Light penetration	PenetrationRatio	2006 – 2024	7	27	38	34	31	35	35	0	0	0	0	0	0

Summarize LNETN events only

lnetn <- sumEvents(park = "LNETN")
print_head(lnetn)

UnitCode	SiteType	SiteName	param_type	Parameter	year_range	num_years	May	Jun	Jul	Aug	Sep	Oct	May_cens	Jun_cens	Jul_cens	Aug_cens	Sep_cens	Oct_cens
MABI	Lake	The Pogue	Lab chemistry	ANC_ueqL	2006 – 2024	18	0	12	0	12	0	0	0	0	0	0	0	0
MABI	Lake	The Pogue	Lab chemistry	TN_mgL	2006 – 2024	18	6	18	6	18	6	6	0	0	0	0	0	0
MABI	Lake	The Pogue	Lab chemistry	TP_ugL	2006 – 2024	18	6	18	6	18	6	6	0	0	0	0	0	0
MABI	Lake	The Pogue	Light penetration	PenetrationRatio	2006 – 2024	18	120	137	130	134	122	120	0	0	0	0	0	0
MABI	Lake	The Pogue	Sonde field meas.	DO_mgL	2006 – 2024	18	16	18	17	18	17	19	0	0	0	0	0	0
MABI	Lake	The Pogue	Sonde field meas.	SpCond_uScm	2006 – 2024	18	16	18	17	18	17	19	0	0	0	0	0	0