Title:	'DBHYDRO' Hydrologic and Water Quality Data
Description:	Client for programmatic access to the South Florida Water Management District's 'DBHYDRO' database at https://www.sfwmd.gov/science-data/dbhydro, with functions for accessing hydrologic and water quality data.
Version:	0.2-8
URL:	https://github.com/ropensci/dbhydroR, https://docs.ropensci.org/dbhydroR/
BugReports:	https://github.com/ropensci/dbhydroR/issues
Depends:	R (≥ 3.0.2)
Imports:	httr, reshape2, XML
License:	GPL-2 | GPL-3 [expanded from: GPL]
LazyData:	true
Suggests:	testthat, knitr, rmarkdown, vcr
RoxygenNote:	7.1.1
VignetteBuilder:	knitr
Encoding:	UTF-8
NeedsCompilation:	no
Packaged:	2021-02-21 02:04:30 UTC; julie
Author:	Joseph Stachelek [aut, cre]
Maintainer:	Joseph Stachelek <stachel2@msu.edu>
Repository:	CRAN
Date/Publication:	2021-02-21 16:50:02 UTC

dbhydroR

Description

dbhydroR is an R interface to the South Florida Water Management District's DBHYDRO database which holds over 35 million hydrologic and water quality records from the Florida Everglades and surrounding areas.

Hydrologic Data

The get_hydro function provides the capability to return:

• weather data

• surfacewater data

• groundwater data

• water-quality sonde data

Water Quality Data

The get_wq function provides the capability to return:

• water quality data

Clean raw hydrologic DBHYDRO data retrievals

Description

Converts output of get_hydro from long (each piece of data on its own row) to wide format (each site x variable combination in its own column). Metadata (station-name, variable, measurement units) is parsed so that it is wholly contained in column names.

Usage

clean_hydro(dt)

Arguments

Examples

## Not run: 
clean_hydro(gethydro(dbkey = "15081", date_min = "2013-01-01", date_max = "2013-02-02", raw = TRUE))

## End(Not run)

Clean raw water quality DBHYDRO data retrievals

Description

Removes extra columns associated with QA flags and QA blanks which are used to check on potential sources of contamination. If raw is set to TRUE, get_wq results are converted from long (each piece of data on its own row) to wide format (each site x variable combination in its own column).

Usage

clean_wq(dt, raw = FALSE, mdl_handling = "raw")

Arguments

Examples

## Not run: 
#check handling of values below MDL
dt <- getwq("FLAB01", "2014-09-14", "2014-09-18", "NITRATE+NITRITE-N",
 raw = TRUE)
clean_wq(dt, mdl_handling = "raw")
clean_wq(dt, mdl_handling = "half")

## End(Not run)

dt <- read.csv(system.file("extdata", "testwq.csv", package = "dbhydroR"))
clean_wq(dt)

Query dbkey information

Description

Retrieve a data.frame summary including dbkeys or a vector of dbkeys corresponding to specified parameters

Usage

get_dbkey(
  category,
  stationid = NA,
  param = NA,
  freq = NA,
  longest = FALSE,
  stat = NA,
  recorder = NA,
  agency = NA,
  strata = NA,
  detail.level = "summary",
  ...
)

Arguments

Details

A dbkey represents a unique station x variable time-series. A value in the "Recorder" field of "PREF" should be used whenever possible. This indicates that the dataset has been checked by the SFWMD modelling group.

Examples

## Not run: 
# Weather
get_dbkey(stationid = "JBTS", category = "WEATHER", param = "WNDS",
detail.level = "summary")
get_dbkey(stationid = "JBTS", category = "WEATHER", param = "WNDS",
detail.level = "dbkey")

# query on multiple values
get_dbkey(stationid = c("MBTS", "JBTS"), category = "WEATHER",
param = "WNDS", freq = "DA", detail.level = "dbkey")


# Surfacewater
get_dbkey(stationid = "C111%", category = "SW")
get_dbkey(category = "SW", stationid = "LAKE%", detail.level = "full")

# Groundwater
get_dbkey(stationid = "C111%", category = "GW")
get_dbkey(stationid = "C111AE", category = "GW", param = "WELL",
freq = "DA", stat = "MEAN", strata = c(9, 22), recorder = "TROL",
 agency = "WMD", detail.level = "full")

# Water Quality
get_dbkey(stationid = "C111%", category = "WQ")

## End(Not run)

Retrieve hydrologic data from the DBHYDRO Environmental Database

Description

Retrieve hydrologic data from the DBHYDRO Environmental Database

Usage

get_hydro(dbkey = NA, date_min = NA, date_max = NA, raw = FALSE, ...)

Arguments

Details

get_hydro can be run in one of two ways.

• The first, is to identify one or more dbkeys before-hand that correspond to unique data series and are passed to the dbkey argument. dbkeys can be found by:

  • iterative calls to get_dbkey (see example)

  • using the Environmental Monitoring Location Maps (https://www.sfwmd.gov/documents-by-tag/emmaps)

  • using the DBHYDRO Browser.

• The second way to run get_hydro is to specify additional arguments to ... which are passed to get_dbkey on-the-fly.

By default, get_hydro returns a cleaned output where metadata (station-name, variable, measurement units) is wholly contained in the column name. This is accomplished internally by the clean_hydro function. If additional metadata such as latitude and longitude are desired set the raw argument to TRUE.

Examples

## Not run: 
#One variable/station time series
get_hydro(dbkey = "15081", date_min = "2013-01-01", date_max = "2013-02-02")

#Multiple variable/station time series
get_hydro(dbkey = c("15081", "15069"),
date_min = "2013-01-01", date_max = "2013-02-02")

#Instantaneous hydro retrieval
get_hydro(dbkey = "IY639", date_min = "2015-11-01", date_max = "2015-11-04")

#Looking up unknown dbkeys on the fly
get_hydro(stationid = "JBTS", category = "WEATHER",
param = "WNDS", freq = "DA", date_min = "2013-01-01",
date_max = "2013-02-02")

## End(Not run)

Retrieve water quality data from the DBHYDRO Environmental Database

Description

Retrieve water quality data from the DBHYDRO Environmental Database

Usage

get_wq(
  station_id = NA,
  date_min = NA,
  date_max = NA,
  test_name = NA,
  mdl_handling = "raw",
  raw = FALSE,
  qc_strip = "N",
  qc_field = "N",
  test_number = NA,
  v_target_code = "file_csv",
  sample_id = NA,
  project_code = NA
)

Arguments

Details

By default, get_wq returns a cleaned output. First, the cleaning function clean_wq converts the raw output from native DBHYDRO long format (each piece of data on its own row) to wide format (each site x variable combination in its own column). Next, the extra columns associated with QA flags, LIMS, and District receiving are removed. Finally, row entries associated with QA field blanks, which are used to check on potential sources of contamination, are removed. Setting the raw flag to TRUE will force getwq to retain information on QA field blanks as well as the other QA fields.

Examples

## Not run: 
#one variable and one station
get_wq(station_id = "FLAB08",
date_min = "2011-03-01", date_max = "2012-05-01",
test_name = "CHLOROPHYLLA-SALINE")

#one variable at multiple stations
get_wq(station_id = c("FLAB08", "FLAB09"),
date_min = "2011-03-01", date_max = "2012-05-01",
test_name = "CHLOROPHYLLA-SALINE")

#One variable at a wildcard station
get_wq(station_id = c("FLAB0%"),
date_min = "2011-03-01",
date_max = "2012-05-01",
test_name = "CHLOROPHYLLA-SALINE")

#multiple variables at multiple stations
get_wq(station_id = c("FLAB08", "FLAB09"),
date_min = "2011-03-01", date_max = "2012-05-01",
test_name = c("CHLOROPHYLLA-SALINE", "SALINITY"))

## End(Not run)