qcMWRcom: Run quality control completeness checks for water quality...

In massbays-tech/MassWateR: Quality Control and Analysis of Massachusetts Water Quality Data

Run quality control completeness checks for water quality monitoring results

Description

Run quality control completeness checks for water quality monitoring results

Usage

qcMWRcom(
  res = NULL,
  frecom = NULL,
  cens = NULL,
  fset = NULL,
  runchk = TRUE,
  warn = TRUE
)

Arguments

res	character string of path to the results file or data.frame for results returned by readMWRresults
frecom	character string of path to the data quality objectives file for frequency and completeness or data.frame returned by readMWRfrecom
cens	character string of path to the censored data file or data.frame returned by readMWRcens, optional
fset	optional list of inputs with elements named res, acc, frecom, sit, or wqx overrides the other arguments
runchk	logical to run data checks with checkMWRresults and checkMWRfrecom, applies only if res or frecom are file paths
warn	logical to return warnings to the console (default)

Details

The function can be used with inputs as paths to the relevant files or as data frames returned by readMWRresults, readMWRfrecom, and readMWRcens (optional). For the former, the full suite of data checks can be evaluated with runkchk = T (default) or suppressed with runchk = F. In the latter case, downstream analyses may not work if data are formatted incorrectly. For convenience, a named list with the input arguments as paths or data frames can be passed to the fset argument instead. See the help file for utilMWRinput.

Note that frequency is only evaluated on parameters in the Parameter column in the data quality objectives frequency and completeness file. A warning is returned if there are parameters in Parameter in the frequency and completeness file that are not in Characteristic Name in the results file.

Similarly, parameters in the results file in the Characteristic Name column that are not found in the data quality objectives frequency and completeness file are not evaluated. A warning is returned if there are parameters in Characteristic Name in the results file that are not in Parameter in the frequency and completeness file.

A similar warning is returned if there are parameters in the censored data, if provided, that are not in the results file. However, an error is returned if there are parameters in the data quality objectives frequency and completeness file that are not in the censored data file.

All warnings can be suppressed by setting warn = FALSE.

Value

The output shows the completeness checks from the combined files. Each row applies to a completeness check for a parameter. The datarec and qualrec columns show the number of data records and qualified records, respectively. The datarec column specifically shows only records not for quality control by excluding those as duplicates, blanks, or spikes in the count. The standard column shows the relevant percentage required for the quality control check from the quality control objectives file, the complete column shows the calculated completeness taken from the input data, and the met column shows if the standard was met by comparing if complete is greater than or equal to standard.

Examples

##
# using file paths

# results path
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')

# frequency and completeness path
frecompth <- system.file('extdata/ExampleDQOFrequencyCompleteness.xlsx', 
     package = 'MassWateR')

# censored path
censpth <- system.file('extdata/ExampleCensored.xlsx', 
     package = 'MassWateR')

qcMWRcom(res = respth, frecom = frecompth, cens = censpth)

##
# using data frames

# results data
resdat <- readMWRresults(respth)

# frequency and completeness data
frecomdat <- readMWRfrecom(frecompth)

# censored data
censdat <- readMWRcens(censpth)

qcMWRcom(res = resdat, frecom = frecomdat, cens = censdat)

massbays-tech/MassWateR documentation built on April 12, 2025, 7:53 p.m.