tabMWRcom: Create a formatted table of quality control completeness...

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

Create a formatted table of quality control completeness checks

Description

Create a formatted table of quality control completeness checks

Usage

tabMWRcom(
  res = NULL,
  frecom = NULL,
  cens = NULL,
  fset = NULL,
  runchk = TRUE,
  warn = TRUE,
  pass_col = "#57C4AD",
  fail_col = "#DB4325",
  digits = 0,
  suffix = "%",
  parameterwd = 1.15,
  noteswd = 3
)

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)
pass_col	character string (as hex code) for the cell color of checks that pass
fail_col	character string (as hex code) for the cell color of checks that fail
digits	numeric indicating number of significant digits to report for percentages
suffix	character string indicating suffix to append to percentage values
parameterwd	numeric indicating width of the parameter column
noteswd	numeric indicating width of notes column

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, as explained in the relevant help files. 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.

Also note that completeness is only evaluated on parameters that are shared between the results file and data quality objectives file for frequency and completeness. A warning is returned for parameters that do not match between the files. A similar warning is returned if there are parameters in the censored data, if provided, that are not in the results file and vice versa. These warnings can be suppressed by setting warn = FALSE.

A summary table showing the number of data records, number of qualified records, and percent completeness is created. The % Completeness column shows cells as green or red if the required percentage of observations for completeness are present as specified in the data quality objectives file. The Hit/ Miss column shows similar information but in text format, i.e., MISS is shown if the quality control standard for completeness is not met.

Inputs for the results and data quality objectives for frequency and completeness are processed internally with qcMWRcom and the same arguments are accepted for this function, in addition to others listed above.

Value

A flextable object with formatted results showing summary counts for all completeness checks for each parameter.

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')

tabMWRcom(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)

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

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