tabMWRfre {MassWateR}

Create a formatted table of quality control frequency checks

Description

Create a formatted table of quality control frequency checks

Usage

tabMWRfre(
  res = NULL,
  acc = NULL,
  frecom = NULL,
  fset = NULL,
  runchk = TRUE,
  warn = TRUE,
  type = c("summary", "percent"),
  pass_col = "#57C4AD",
  fail_col = "#DB4325",
  digits = 0,
  suffix = "%"
)

Arguments

res

character string of path to the results file or data.frame for results returned by readMWRresults

acc

character string of path to the data quality objectives file for accuracy or data.frame returned by readMWRacc

frecom

character string of path to the data quality objectives file for frequency and completeness or data.frame returned by readMWRfrecom

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)

type

character string indicating summary or percent tabular output, see datails

pass_col

character string (as hex code) for the cell color of checks that pass, applies only if type = 'percent'

fail_col

character string (as hex code) for the cell color of checks that fail, applies only if type = 'percent'

digits

numeric indicating number of significant digits to report for percentages

suffix

character string indicating suffix to append to percentage values

Details

The function can be used with inputs as paths to the relevant files or as data frames returned by readMWRresults, readMWRacc, and readMWRfrecom. 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. This warning can be suppressed by setting warn = FALSE.

The quality control tables for frequency show the number of records that apply to a given check (e.g., Lab Blank, Field Blank, etc.) relative to the number of "regular" data records (e.g., field samples or measures) for each parameter. A summary of all frequency checks for each parameter is provided if type = "summary" or a color-coded table showing similar information as percentages for each parameter is provided if type = "percent".

Inputs for the results and data quality objectives for accuracy and 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.

Examples

##
# using file paths

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

# dqo accuracy data path
accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx', package = 'MassWateR')

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

# table as summary
tabMWRfre(res = respth, acc = accpth, frecom = frecompth, type = 'summary')

# table as percent
tabMWRfre(res = respth, acc = accpth, frecom = frecompth, type = 'percent')

##
# using data frames

# results data
resdat <- readMWRresults(respth)

# accuracy data
accdat <- readMWRacc(accpth)

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

# table as summary
tabMWRfre(res = resdat, acc = accdat, frecom = frecomdat, type = 'summary')

# table as percent
tabMWRfre(res = resdat, acc = accdat, frecom = frecomdat, type = 'percent')