Create the quality control review report

Usage

qcMWRreview(
  res = NULL,
  acc = NULL,
  frecom = NULL,
  fset = NULL,
  output_dir,
  output_file = NULL,
  rawdata = TRUE,
  dqofontsize = 7.5,
  tabfontsize = 9,
  padding = 0,
  warn = TRUE,
  runchk = TRUE
)

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
output_dir: character string of the output directory for the rendered file
output_file: optional character string for the file name
rawdata: logical to include quality control accuracy summaries for raw data, e.g., field blanks, etc.
dqofontsize: numeric for font size in the data quality objective tables in the first page of the review
tabfontsize: numeric for font size in the review tables
padding: numeric for row padding for table output
warn: logical indicating if warnings from the table functions are included in the file output
runchk: logical to run data checks with checkMWRresults, checkMWRacc, checkMWRfrecom, applies only if res, acc, or frecom are file paths

Value

A compiled review report named qcreview.docx (or name passed to output_file) will be saved in the directory specified by output_dir

Details

The function compiles a review report as a Word document for all quality control checks included in the MassWateR package. The report shows several tables, including the data quality objectives files for accuracy, frequency, and completeness, summary results for all accuracy checks, summary results for all frequency checks, summary results for all completeness checks, and individual results for all accuracy checks. The report uses the individual table functions (which can be used separately) to return the results, which include tabMWRacc, tabMWRfre, and tabMWRcom. The help files for each of these functions can be consulted for a more detailed explanation of the quality control checks.

The workflow for using this function is to import the required data (results and data quality objective files) and to fix any errors noted on import prior to creating the review report. Additional warnings that may be of interest as returned by the individual table functions can be returned in the console by setting warn = TRUE.

Optional arguments that can be changed as needed include specifying the file name with output_file, suppressing the raw data summaries at the end of the report with rawdata = FALSE, and changing the table font sizes (dqofontsize for the data quality objectives on the first page, tabfontsize for the remainder).

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.

Examples

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

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

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

# results data
resdat <- readMWRresults(respth)
#> Running checks on results data...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking valid Activity Types... OK
#> 	Checking Activity Start Date formats... OK
#> 	Checking depth data present... OK
#> 	Checking for non-numeric values in Activity Depth/Height Measure... OK
#> 	Checking Activity Depth/Height Unit... OK
#> 	Checking Activity Relative Depth Name formats... OK
#> 	Checking values in Activity Depth/Height Measure > 1 m / 3.3 ft... OK
#> 	Checking Characteristic Name formats... OK
#> 	Checking Result Values... OK
#> 	Checking for non-numeric values in Quantitation Limit... OK
#> 	Checking QC Reference Values... OK
#> 	Checking for missing entries for Result Unit... OK
#> 	Checking if more than one unit per Characteristic Name... OK
#> 	Checking acceptable units for each entry in Characteristic Name... OK
#> 
#> All checks passed!

# accuracy data
accdat <- readMWRacc(accpth)
#> Running checks on data quality objectives for accuracy...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking column types... OK
#> 	Checking no "na" in Value Range... OK
#> 	Checking for text other than <=, ≤, <, >=, ≥, >, ±, %, AQL, BQL, log, or all... OK
#> 	Checking overlaps in Value Range... OK
#> 	Checking gaps in Value Range... OK
#> 	Checking Parameter formats... OK
#> 	Checking for missing entries for unit (uom)... OK
#> 	Checking if more than one unit (uom) per Parameter... OK
#> 	Checking acceptable units (uom) for each entry in Parameter... OK
#> 	Checking empty columns... OK
#> 
#> All checks passed!

# frequency and completeness data
frecomdat <- readMWRfrecom(frecompth)
#> Running checks on data quality objectives for frequency and completeness...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking for non-numeric values... OK
#> 	Checking for values outside of 0 and 100... OK
#> 	Checking Parameter formats... OK
#> 	Checking empty columns... OK
#> 
#> All checks passed!

# \donttest{
# create report
qcMWRreview(res = resdat, acc = accdat, frecom = frecomdat, output_dir = tempdir())
#> Report created successfully! File located at /tmp/RtmpgGd0ja/qcreview.docx
# }