qcMWRreview {MassWateR}

Create the quality control review report

Description

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

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.

Value

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

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)

# accuracy data
accdat <- readMWRacc(accpth)

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


# create report
qcMWRreview(res = resdat, acc = accdat, frecom = frecomdat, output_dir = tempdir())