Create a formatted table of quality control frequency checks

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

Value

A flextable object with formatted results.

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.

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')
#> 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!
#> 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!
#> 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!
Type
Parameter
Number of Data Records
Number of Dups/Blanks/Spikes
Frequency %
Hit/Miss
Field Duplicates
Ammonia
43
4
9%
MISS
DO
49
11
22%
E.coli
12
2
17%
Nitrate
20
2
10%
pH
49
11
22%
Sp Conductance
49
11
22%
TP
48
5
10%
Water Temp
49
11
22%
Lab Duplicates
Ammonia
43
10
23%
E.coli
12
4
33%
Nitrate
20
10
50%
pH
49
17
35%
Sp Conductance
49
17
35%
TP
48
16
33%
Water Temp
49
17
35%
Field Blanks
Ammonia
43
7
16%
E.coli
12
4
33%
Nitrate
20
7
35%
TP
48
11
23%
Lab Blanks
Ammonia
43
7
16%
E.coli
12
0
0%
MISS
Nitrate
20
5
25%
Sp Conductance
49
21
43%
TP
48
5
10%
Lab Spikes / Instrument Checks
Ammonia
43
9
21%
Nitrate
20
10
50%
pH
49
20
41%
Sp Conductance
49
21
43%
TP
48
15
31%
Water Temp
49
19
39%

# table as percent
tabMWRfre(res = respth, acc = accpth, frecom = frecompth, type = 'percent')
#> 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!
#> 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!
#> 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!
Parameter
Field Duplicate
Lab Duplicate
Field Blank
Lab Blank
Spike/Check Accuracy
Ammonia
9%
23%
16%
16%
21%
DO
22%
-
-
-
-
E.coli
17%
33%
33%
0%
-
Nitrate
10%
50%
35%
25%
50%
Sp Conductance
22%
35%
-
43%
43%
TP
10%
33%
23%
10%
31%
Water Temp
22%
35%
-
-
39%
pH
22%
35%
-
-
41%

##
# using data frames

# 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!

# table as summary
tabMWRfre(res = resdat, acc = accdat, frecom = frecomdat, type = 'summary')
Type
Parameter
Number of Data Records
Number of Dups/Blanks/Spikes
Frequency %
Hit/Miss
Field Duplicates
Ammonia
43
4
9%
MISS
DO
49
11
22%
E.coli
12
2
17%
Nitrate
20
2
10%
pH
49
11
22%
Sp Conductance
49
11
22%
TP
48
5
10%
Water Temp
49
11
22%
Lab Duplicates
Ammonia
43
10
23%
E.coli
12
4
33%
Nitrate
20
10
50%
pH
49
17
35%
Sp Conductance
49
17
35%
TP
48
16
33%
Water Temp
49
17
35%
Field Blanks
Ammonia
43
7
16%
E.coli
12
4
33%
Nitrate
20
7
35%
TP
48
11
23%
Lab Blanks
Ammonia
43
7
16%
E.coli
12
0
0%
MISS
Nitrate
20
5
25%
Sp Conductance
49
21
43%
TP
48
5
10%
Lab Spikes / Instrument Checks
Ammonia
43
9
21%
Nitrate
20
10
50%
pH
49
20
41%
Sp Conductance
49
21
43%
TP
48
15
31%
Water Temp
49
19
39%

# table as percent
tabMWRfre(res = resdat, acc = accdat, frecom = frecomdat, type = 'percent')
Parameter
Field Duplicate
Lab Duplicate
Field Blank
Lab Blank
Spike/Check Accuracy
Ammonia
9%
23%
16%
16%
21%
DO
22%
-
-
-
-
E.coli
17%
33%
33%
0%
-
Nitrate
10%
50%
35%
25%
50%
Sp Conductance
22%
35%
-
43%
43%
TP
10%
33%
23%
10%
31%
Water Temp
22%
35%
-
-
39%
pH
22%
35%
-
-
41%