Run quality control accuracy checks for water quality monitoring results

Usage

qcMWRacc(
  res = NULL,
  acc = NULL,
  frecom = NULL,
  fset = NULL,
  runchk = TRUE,
  warn = TRUE,
  accchk = c("Field Blanks", "Lab Blanks", "Field Duplicates", "Lab Duplicates",
    "Lab Spikes / Instrument Checks"),
  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 checkMWRacc, applies only if res or acc are file paths
warn: logical to return warnings to the console (default)
accchk: character string indicating which accuracy check to return, one to any of "Field Blanks", "Lab Blanks", "Field Duplicates", "Lab Duplicates", or "Lab Spikes / Instrument Checks"
suffix: character string indicating suffix to append to percentage values

Value

The output shows the accuracy checks from the input files returned as a list, with each element of the list corresponding to a specific accuracy check specified with accchk.

Details

The function can be used with inputs as paths to the relevant files or as data frames returned by readMWRresults and readMWRacc. For the former, the full suite of data checks can be evaluated with runkchk = T (default) or suppressed with runchk = F. 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.

Note that accuracy is only evaluated on parameters in the Parameter column in the data quality objectives accuracy file. A warning is returned if there are parameters in Parameter in the accuracy file that are not in Characteristic Name in the results file.

Similarly, parameters in the results file in the Characteristic Name column that are not found in the data quality objectives accuracy file are not evaluated. A warning is returned if there are parameters in Characteristic Name in the results file that are not in Parameter in the accuracy file.

The data quality objectives file for frequency and completeness is used to screen parameters in the results file for inclusion in the accuracy tables. Parameters with empty values in the frequency and completeness table are not returned.

Examples

##
# using file paths

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

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

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

qcMWRacc(res = respth, acc = accpth, frecom = frecompth)
#> 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!
#> $`Field Blanks`
#> # A tibble: 29 × 6
#>    Parameter Date                Site  Result Threshold   `Hit/Miss`
#>    <chr>     <dttm>              <chr> <chr>  <chr>       <chr>     
#>  1 Ammonia   2022-05-15 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  2 Ammonia   2022-06-12 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  3 Ammonia   2022-07-17 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  4 Ammonia   2022-07-17 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  5 Ammonia   2022-08-14 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  6 Ammonia   2022-08-14 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  7 Ammonia   2022-09-11 00:00:00 NA    BDL    0.1 mg/l    NA        
#>  8 E.coli    2022-06-13 00:00:00 NA    BDL    1 MPN/100ml NA        
#>  9 E.coli    2022-07-18 00:00:00 NA    BDL    1 MPN/100ml NA        
#> 10 E.coli    2022-08-01 00:00:00 NA    BDL    1 MPN/100ml NA        
#> # ℹ 19 more rows
#> 
#> $`Lab Blanks`
#> # A tibble: 38 × 6
#>    Parameter Date                `Sample ID` Result   Threshold `Hit/Miss`
#>    <chr>     <dttm>              <chr>       <chr>    <chr>     <chr>     
#>  1 Ammonia   2022-05-15 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  2 Ammonia   2022-06-12 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  3 Ammonia   2022-07-17 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  4 Ammonia   2022-07-17 00:00:00 NA          0.1 mg/l 0.1 mg/l  MISS      
#>  5 Ammonia   2022-08-14 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  6 Ammonia   2022-08-14 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  7 Ammonia   2022-09-11 00:00:00 NA          BDL      0.1 mg/l  NA        
#>  8 Nitrate   2022-05-15 00:00:00 NA          BDL      0.05 mg/l NA        
#>  9 Nitrate   2022-06-12 00:00:00 NA          BDL      0.05 mg/l NA        
#> 10 Nitrate   2022-07-17 00:00:00 NA          BDL      0.05 mg/l NA        
#> # ℹ 28 more rows
#> 
#> $`Field Duplicates`
#> # A tibble: 57 × 7
#>    Parameter Date                Site    `Initial Result` `Dup. Result`
#>    <chr>     <dttm>              <chr>   <chr>            <chr>        
#>  1 Ammonia   2022-05-15 00:00:00 ABT-312 BDL              BDL          
#>  2 Ammonia   2022-05-15 00:00:00 DAN-013 BDL              BDL          
#>  3 Ammonia   2022-06-12 00:00:00 ABT-301 BDL              0.2 mg/l     
#>  4 Ammonia   2022-09-11 00:00:00 ABT-301 BDL              BDL          
#>  5 DO        2022-05-15 00:00:00 ABT-026 7.58 mg/l        7.6 mg/l     
#>  6 DO        2022-05-15 00:00:00 ELZ-004 5.81 mg/l        5.94 mg/l    
#>  7 DO        2022-05-15 00:00:00 NSH-002 8.32 mg/l        8.33 mg/l    
#>  8 DO        2022-06-12 00:00:00 ABT-062 8.56 mg/l        8.56 mg/l    
#>  9 DO        2022-06-12 00:00:00 ABT-237 7.81 mg/l        8.1 mg/l     
#> 10 DO        2022-06-12 00:00:00 HOP-011 7.8 mg/l         7.79 mg/l    
#> # ℹ 47 more rows
#> # ℹ 2 more variables: `Diff./RPD` <chr>, `Hit/Miss` <chr>
#> 
#> $`Lab Duplicates`
#> # A tibble: 91 × 7
#>    Parameter Date                `Sample ID` `Initial Result` `Dup. Result`
#>    <chr>     <dttm>              <chr>       <chr>            <chr>        
#>  1 Ammonia   2022-05-15 00:00:00 NA          0.21 mg/l        0.21 mg/l    
#>  2 Ammonia   2022-05-15 00:00:00 NA          BDL              BDL          
#>  3 Ammonia   2022-06-12 00:00:00 NA          0.1 mg/l         0.1 mg/l     
#>  4 Ammonia   2022-06-12 00:00:00 NA          0.19 mg/l        0.19 mg/l    
#>  5 Ammonia   2022-07-17 00:00:00 NA          BDL              BDL          
#>  6 Ammonia   2022-07-17 00:00:00 NA          BDL              BDL          
#>  7 Ammonia   2022-08-14 00:00:00 NA          BDL              BDL          
#>  8 Ammonia   2022-08-14 00:00:00 NA          BDL              BDL          
#>  9 Ammonia   2022-09-11 00:00:00 NA          BDL              BDL          
#> 10 Ammonia   2022-09-11 00:00:00 NA          BDL              BDL          
#> # ℹ 81 more rows
#> # ℹ 2 more variables: `Diff./RPD` <chr>, `Hit/Miss` <chr>
#> 
#> $`Lab Spikes / Instrument Checks`
#> # A tibble: 94 × 7
#>    Parameter Date                `Sample ID` `Spike/Standard` Result        
#>    <chr>     <dttm>              <chr>       <chr>            <chr>         
#>  1 Ammonia   2022-05-15 00:00:00 NA          100 % recovery   86 % recovery 
#>  2 Ammonia   2022-06-12 00:00:00 NA          100 % recovery   94 % recovery 
#>  3 Ammonia   2022-06-12 00:00:00 NA          100 % recovery   106 % recovery
#>  4 Ammonia   2022-07-17 00:00:00 NA          100 % recovery   92 % recovery 
#>  5 Ammonia   2022-07-17 00:00:00 NA          100 % recovery   108 % recovery
#>  6 Ammonia   2022-08-14 00:00:00 NA          100 % recovery   96 % recovery 
#>  7 Ammonia   2022-08-14 00:00:00 NA          100 % recovery   102 % recovery
#>  8 Ammonia   2022-09-11 00:00:00 NA          100 % recovery   88 % recovery 
#>  9 Ammonia   2022-09-11 00:00:00 NA          100 % recovery   89 % recovery 
#> 10 Nitrate   2022-05-15 00:00:00 NA          100 % recovery   99 % recovery 
#> # ℹ 84 more rows
#> # ℹ 2 more variables: `Diff./Accuracy` <chr>, `Hit/Miss` <chr>
#>