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Check data quality objectives

Source: R/checkASRdqo.R
checkASRdqo.Rd

Check data quality objectives

Usage

checkASRdqo(dqodat)

Arguments

dqodat

input data frame fordata quality objectives

Value

dqodat is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding.

Details

This function is used internally within readASRdqo to run several checks on the input data to verify correct formatting before downstream analysis.

The following checks are made:

  • Column names: Should include only Parameter, Flag, GrMin, GrMax, Spike, FlatN, FlatDelta, RoCN, and RoCHours

  • All columns present: All columns from the previous check should be present

  • At least one parameter is present: At least one parameter in the Parameter column matches the Parameter column in paramsASR

  • Parameter format: All parameters listed in the Parameter column should match those in the Parameter column in paramsASR

  • Flag column: The Flag column should contain only "Fail" or "Suspect" entries

  • Rate of Change: No entries for Fail Flag rows

  • Numeric columns: All columns except Parameter and Flag should be numeric values

Examples

library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union

dqopth <- system.file('extdata/ExampleDQO.xlsx', package = 'AquaSensR')

dqodat <- suppressWarnings(readxl::read_excel(dqopth, na = c('NA', 'na', ''),
     guess_max = Inf))

checkASRdqo(dqodat)
#> Running checks on data quality objectives...
#> 	Checking column names... OK
#> 	Checking all columns present... OK
#> 	Checking at least one parameter is present... OK
#> 	Checking parameter format... OK
#> 	Checking Flag column... OK
#> 	Checking Rate of Change flags... OK
#> 	Checking columns for non-numeric values... OK
#> 
#> All checks passed!
#> # A tibble: 14 × 9
#>    Parameter          Flag    GrMin GrMax Spike FlatN FlatDelta  RoCN RoCHours
#>    <chr>              <chr>   <dbl> <dbl> <dbl> <dbl>     <dbl> <dbl>    <dbl>
#>  1 Water Temp_C       Suspect  -0.5    28   1.5    60      0.01     6       25
#>  2 Water Temp_C       Fail     -1      30   2     100      0.01    NA       NA
#>  3 DO_pctsat          Suspect   0     100  10      30      0.01     6       25
#>  4 DO_pctsat          Fail     -1     120  25      60      0.01    NA       NA
#>  5 DO_mg_l            Suspect   2      16   2      30      0.01     6       25
#>  6 DO_mg_l            Fail      1      18   4      60      0.01    NA       NA
#>  7 Conductivity_uS_cm Suspect  20    1200   5      30      0.01     6       25
#>  8 Conductivity_uS_cm Fail     10    1500  10      60      0.01    NA       NA
#>  9 TDS_mg_l           Suspect  20    1200  50      30      0.01     6       25
#> 10 TDS_mg_l           Fail     10    1500 100      60      0.01    NA       NA
#> 11 Salinity_ppt       Suspect   3      37   3      30      0.01     6       25
#> 12 Salinity_ppt       Fail      2      41   5      60      0.01    NA       NA
#> 13 pH_SU              Suspect   4      11   5      30      0.01     6       25
#> 14 pH_SU              Fail      3      12  10      60      0.01    NA       NA