pre_checks: Basic pre-processing completeness review.

In DEQrmichie/odeqcdr: ODEQ Continuous Data Review

Basic pre-processing completeness review.

Description

This function will execute a basic completeness review for Oregon DEQ's continuous data submission template xlsx file v2.03. The function checks for missing data, missing values in required columns, invalid domain values, and flags potential errors. If a check result is TRUE, it means the check failed and something is missing or there is an invalid value.

Usage

pre_checks(
  template_list = NULL,
  org = NULL,
  projects = NULL,
  mloc = NULL,
  deployment = NULL,
  results = NULL,
  prepost = NULL,
  audits = NULL
)

Arguments

template_list	A continuous data list object with each list holding a different worksheet from the xlsx data template. Use contin_import() to make the list. Default is NULL. If NULL all individual worksheet data frames must be supplied instead.
org	data frame holding Organization Details. Default is NULL.
projects	data frame with Projects. Default is NULL.
mloc	data frame holding Monitoring_Locations. Default is NULL.
deployment	data frame holding Deployment. Default is NULL.
results	data frame holding Results. Default is NULL.
prepost	data frame holding PrePost. Default is NULL.
audits	Dataframe of audits. Default is NULL.

Details

Complete list of checks:

Organizational Details worksheet checks:

1. Missing Organization Name

2. Missing Address

3. Missing Phone Number

4. Missing Email

5. Missing response to Type(s) of Data Submitted

6. Missing response to Prior DEQ Data Submission

Project worksheet checks:

1. Project worksheet is empty

2. Missing value in column Project.IDs

3. Missing value in column Project.Name

4. Missing value in column Project.Description

5. Missing value in column Approved.QAPP.Indicator

6. Value in column QAPP.Approval.Agency.Name is NA but value in column Approved.QAPP.Indicator = 'Yes'

Monitoring Locations worksheet checks:

1. Monitoring Locations worksheet is empty

2. Monitoring Location ID in results and not in Monitoring_Locations

3. Value in column Monitoring.Location.ID has been entered more than once.

4. Value in column Monitoring.Location.ID is > 22 characters

5. Value in column in Monitoring.Location.ID has an invalid character: ‘ ~ ! @ # $ % ^ & * ( ) [ { ] } \ | ; ’ " < > / ? [space].

6. Missing value in column Monitoring.Location.Name

7. Invalid value in column Monitoring.Location.Type

8. Missing value in column Latitude

9. Missing value in column Longitude

10. Invalid value in column Horizontal.Datum

11. Invalid value in column Coordinate.Collection.Method

12. Invalid value in column Tribal.Land

13. Invalid value in column County.Name

14. Invalid value in column State.Code

15. Invalid value in column HUC.8.Code

16. Value in column Latitude is outside of Oregon

17. Value in column Longitude is outside of Oregon

18. Value in column Source.Map.Scale is NA but column Coordinate.Collection.Method ='Interpolation-Map'

19. Value in column County.Name is NA but value in column State.Code = 'OR', 'WA', 'ID', 'CA', or 'NV'

20. Missing value in column Alternate.Context.1 because column Alternate.ID.1 has information

21. Missing value in column Alternate.Context.2 because column Alternate.ID.2 has information

22. Missing value in column Reachcode

23. Missing value in column Measure

24. Missing value in column LLID

25. Missing value in column River.Mile

Deployment worksheet checks:

1. Deployment worksheet is empty

2. Deployments '[Monitoring.Location.ID - Equipment.ID - Characteristic.Name]' in Results and not in Deployment.

3. Deployments '[Monitoring.Location.ID - Equipment.ID - Characteristic.Name]' not in Results.

4. There is more than one row of the same deployment '[Monitoring.Location.ID - Equipment.ID - Characteristic.Name]'. Make them unique or expand deployment start and end dates.

5. There are results from a deployment '[Monitoring.Location.ID - Equipment.ID - Characteristic.Name]' sampled outside of the deployment period.

6. Missing value in column Equipment.ID

7. Invalid value in column Characteristic.Name

8. Missing value in column Deployment.Start.Date

9. Missing value in column Deployment.End.Date

10. Missing value in column Sample.Depth

11. Invalid value in column Sample.Depth.Unit

12. Invalid value in column Sample.Media

13. Invalid value in column Sample.Sub.Media

Results worksheet checks:

1. Results worksheet is empty

2. Monitoring Location ID in Monitoring_Locations and not in Results

3. Missing value in column Activity.Start.Date

4. Missing value in column Activity.Start.Time

5. Invalid value in column Activity.Start.End.Time.Zone

6. Missing value in column Equipment.ID

7. Invalid value in column Characteristic.Name

8. Missing value in column Result.Value

9. Invalid value in column Result.Unit

10. Invalid value in column Result.Status.ID

PrePost worksheet checks:

1. PrePost worksheet is empty

2. Missing PrePost Results for '[Equipment.ID - Characteristic.Name]' that are in Results worksheet.

3. Invalid value in column Characteristic.Name

4. Missing value in column Equipment.Result.Value

5. Invalid value in column Equipment.Result.Unit

6. Missing value in column Reference.Result.Value

7. Invalid value in column Reference.Result.Unit

8. Missing value in column Reference.ID

Audit Data worksheet checks:

1. Audit Data worksheet is empty

2. Audits missing for some deployments '[Monitoring.Location.ID - Equipment.ID - Characteristic.Name]'.

3. Missing value in column Project.ID

4. Missing value in column Activity.Start.Date

5. Missing value in column Activity.Start.Time

6. Missing value in column Activity.End.Date

7. Missing value in column Activity.End.Time

8. Invalid value in column Activity.Start.End.Time.Zone

9. Invalid value in column Activity.Type

10. Missing value in column Activity.ID

11. Missing value in column Equipment.ID

12. Invalid value in column Sample.Collection.Method

13. Invalid value in column Characteristic.Name

14. Missing value in column Result.Value

15. Invalid value in column Result.Unit

16. Invalid value in column Result.Analytical.Method.ID

17. Invalid value in column Result.Analytical.Method.Context

18. Invalid value in column Result.Value.Type

19. Invalid value in column Result.Status.ID

20. Invalid value in column Result.Measure.Qualifier

Value

data frame of the check and check result.

DEQrmichie/odeqcdr documentation built on Feb. 15, 2025, 10:01 a.m.