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QAQC-Tools

The purpose of this repository is to act as a store of any scripts relevent to the internal QAQC process within SEACAR. Many scripts contain the variable "seacar_data_location" which points to the location where SEACAR combined tables can be found. Must be set by the user.

/comparison/

  • Script intended to highlighted differences in structure between Combined export tables
  • Generates LaTeX-based .PDF reports outlining differences
  • Currently highlights differences between exports for the following:
    • number of records (data entries)
    • number of programs
    • number of columns

ContinuousThresholdCheck.R

  • Loops through the data location (specified using the variable seacar_data_location) and looks for relevant Continuous combined tables
  • Applies thresholds as specified in the Ref_WQ_Include sheet of SEACAR_DatExportFile_Metadata (hard-coded, future solutions can include updating via Metadata file directly)
  • Stores the results that fall above or below the given threshold for each parameter, listing them in table format in threshold_data_combined
  • Summary results are viewed using View(group_df)
  • Unique SEACAR_QAQCFlagCode values are provided to see which QAQCFlagCodes are being applied by the database
  • Assuming the thresholds and their respective QAQCFlagCodes are being applied correctly on the database side, threshold_data_combined should return 0 results, and group_df will return an error upon compiling

unzip.R

  • unzip.R can be used to unzip the Combined Export Table files
  • Script should be placed into the folder where your most recent files have been downloaded
  • downloaddate variable should be set to the date listed in the .zip files using the format "YYYY-MM-DD"
  • folder_name variable is set to determine where unzipped files should be placed. Default is "SEACARdata"
  • .zip files are removed upon completion. Comment out lines 25 and 29 to keep .zip files

ParameterList.R

  • Generates a .xlsx file that records which parameters are included in Combined Export Tables and records the number of records and the data file used.

species_crosswalk_check.R

  • Generates a .csv file outlining each Habitat and CommonIdentifier, SpeciesGroup1, SpeciesGroup2 combinations available in latest combined table exports.
  • Requires the latest SEACAR_Metdata.xlsx file as an input to verify correct implementation of Mthd_SpeciesCrosswalk tab in latest exports.
  • match column (TRUE or FALSE) is created to confirm correct implementation. If all values are TRUE, the species crosswalk has been implemented correctly.

DDICitations_to_Zotero.R

  • Walks through the program list on the DDI and compiles a list of the "suggested citation" text from them.

  • Converts each citation to "Better BibLaTeX" format and saves it as a .bib file that can be imported into reference management software (e.g., for the SEACAR Zotero library).