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).