executeDbProfile — executeDbProfile • DbDiagnostics

executeDbProfile

executeDbProfile(
  connectionDetails,
  cdmDatabaseSchema,
  resultsDatabaseSchema,
  writeTo,
  vocabDatabaseSchema,
  cdmSourceName = NA,
  siteName = NA,
  siteOHDSIParticipation = NA,
  siteOHDSIRunPackage = NA,
  dataFullName = NA,
  dataShortName = NA,
  dataContactName = NA,
  dataContactEmail = NA,
  dataDoiType = NA,
  governanceTime = NA,
  dataProvenance = NA,
  refreshTime = NA,
  outputFolder = getwd(),
  cdmVersion = "5.3",
  appendAchilles = FALSE,
  minCellCount = 5,
  roundTo = 10,
  excludedConcepts = c(),
  addDQD = FALSE,
  tableCheckThresholds = "default",
  fieldCheckThresholds = "default",
  conceptCheckThresholds = "default"
)

Arguments

connectionDetails: A connectionDetails object for connecting to the CDM database
cdmDatabaseSchema: The fully qualified database name of the CDM schema
resultsDatabaseSchema: The fully qualified database name of the results schema where achilles results are held
writeTo: The fully qualified schema you have write access to. This will be used to store any missing analyses that need to be run.
vocabDatabaseSchema: The fully qualified database name of the vocabulary schema
cdmSourceName: A string containing the name of the database
siteName: The name of the site or institution that owns or licenses the data.
siteOHDSIParticipation: Yes/No if the site contributed to an OHDSI study in the past
siteOHDSIRunPackage: Yes/No if site has someone who can run and/or debug an OHDSI study package
dataFullName: The full name of the database
dataShortName: The short name or nickname of the database
dataContactName: The name of the person who should be contacted in the event this database is identified as a good candidate for a study
dataContactEmail: The email address of the person who should be contacted in the event this database is identified as a good candidate for a study
dataDoiType: The type of data object identifier (DOI) the database has. Options are "DOI", "CURIE", "ARK", "Other",
governanceTime: How long (in weeks) it typically takes to receive approval to run a study on this database
dataProvenance: The type(s) of data that are present in your database. Options are "Electronic Health Records", "Administrative Claims", "Disease-specific Registry", "Wearable or Sensor Data", "Other".
refreshTime: How often the data are refreshed
outputFolder: Results will be written to this directory, Default = getwd()
cdmVersion: The CDM version to target for the data source. Default = "5.3"
appendAchilles: Specify if any missing achilles analyses should be appended to existing achilles results tables. This requires write access to the schema specified in the resultsDatabaseSchema. Default is FALSE meaning any missing analyses will be written to the schema specified in the writeTo parameter.
minCellCount: Minimum cell count to allow in analyses. Default = 0
roundTo: Specify whether to round to the 10s or 100s place. Valid inputs are 10 or 100, default is 10.
excludedConcepts: A vector of concepts that should not be included in the final file "achilles_results_augmented.csv". This is the file that is shared with as part of the OHDSI network initiative.
addDQD: Specify if DQD should be run. Default = TRUE
tableCheckThresholds: OPTIONAL Location of the custom threshold file for the DQD table checks. In absence of this parameter the default thresholds are used.
fieldCheckThresholds: OPTIONAL Location of the custom threshold file for the DQD field checks. In absence of this parameter the default thresholds are used.
conceptCheckThresholds: OPTIONAL Location of the custom threshold file for the DQD concept checks. In absence of this parameter the default thresholds are used.