This function runs a set of prediction diagnoses to help pick a suitable T, O, TAR and determine whether the prediction problem is worth executing.
diagnostic(
plpData = NULL,
cdmDatabaseName,
connectionDetails,
cdmDatabaseSchema,
oracleTempSchema = NULL,
cohortId,
cohortName = cohortId,
outcomeIds,
outcomeNames = outcomeIds,
cohortDatabaseSchema,
cohortTable = "cohort",
outcomeDatabaseSchema = cohortDatabaseSchema,
outcomeTable = cohortTable,
cdmVersion = 5,
riskWindowStart = c(1, 1, 1, 1, 1),
startAnchor = rep("cohort start", 5),
riskWindowEnd = c(365, 365 * 2, 365 * 3, 365 * 4, 365 * 5),
endAnchor = rep("cohort start", 5),
outputFolder = NULL,
sampleSize = NULL,
minCellCount = 5
)The data object to do the diagnostic on - if NULL you need to specify the connection settings below
Name of the database
An R object of typeconnectionDetails created using the
function createConnectionDetails in the
DatabaseConnector package.
The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
For Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database.
A unique identifier to define the at risk cohorts. CohortId is used to select the cohort_concept_id in the cohort-like table.
A string specifying the name of the target cohort
A vector of cohort_definition_ids used to define outcomes.
A vector of names for each outcome.
The name of the database schema that is the location where the cohort data used to define the at risk cohort is available. If cohortTable = DRUG_ERA, cohortDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
The tablename that contains the at risk cohort. If cohortTable <> DRUG_ERA, then expectation is cohortTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
The name of the database schema that is the location where the data used to define the outcome cohorts is available. If cohortTable = CONDITION_ERA, exposureDatabaseSchema is not used by assumed to be cdmSchema. Requires read permissions to this database.
The tablename that contains the outcome cohorts. If outcomeTable <> CONDITION_OCCURRENCE, then expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
Define the OMOP CDM version used: currently support "4" and "5".
The start of the risk window (in days) relative to the startAnchor.
The anchor point for the start of the risk window. Can be "cohort start" or "cohort end".
The end of the risk window (in days) relative to the endAnchor parameter
The anchor point for the end of the risk window. Can be "cohort start" or "cohort end".
Location to save results for shiny app
Sample from the target population
The minimum count that will be displayed
An object containing the model or location where the model is save, the data selection settings, the preprocessing and training settings as well as various performance measures obtained by the model.
list for each O of a data.frame containing: i) Time to observation end distribution, ii) Time from observation start distribution, iii) Time to event distribution and iv) Time from last prior event to index distribution (only for patients in T who have O before index)
list for each O of incidence of O in T during TAR
list for each O of Characterization of T, TnO, Tn~O
Users can define set of Ts, Os, databases and population settings. A list of data.frames containing details such as follow-up time distribution, time-to-event information, characteriszation details, time from last prior event, observation time distribution.
# NOT RUN {
#******** EXAMPLE 1 *********
# }
Run the code above in your browser using DataLab