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Extract the model design diagnostics for a specific development database

Source: R/PredictionQueries.R
getPredictionDiagnostics.Rd

This function extracts the PROBAST diagnostics

Usage

getPredictionDiagnostics(
  connectionHandler,
  schema,
  plpTablePrefix = "plp_",
  cgTablePrefix = "cg_",
  databaseTable = "database_meta_data",
  databaseTablePrefix = "",
  modelDesignId = NULL,
  threshold1_2 = 0.9
)

Arguments

connectionHandler

A connection handler that connects to the database and extracts sql queries. Create a connection handler via `ResultModelManager::ConnectionHandler$new()`.

schema

The result database schema (e.g., 'main' for sqlite)

plpTablePrefix

The prefix used for the patient level prediction results tables

cgTablePrefix

The prefix used for the cohort generator results tables

databaseTable

The name of the table with the database details (default 'database_meta_data')

databaseTablePrefix

The prefix for the database table either ” or 'plp_'

modelDesignId

The identifier for a model design to restrict results to

threshold1_2

A threshold for probast 1.2

Value

Returns a data.frame with the columns:

  • modelDesignId the unique identifier for the model design

  • diagnosticId the unique identifier for diagnostic result

  • developmentDatabaseName the name for the database used to develop the model

  • developmentTargetName the name for the development target population

  • developmentOutcomeName the name for the development outcome

  • probast1_1 Were appropriate data sources used, e.g., cohort, RCT, or nested case-control study data?

  • probast1_2 Were all inclusions and exclusions of paticipants appropriate?

  • probast2_1 Were predictors defined and assessed in a similar way for all participants?

  • probast2_2 Were predictors assessments made without knowledge of outcome data?

  • probast2_3 All all predictors available at the time the model is intended to be used?

  • probast3_4 Was the outcome defined and determined in a similar way for all participants?

  • probast3_6 Was the time interval between predictor assessment and outcome determination appropriate?

  • probast4_1 Were there a reasonable number of participants with the outcome?

Details

Specify the connectionHandler, the resultDatabaseSettings and (optionally) a modelDesignId and threshold1_2 a threshold value to use for the PROBAST 1.2

See also

Other Prediction: getPredictionCohorts(), getPredictionDiagnosticTable(), getPredictionHyperParamSearch(), getPredictionIntercept(), getPredictionModelDesigns(), getPredictionPerformanceTable(), getPredictionPerformances(), getPredictionTopPredictors()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver

diag <- getPredictionDiagnostics(
  connectionHandler = connectionHandler, 
  schema = 'main'
)