Run a list of predictions

runPlpAnalyses(connectionDetails, cdmDatabaseSchema, cdmDatabaseName,
  oracleTempSchema = cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema, cohortTable = "cohort",
  outcomeDatabaseSchema = cdmDatabaseSchema, outcomeTable = "cohort",
  cdmVersion = 5, outputFolder = "./PlpOutput", modelAnalysisList,
  cohortIds, cohortNames, outcomeIds, outcomeNames, washoutPeriod = 0,
  maxSampleSize = NULL, minCovariateFraction = 0, normalizeData = T,
  testSplit = "person", testFraction = 0.25, splitSeed = NULL,
  nfold = 3, verbosity = "INFO")

Arguments

connectionDetails

An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.

cdmDatabaseSchema

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'.

cdmDatabaseName

A string with a shareable name of the database (this will be shown to OHDSI researchers if the results get transported)

oracleTempSchema

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.

cohortDatabaseSchema

The name of the database schema that is the location where the target cohorts are available. Requires read permissions to this database.

cohortTable

The tablename that contains the target cohorts. Expectation is cohortTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.

outcomeDatabaseSchema

The name of the database schema that is the location where the data used to define the outcome cohorts is available. Requires read permissions to this database.

outcomeTable

The tablename that contains the outcome cohorts. Expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.

cdmVersion

Define the OMOP CDM version used: currently support "4" and "5".

outputFolder

Name of the folder where all the outputs will written to.

modelAnalysisList

A list of objects of type modelSettings as created using the createPlpModelSettings function.

cohortIds

A vector of cohortIds that specify all the target cohorts

cohortNames

A vector of cohortNames corresponding to the cohortIds

outcomeIds

A vector of outcomeIds that specify all the outcome cohorts

outcomeNames

A vector of outcomeNames corresponding to the outcomeIds

washoutPeriod

Minimum number of prior observation days

maxSampleSize

Max number of target people to sample from to develop models

minCovariateFraction

Any covariate with an incidence less than this value if ignored

normalizeData

Whether to normalize the covariates

testSplit

How to split into test/train (time or person)

testFraction

Fraction of data to use as test set

splitSeed

The seed used for the randomization into test/train

nfold

Number of folds used to do cross validation

verbosity

The logging level

Value

A data frame with the following columns:

analysisId
The unique identifier
for a set of analysis choices.
cohortId
The ID of the target cohort populations.
outcomeId
The ID of the outcomeId.
plpDataFolder
The location where the plpData was saved
studyPopFile
Thename of the file containing the study population
evaluationFolder
The name of file containing the evaluation saved as a csv
modelFolder
The name of the file containing the developed model.

Details

Run a list of predictions for the target cohorts and outcomes of interest. This function will run all specified predictions, meaning that the total number of outcome models is `length(cohortIds) * length(outcomeIds) * length(modelAnalysisList)`.