savePredictionAnalysisList: Saves a json prediction settings given R settings

In hxia/plp-git-demo: Package for patient level prediction using data in the OMOP Common Data Model

Description

Saves a json prediction settings given R settings

Usage

savePredictionAnalysisList(
  workFolder = "inst/settings",
  cohortIds,
  outcomeIds,
  cohortSettingCsv = file.path(workFolder, "CohortsToCreate.csv"),
  covariateSettingList,
  populationSettingList,
  modelSettingList,
  maxSampleSize = NULL,
  washoutPeriod = 0,
  minCovariateFraction = 0,
  normalizeData = T,
  testSplit = "person",
  testFraction = 0.25,
  splitSeed = 1,
  nfold = 3
)

Arguments

workFolder	Location to save json specification
cohortIds	Vector of target population cohort ids
outcomeIds	Vector of outcome cohort ids
cohortSettingCsv	The location to the csv containing the cohort details
covariateSettingList	A list of covariate settings
populationSettingList	A list of population settings
modelSettingList	A list of model settings
maxSampleSize	If not NULL then max number of target population to sample for model training
washoutPeriod	Minimum prior observation for each person in target pop to be included
minCovariateFraction	Minimum covariate fraction to include
normalizeData	Whether to normalise data
testSplit	Split by person or time
testFraction	Fractiuon of data to use for test set
splitSeed	Seed used in test split
nfold	Number of folds used when training model

Details

This function interprets a json with the multiple prediction settings and creates a list that can be combined with connection settings to run a multiple prediction study

hxia/plp-git-demo documentation built on March 19, 2021, 1:54 a.m.