Creates propensity scores using a regularized logistic regression.
createPs( cohortMethodData, population = NULL, excludeCovariateIds = c(), includeCovariateIds = c(), maxCohortSizeForFitting = 250000, errorOnHighCorrelation = TRUE, stopOnError = TRUE, prior = createPrior("laplace", exclude = c(0), useCrossValidation = TRUE), control = createControl(noiseLevel = "silent", cvType = "auto", seed = 1, tolerance = 2e-07, cvRepetitions = 10, startingVariance = 0.01) )
A data frame describing the population. This should at least have a
Exclude these covariates from the propensity model.
Include only these covariates in the propensity model.
If the target or comparator cohort are larger than this number, they will be downsampled before fitting the propensity model. The model will be used to compute propensity scores for all subjects. The purpose of the sampling is to gain speed. Setting this number to 0 means no downsampling will be applied.
If true, the function will test each covariate for correlation with the treatment assignment. If any covariate has an unusually high correlation (either positive or negative), this will throw and error.
If an error occurr, should the function stop? Else, the two cohorts will be assumed to be perfectly separable.
The prior used to fit the model. See
The control object used to control the cross-validation used to
determine the hyperparameters of the prior (if applicable). See
data(cohortMethodDataSimulationProfile) cohortMethodData <- simulateCohortMethodData(cohortMethodDataSimulationProfile, n = 1000)#> Generating covariates #> Generating treatment variable #> Generating cohorts #> Generating outcomes after index date #> Generating outcomes before index dateps <- createPs(cohortMethodData)#> Removing 1 redundant covariates #> Removing 1 infrequent covariates #> Normalizing covariates #> Tidying covariates took 0.652 secs#> Warning: All coefficients (except maybe the intercept) are zero. Either the covariates are completely uninformative or completely predictive of the treatment. Did you remember to exclude the treatment variables from the covariates?#> Creating propensity scores took 3.48 secs