Merge pull request #149 from OHDSI/fitOutcomeModel-tests

Fit outcome model tests

R/OutcomeModels.R

@@ -80,6 +80,10 @@ fitOutcomeModel <- function(population,
  )) {
  errorMessages <- checkmate::makeAssertCollection()
  checkmate::assertDataFrame(population, null.ok = TRUE, add = errorMessages)
+ checkmate::assertNames(names(population), must.include = c("rowId", "outcomeCount", "treatment", "timeAtRisk", "personSeqId"), add = errorMessages)
+ if (!is.null(cohortMethodData)) {
+ checkmate::assertNames(names(cohortMethodData), must.include = c("analysisRef", "cohorts", "covariateRef", "covariates", "outcomes"), add = errorMessages)
+ }
  checkmate::assertClass(cohortMethodData, "CohortMethodData", null.ok = TRUE, add = errorMessages)
  checkmate::assertChoice(modelType, c("logistic", "poisson", "cox"), add = errorMessages)
  checkmate::assertLogical(stratified, len = 1, add = errorMessages)
@@ -96,9 +100,6 @@ fitOutcomeModel <- function(population,
  if (stratified && nrow(population) > 0 && is.null(population$stratumId)) {
  stop("Requested stratified analysis, but no stratumId column found in population. Please use matchOnPs or stratifyByPs to create strata.")
  }
- if (is.null(population$outcomeCount)) {
- stop("No outcome variable found in population object. Use createStudyPopulation to create variable.")
- }
  if (is.null(cohortMethodData) && useCovariates) {
  stop("Requested all covariates for model, but no cohortMethodData object specified")
  }
@@ -108,6 +109,9 @@ fitOutcomeModel <- function(population,
  if (any(excludeCovariateIds %in% interactionCovariateIds)) {
  stop("Can't exclude covariates that are to be used for interaction terms")
  }
+ if (any(includeCovariateIds %in% excludeCovariateIds)) {
+ stop("Can't exclude covariates that are to be included")
+ }
  if (inversePtWeighting && is.null(population$iptw)) {
  stop("Requested inverse probability weighting, but no IPTW are provided. Use createPs to generate them")
  }