Phevaluator module - #294
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![O'Brien, William [JRDUS]](https://github.githubassets.com/images/gravatars/gravatar-user-420.png){kind=avatar}
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@ob325 thanks for adding this new module! I see that some of the new PheValuator unit tests are failing when running the R CMD checks. Could you take a look and fix those up? I'll then give this a closer review. Thanks! |
| #' } | ||
| #' } | ||
| createModuleSpecifications = function(analysisName = "Main", | ||
| cohortDefinitionSet = data.frame(), |
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@ob325 - we specify the cohort definition set as part of the "Shared Resources" section when constructing the overall Strategus analysis specification. So I'd expect that all cohorts you would have in your pheValuatorAnalysisList are included in that section of the analysis specification. This would include the phenotypeCohortId, xSpecCohortId, xSensCohortId, prevalenceCohortId.
| for (analysisSpec in spec$pheValuatorAnalysisList) { | ||
| private$.executeAnalysis( | ||
| analysisSpec = analysisSpec, | ||
| connectionDetails = connectionDetails, | ||
| executionSettings = executionSettings, | ||
| jobContext = jobContext, | ||
| outputFolder = outputFolder, | ||
| resultsFolder = resultsFolder | ||
| ) | ||
| } |
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Can we consider adding some messages using the cli package to indicate progress through this loop?
| pvModuleSpecifications <- pvModuleSettingsCreator$createModuleSpecifications( | ||
| phenotype = "Type 2 Diabetes", | ||
| pheValuatorAnalysisList = list( | ||
| list( | ||
| analysisId = 1, | ||
| description = "Test PheValuator analysis", | ||
| createEvaluationCohortArgs = list(xSpecCohortId = 1), | ||
| testPhenotypeAlgorithmArgs = list(phenotypeCohortId = 3, cutPoints = c("EV")) | ||
| ) | ||
| ) | ||
| ) |
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This code is currently failing in the unit tests since the function signature changed.
2 participants
This adds the PheValuator module, closes #279