Introduction | Overview of Process | Creating the Extremely Specific (xSpec), Extremely Sensitive (xSens), Prevalence, and Evaluation Cohorts | Evaluating phenotype algorithms for health conditions | Output from the process
Package: PheValuator 2.2.18
William J. OBrien
PheValuator: Rapid Phenotype Evaluation
Evaluates phenotype algorithms by developing a diagnostic prediction model using a set of noisy positives and noisy negatives. It can then apply the model to a large cohort to create a set of subjects each with a predicted probability for the health outcome of interest. This cohort can then be used to evaluate phenotype algorithms through the calculation of the necessary performance characteristics - sensitivity, specificity, and positive and negative predictive value. Based on work by Swerdel (2022) <doi:10.1016/j.jbi.2022.104177> and Swerdel (2019) <doi:10.1016/j.jbi.2019.103258>.
Authors:
PheValuator_2.2.18.tar.gz
PheValuator_2.2.18.zip(r-4.7-any)PheValuator_2.2.18.zip(r-4.6-any)
PheValuator_2.2.18.tar.gz(r-4.7-any)PheValuator_2.2.18.tar.gz(r-4.6-any)
PheValuator_2.2.18.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PheValuator/json (API)
| # Install 'PheValuator' in R: |
| install.packages('PheValuator', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ohdsi/phevaluator/issues
Pkgdown/docs site:https://ohdsi.github.io
Last updated from:65148cdd17. Checks:4 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 160 | ||
| source / vignettes | OK | 273 | ||
| linux-release | WARNING | 157 | ||
| windows-devel | WARNING | 107 | ||
| windows-release | WARNING | 109 | ||
| wasm-release | OK | 147 |
Exports:computePerformanceMetricsFromCountscreateCreateEvaluationCohortArgscreateDefaultCovariateSettingscreateEvaluationCohortcreatePheValuatorAnalysiscreateTestPhenotypeAlgorithmArgsloadPheValuatorAnalysisListrunPheValuatorAnalysessavePheValuatorAnalysisListsummarizePheValuatorAnalysestestPhenotypeAlgorithm
Dependencies:Andromedabackportsbitbit64blobcachemcheckmateclicliprcpp11crayonCyclopsDatabaseConnectorDBIdbplyrdigestdplyrduckdbfastmapFeatureExtractiongenericsgluehmsjsonlitelatticelifecyclemagrittrMatrixmemoisememuseParallelLoggerPatientLevelPredictionpillarpkgconfigprettyunitspROCprogressPRROCpurrrR6RcppRcppEigenreadrrJavarlangRSQLiterstudioapisnowSqlRenderstringistringrsurvivaltibbletidyrtidyselecttriebeardtzdburltoolsutf8vctrsvroomwithrxml2zip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute performance metrics based on a 2-by-2 counts table | computePerformanceMetricsFromCounts |
| Create a parameter object for the function createEvaluationCohort | createCreateEvaluationCohortArgs |
| Create the default covariate settings | createDefaultCovariateSettings |
| Create the evaluation cohort | createEvaluationCohort |
| Create a PheValuator analysis specification | createPheValuatorAnalysis |
| Create a parameter object for the function testPhenotypeAlgorithm | createTestPhenotypeAlgorithmArgs |
| Load a list of phevaluatorAnalysis from file | loadPheValuatorAnalysisList |
| Run a list of analyses | runPheValuatorAnalyses |
| Save a list of phevaluatorAnalysis to file | savePheValuatorAnalysisList |
| Summarize results of PheValuator analyses | summarizePheValuatorAnalyses |
| Test phenotype algorithms | testPhenotypeAlgorithm |