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 2.2.17
Joel N. Swerdel
PheValuator: Rapid Phenotype Evaluation
A package for evaluating phenotype algorithms. The package develops 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 preditive value.
Authors:
PheValuator_2.2.17.tar.gz
PheValuator_2.2.17.zip(r-4.7-any)PheValuator_2.2.17.zip(r-4.6-any)PheValuator_2.2.17.zip(r-4.5-any)
PheValuator_2.2.17.tgz(r-4.6-any)PheValuator_2.2.17.tgz(r-4.5-any)
PheValuator_2.2.17.tar.gz(r-4.7-any)PheValuator_2.2.17.tar.gz(r-4.6-any)
PheValuator_2.2.17.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://ohdsi.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:81cdb797d1. Checks:7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 197 | ||
| source / vignettes | OK | 454 | ||
| linux-release | WARNING | 205 | ||
| macos-release | WARNING | 132 | ||
| macos-oldrel | WARNING | 140 | ||
| windows-devel | WARNING | 169 | ||
| windows-release | WARNING | 182 | ||
| windows-oldrel | WARNING | 122 | ||
| wasm-release | OK | 143 |
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 |