Comprehensive Collection of Curated Benchmarking Datasets and
their Evaluation
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Documentation for package ‘BenchHub’ version 0.99.15
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| ARImetric | Adjusted Rand Index (ARI) Metric |
| balAccMetric | Balanced Accuracy Metric |
| balErrMetric | Balanced Error Metric |
| beggCIndexMetric | Begg's C-Index Metric |
| BenchmarkInsights | A BenchmarkInsights object |
| BenchmarkStudy | BenchmarkStudy Class |
| brierScoreMetric | Brier Score Metric |
| buildDatasetEvidenceSubmission | Build DatasetEvidence submission rows from a Trio object |
| buildDatasetSubmission | Build a Dataset submission row from a Trio object |
| buildDatasetTaskMetricSubmission | Build DatasetTaskMetric submission rows from a Trio object |
| buildDatasetTaskSubmission | Build DatasetTask submission rows from a Trio object |
| buildMetricSubmission | Build Metric submission rows from a Trio object |
| buildStudySubmission | Build Study and StudyDataset submission tables |
| buildStudySubmissionPayload | Convert a Study submission to payload structure |
| buildTrioSubmission | Build a combined Trio submission object |
| buildTrioSubmissionPayload | Convert a combined Trio submission to payload structure |
| collectDatasetSubmissionInfo | Collect Dataset submission metadata interactively |
| collectDatasetTaskMetricSubmission | Collect DatasetTaskMetric submission rows from Trio assignments |
| collectEvidenceSubmissionInfo | Collect DatasetEvidence submission metadata interactively |
| collectMetricSubmissionInfo | Collect Metric submission metadata interactively |
| collectStudySubmissionInfo | Collect Study submission metadata |
| collectTaskSubmissionInfo | Collect DatasetTask submission metadata interactively |
| downloadSubmissionStudy | Download a BenchmarkStudy from the submission database |
| downloadSubmissionTrio | Download a Trio from the five-table submission database |
| getSubmissionStudy | Get one existing Study row by studyID |
| getSubmissionStudyDatasets | Get linked StudyDataset rows by studyID |
| ghCIndexMetric | GH C-Index Metric |
| harrelCIndexMetric | Harrel's C-Index Metric |
| interactivePrepareStudySubmission | Interactively prepare a Study submission |
| interactivePrepareStudyUpdateSubmission | Interactively prepare a Study update submission |
| JSDmetric | Jensen-Shannon Divergence (JSD) Metric |
| kdeMetric | Kernel Density Estimation (KDE) Metric |
| listCuratedTrioDatasets | List the curated Trio datasets |
| listCuratedTrioStudies | List the curated Trio studies |
| listSubmissionStudies | List existing Study rows |
| listSubmissionStudyDatasets | List available datasets for Study submission |
| lubomPD | Human Gut Microbiome Abundance and Patient Classes |
| lubomski_microbiome_data | Human Gut Microbiome Abundance and Patient Classes |
| macroF1Metric | Macro F1 Score Metric |
| macroPrecMetric | Macro Precision Metric |
| macroRecMetric | Macro Recall Metric |
| MCCmetric | Matthews Correlation Coefficient (MCC) Metric |
| microF1Metric | Micro F1 Score Metric |
| microPrecMetric | Micro Precision Metric |
| microRecMetric | Micro Recall Metric |
| MSEmetric | Mean Squared Error (MSE) Metric |
| NMImetric | Normalized Mutual Information (NMI) Metric |
| prepareStudySubmission | Prepare a Study submission bundle |
| prepareStudyUpdateSubmission | Prepare an update submission from an existing Study version |
| prepareTrioSubmissionBundle | Build a pre-submit Trio submission bundle |
| prepareTrioSubmissionFiles | Prepare Trio files and download metadata for submission |
| prepareTrioSubmissionMetrics | Prepare Trio metric metadata for submission |
| RMSEmetric | Root Mean Squared Error (RMSE) Metric |
| studySubmissionToJSON | Convert a Study submission to JSON |
| submitStudySubmission | Submit a Study submission payload to Google Apps Script |
| submitTrioSubmission | Submit a Trio submission payload to Google Apps Script |
| timeDependentAUCMetric | Time-Dependent AUC Metric |
| Trio | A Trio object |
| trioSubmissionToJSON | Convert a combined Trio submission to JSON |
| unoCIndexMetric | Uno's C-Index Metric |
| writeSubmission | Interactively prepare a Trio submission bundle |
| x | Human Gut Microbiome Abundance and Patient Classes |