Man pages for n8thangreen/IDEAdectree
The IDEA study clinical data health economics analysis with decision trees
| addLevel_Nottaken | Prepend Not Taken as Extra Level |
| as.Date.POSIX | Convert Different Classes to Date Class |
| assert.dateinpast | Assert dates are in the past |
| boot.calcIdealisedTestCosts | Bootstrap calculate idealised test costs [DEPRECATED] |
| bootstrap.data | Bootstrap data |
| boot.testPerformanceMetricTable | Make array of statistics for each bootstrap sample of IDEA... |
| calc.enhancedDiagTimeAndCost.bootsample | Create an enhanced pathway individual-level dataset of time... |
| calc.EVPI | Calculate Expected Value of Information |
| calcExpectedINMB | Calculate Expected INMB |
| calcIdealisedTestCosts | Calculate NICE Idealised Test Costs |
| calcIdealisedTimetoDiag | Calculate NICE Idealised Time to Diagnosis |
| calcPatientCostofTests | Sum the Cost of All Specified Tests for Each Patient |
| calcRiskFactorScore | Calculate a risk factor score for each patient |
| calc.statOutcomeByCovariate | calc.statOutcomeByCovariate |
| calc.summarystats_Dosanjh_TimeCost | Calculate summary statistics to include in final tables |
| calc.testDate.min | Calculate the First Test Dates for Each Patient |
| cleanData | Clean IDEA Study Clinical Data Wrapper |
| combineTestResults | Combine test results |
| COST.distns | Probability Distribution Parameter Values for the Test and... |
| create.indivpathmatrix | create.indivpathmatrix |
| data | Cleaned IDEA Study Clinical Data With Derived Fields |
| diag_Sxest | Idealised pathway input-diagnosis/action look-up table |
| diag_Sxobs | Idealised pathway input-diagnosis/action look-up table |
| EstimateSymptomsResolved | Estimate Symptoms Resolved by Whether There Was a Response to... |
| estimateTimeToDiagnosis | Rule-based Time to Diagnosis Estimation |
| fillInEndOfTreatmentDate | Fill-in End Of Treatment Dates |
| get.allDataTestCombinations | Get All Data Test Combinations |
| getDateFrequencies | Get the Date Frequencies |
| get.meansdOutcomeByCovariate | get.meansdOutcomeByCovariate |
| get.meansdStartToDiagByCovariate | get.meansdStartToDiagByCovariate |
| get.sd.from.normalCI | Get standard deviation from Normal confidence interval |
| get.statStartToDiagByCovariate | get.statStartToDiagByCovariate |
| get.uniqueDataTestCombinations | get.uniqueDataTestCombinations |
| GroupDiagOutcomes | Group Together Diagnosis Outcomes |
| IDEAdectree.simple | IDEA Decision Tree Calculation |
| INMB | Incremental Net Monetary Benefit for IDEA enhanced diagnostic... |
| is.diagByClinicalFeatures | Distiguish Between When Clinical Features Used to Rule-in or... |
| is.empty | TRUE element if NA or "" |
| joinLevels | Read From Database Extract |
| join.stratifiedOutcomeTables | join.stratifiedOutcomeTables |
| joinWithLookups | Join Data Set With Demographic Look-up Tables |
| makeExpectedINMBtable | Make Expected INMB Table |
| make.ruleoutTable.bootsample | Make rule-out table of bootstrapped samples of patients |
| make.ruleoutTable.cat4percent | Make rule-out table for multiple cohort prevalences |
| make.ruleoutTable.fixed | make.ruleoutTable.fixed DEPRECATED |
| make.ruleoutTable.FNtime | Make rule-out table for multiple follow-up times |
| make.ruleoutTable.highrisk | Make rule-out table of multiple clinically judged highrisk... |
| make.ruleoutTable.pre | make.ruleoutTable.pre |
| maketable.CEAC_estimates | Print a Table of Cost-Effectiveness Acceptability Curve... |
| make.tableDiagCost_bootmeanse | Make a table of time to diagnosis and total test costs |
| make.testFreqTable | Make test frequency table |
| make.testPerformanceMetricsTable | Make test performance metrics table |
| MoM.beta | Method of Moments Beta Distribution Parameter Transformation |
| MoM.gamma | Method of Moments Gamma Distribution Parameter Transformation |
| my.plot.bcea | my.plot.bcea |
| my.plot.ceac | My Version of the Cost-Effectiveness Acceptability Curve Plot |
| plotCEAC.xSens.groupSpecCost | Plot Cost-effectiveness Acceptability Curves |
| plotCEplane | Plot Cost-Effectiveness Plane With Contours |
| plot.EVPI | Plot Expected Value of Information curves |
| plot.riskprofile | Plot Risk Profile Discrete Distribution |
| readFromDatabaseExtract | Read From original IDEA Database Extract and Flatten (Tidy) |
| rmPatientsInCleaning | Remove Patients Records In Data Cleaning |
| rm.TooEarly | Remove Dates That are Before the Earliest Time For the Given... |
| rpert | Beta-PERT |
| senspec.env | An Environment Containing the Sensitivity and Specificity... |
| summaryTable | summaryTable |
| tests | Idealised pathway input-diagnosis/action look-up table |
| testsdummy.allIdeaTests | Idealised pathway input-diagnosis/action look-up table |
| testsdummy.allPossTests | Idealised pathway input-diagnosis/action look-up table |
| testsdummy.preCultTreatAll | Idealised pathway input-diagnosis/action look-up table |
| tidyBALSputumdata | Separate and combine BAL and sputum information |
| tidyCSFdata | Combine CSF information |
| tidyCTdata | Tidy multiple chest X-ray data |
| tidyCXRdata | Tidy multiple chest X-ray data |
