Man pages for n8thangreen/IDEAdectree
Compares IDEA study clinical data with decision tree idealised pathway

addLevel_NottakenPrepend Not Taken as Extra Level
addMissingEntriesaddMissingEntries
as.Date.POSIXConvert Different Classes to Date Class
assert.dateinpastAssert dates are in the past
boot.calcIdealisedTestCostsBootstrap calculate idealised test costs [DEPRECATED]
bootstrap.dataBootstrap data
boot.testPerformanceMetricTableMake array of statistics for each bootstrap sample of IDEA...
calc.enhancedDiagTimeAndCost.bootsampleCreate an enhanced pathway individual-level dataset of time...
calc.EVPICalculate Expected Value of Information
calcExpectedINMBCalculate Expected INMB
calcIdealisedTestCostsCalculate NICE Idealised Test Costs
calcIdealisedTimetoDiagCalculate NICE Idealised Time to Diagnosis
calcPatientCostofTestsSum the Cost of All Specified Treatments for Each Patient
calcRiskFactorScoreCalculate a risk factor score for each patient
calc.statOutcomeByCovariatecalc.statOutcomeByCovariate
calc.summarystats_Dosanjh_TimeCostCalculate summary statistics to include in final tables
calcSumRowcalcSumRow
calc.testDate.minCalculate the First Test Dates for Each Patient
cleanDataClean IDEA Study Clinical Data Wrapper
combineTestResultsCombine test results
COST.distnsProbability Distribution Parameter Values for the Test and...
createCombinedGridCreate a combined grid
createDecisionTreecreateDecisionTree
createDTobjCreate Decision Tree object
create.indivpathmatrixcreate.indivpathmatrix
crosstabDosanjhCreate contingency table by Dosanjh categories of data and...
dataCleaned IDEA Study Clinical Data With Derived Fields
decisionTreeMultiple.plotPlot multiple data paths of decision tree with frequencies
decisionTree.plotPlot data paths of decision tree with frequencies
diag_SxestIdealised pathway input-diagnosis/action look-up table
diag_SxobsIdealised pathway input-diagnosis/action look-up table
EstimateSymptomsResolvedEstimate Symptoms Resolved by Whether There Was a Response to...
estimateTimeToDiagnosisRule-based Time to Diagnosis Estimation
fillInEndOfTreatmentDateFill-in End Of Treatment Dates
freqTable.DecisionTreefreqTable.DecisionTree
get.allDataTestCombinationsGet All Data Test Combinations
getDateFrequenciesGet the Date Frequencies
get.meansdOutcomeByCovariateget.meansdOutcomeByCovariate
get.meansdStartToDiagByCovariateget.meansdStartToDiagByCovariate
get.sd.from.normalCIGet standard deviation from Normal confidence interval
get.statStartToDiagByCovariateget.statStartToDiagByCovariate
get.uniqueDataTestCombinationsget.uniqueDataTestCombinations
GroupDiagOutcomesGroup Together Diagnosis Outcomes
IDEAdectree.simpleIDEA Decision Tree Calculation
INMBIncremental Net Monetary Benefit for IDEA enhanced diagnostic...
is.diagByClinicalFeaturesDistiguish Between When Clinical Features Used to Rule-in or...
is.emptyTRUE element if NA or ""
joinDataAndRulesjoinDataAndRules
joinLevelsRead From Database Extract
join.stratifiedOutcomeTablesjoin.stratifiedOutcomeTables
joinWithLookupsJoin Data Set With Demographic Look-up Tables
makeExpectedINMBtableMake Expected INMB Table
makeFollowupPlotsmakeFollowupPlots
make.ruleoutTable.bootsampleMake rule-out table of bootstrapped samples of patients
make.ruleoutTable.cat4percentMake rule-out table for multiple cohort prevalences
make.ruleoutTable.fixedmake.ruleoutTable.fixed DEPRECATED
make.ruleoutTable.FNtimeMake rule-out table for multiple follow-up times
make.ruleoutTable.highriskMake rule-out table of multiple clinically judged highrisk...
make.ruleoutTable.premake.ruleoutTable.pre
maketable.CEAC_estimatesPrint a Table of Cost-Effectiveness Acceptability Curve...
make.tableDiagCost_bootmeanseMake a table of time to diagnosis and total test costs
make.testFreqTableMake test frequency table
make.testPerformanceMetricsTableMake test performance metrics table
MoM.betaMethod of Moments Beta Distribution Parameter Transformation
MoM.gammaMethod of Moments Gamma Distribution Parameter Transformation
my.plot.bceamy.plot.bcea
my.plot.ceacMy Version of the Cost-Effectiveness Acceptability Curve Plot
plotCEAC.xSens.groupSpecCostPlot Cost-effectiveness Acceptability Curves
plotCEplanePlot Cost-Effectiveness Plane With Contours
plot.EVPIPlot Expected Value of Information curves
plot.FollowUpChartplot.FollowUpChart
plot.riskprofilePlot Risk Profile Discrete Distribution
prepDataForDecTreeprepDataForDecTree
pwayComparisonCompare data and idealised care pathways.
pwayComparison.simpleA simplified version of comparison of care pathways.
readFromDatabaseExtractRead From original IDEA Database Extract and Flatten (Tidy)
relabelDecTreeOutcomesrelabelDecTreeOutcomes
rmPatientsInCleaningRemove Patients Records In Data Cleaning
rm.TooEarlyRemove Dates That are Before the Earliest Time For the Given...
rpertBeta-PERT
sample.distributionsSample from Standard Distributions
senspec.envAn Environment Containing the Sensitivity and Specificity...
summaryTablesummaryTable
testsIdealised pathway input-diagnosis/action look-up table
testsdummy.allIdeaTestsIdealised pathway input-diagnosis/action look-up table
testsdummy.allPossTestsIdealised pathway input-diagnosis/action look-up table
testsdummy.preCultTreatAllIdealised pathway input-diagnosis/action look-up table
tidyBALSputumdataSeparate and combine BAL and sputum information
tidyCSFdataCombine CSF information
tidyCTdataTidy multiple chest X-ray data
tidyCXRdataTidy multiple chest X-ray data
writeAllFreqTableswriteAllFreqTables
n8thangreen/IDEAdectree documentation built on May 23, 2017, 9:32 a.m.