Reference Interval Estimation using Real-World Data

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Documentation for package ‘refineR’ version 2.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

refineR-package	refineR: Reference Interval Estimation using Real-World Data (RWD)
addGrid	Add a grid to an existing plot.
alignVec	Helper function to align the content of printed tables
as.rgb	Convert color-names or RGB-code to possibly semi-transparent RGB-code.
ashDensity	Estimate density of distribution employing the R package "ash" using R-wrapper function.
BoxCox	One-parameter Box-Cox transformation.
calculateCostHist	Calculate costs for a specific combinations of lambda, muVec and sigmaVec.
cdfTruncatedBoxCox	Function to calculate the RI from a set of parameters
checkInvalidArgs	Check Invalid Arguments
createVerificationTab	Create Verification Table
defineSearchRegions	Helper function to define search regions for mu and sigma and to get the region around the main peak 'ab'
estimateAB	Helper function to find region around the main peak of a distribution
findMainPeak	Helper function to find the main peak of a distribution
findPeaksAndValleys	Find the index of the peaks and valleys of the density estimation.
findRI	Function to estimate reference intervals for a single population
findRoundingBase	Estimate rounding base of the input data.
generateHistData	Generate list with histogram data.
getEquivalenceLimits	Calculate equivalence limits
getRI	Method to calculate reference intervals (percentiles) for objects of class 'RWDRI'
getRIfromRWDRI	Get Reference Interval from RWDRI
getRIMargins	Calculate uncertainty margins for a reference interval using the asymptotic method
getRISimilarity	Calculate similarity of two reference intervals
getSumForPArea	Helper function to calculate the amount of observed and estimated data points within specified regions around the peak.
getVerificationArgs	Get the correct values for RI, RIperc, Lambda, and Shift for the verification
invBoxCox	Inverse of the one-parameter Box-Cox transformation.
optimizeGrid	Helper function for grid search for mu and sigma.
perc_ci_asymptotic	Function to approximate the sampling uncertainty of quantiles using the asymptotic method
plot.RWDRI	Standard plot method for objects of class 'RWDRI'
plotRIVerification	Plot method for RI verification
pnormApprox	Approximate calculation of CDF of normal distribution.
print.RWDRI	Standard print method for objects of class 'RWDRI'
printDataFractionWithinOutsideRI	Print Data Fractions Within and Outside Reference Intervals
printSimilarityTable	Helper function to print the results of getRISimilarity
printTableHeader	Helper function to print Table Header
printTableRows	Helper function to print Table Rows
printVerificationTable	Print Verification Table
refineR	refineR: Reference Interval Estimation using Real-World Data (RWD)
testcase1	Simulated Testcase 1.
testcase2	Simulated Testcase 2.
testcase3	Simulated Testcase 3.
testcase4	Simulated Testcase 4.
testcase5	Simulated Testcase 5.
testParam	Helper function to find optimal parameters lambda, mu and sigma.
verifyRI	Verify Reference Intervals