Package: refineR 1.6.2

Tatjana Ammer

refineR: Reference Interval Estimation using Real-World Data

Indirect method for the estimation of reference intervals using Real-World Data ('RWD'). It takes routine measurements of diagnostic tests, containing pathological and non-pathological samples as input and uses sophisticated statistical methods to derive a model describing the distribution of the non-pathological samples. This distribution can then be used to derive reference intervals. Furthermore, the package offers functions for printing and plotting the results of the algorithm. See ?refineR for a more comprehensive description of the features. Version 1.0 of the algorithm is described in detail in 'Ammer et al. (2021)' <doi:10.1038/s41598-021-95301-2>. Additional guidance on the usage of the algorithm is given in 'Ammer et al. (2023)' <doi:10.1093/jalm/jfac101>.

Authors:Tatjana Ammer [aut, cre], Christopher M Rank [aut], Andre Schuetzenmeister [aut]

refineR_1.6.2.tar.gz
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refineR_1.6.2.tgz(r-4.4-emscripten)refineR_1.6.2.tgz(r-4.3-emscripten)
refineR.pdf |refineR.html✨
refineR/json (API)
NEWS

# Install 'refineR' in R:
install.packages('refineR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.18 score 1 stars 15 scripts 257 downloads 1 mentions 6 exports 8 dependencies

Last updated 4 months agofrom:fc1ab46f12. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-linuxOKNov 20 2024

Exports:BoxCoxfindRIgetRIinvBoxCoxplot.RWDRIprint.RWDRI

Dependencies:ashcodetoolsdigestfuturefuture.applyglobalslistenvparallelly

refineR: Reference Interval Estimation using Real-World Data (RWD)

Tatjana Ammer & Christopher M Rank

Rendered fromrefineR_package.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2023-11-15
Started: 2022-07-19

Readme and manuals

Help Manual

Help pageTopics
refineR: Reference Interval Estimation using Real-World Data (RWD)refineR-package refineR
Add a grid to an existing plot.addGrid
Convert color-names or RGB-code to possibly semi-transparent RGB-code.as.rgb
Estimate density of distribution employing the R package "ash" using R-wrapper function.ashDensity
One-parameter Box-Cox transformation.BoxCox
Calculate costs for a specific combinations of lambda, muVec and sigmaVec.calculateCostHist
Helper function to define search regions for mu and sigma and to get the region around the main peak 'ab'defineSearchRegions
Helper function to find region around the main peak of a distributionestimateAB
Helper function to find the main peak of a distributionfindMainPeak
Find the index of the peaks and valleys of the density estimation.findPeaksAndValleys
Function to estimate reference intervals for a single populationfindRI
Estimate rounding base of the input data.findRoundingBase
Generate list with histogram data.generateHistData
Method to calculate reference intervals (percentiles) for objects of class 'RWDRI'getRI
Helper function to calculate the amount of observed and estimated data points within specified regions around the peak.getSumForPArea
Inverse of the one-parameter Box-Cox transformation.invBoxCox
Helper function for grid search for mu and sigma.optimizeGrid
Standard plot method for objects of class 'RWDRI'plot.RWDRI
Approximate calculation of CDF of normal distribution.pnormApprox
Standard print method for objects of class 'RWDRI'print.RWDRI
Simulated Testcase 1.testcase1
Simulated Testcase 2.testcase2
Simulated Testcase 3.testcase3
Simulated Testcase 4.testcase4
Simulated Testcase 5.testcase5
Helper function to find optimal parameters lambda, mu and sigma.testParam