Package: lrstat 0.2.10

lrstat: Power and Sample Size Calculation for Non-Proportional Hazards and Beyond

Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), and Bayesian optimal interval (BOIN) trials. For count data, it can design group sequential trials for negative binomial endpoints with censoring. Additionally, it facilitates group sequential equivalence trials for all supported data types. Moreover, it can design adaptive group sequential trials for changes in sample size, error spending function, number and spacing or future looks. Finally, it offers various options for adjusted p-values, including graphical and gatekeeping procedures.

Authors:Kaifeng Lu [aut, cre]

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lrstat.pdf |lrstat.html✨
lrstat/json (API)

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

Peer review:

Bug tracker:https://github.com/kaifenglu/lrstat/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

    On CRAN:

    5.36 score 30 scripts 571 downloads 179 exports 32 dependencies

    Last updated 15 days agofrom:79df66aa5a. Checks:OK: 1 WARNING: 8. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 22 2024
    R-4.5-win-x86_64WARNINGOct 22 2024
    R-4.5-linux-x86_64WARNINGOct 22 2024
    R-4.4-win-x86_64WARNINGOct 22 2024
    R-4.4-mac-x86_64WARNINGOct 22 2024
    R-4.4-mac-aarch64WARNINGOct 22 2024
    R-4.3-win-x86_64WARNINGOct 22 2024
    R-4.3-mac-x86_64WARNINGOct 22 2024
    R-4.3-mac-aarch64WARNINGOct 22 2024

    Exports:accrualadadaptDesignbinary_tte_simBOINTablecaltimeClopperPearsonCIcovrmsterrorSpentexitprobfadjpbonfadjpdunfadjpsimfindInterval3fmodmixfquantilefseqbonfstdmixfstp2seqftruncfwgtmatgetAccrualDurationFromNgetADCIgetADRCIgetBoundgetCIgetCPgetDesigngetDesignAgreementgetDesignANOVAgetDesignANOVAContrastgetDesignEquivgetDesignFisherExactgetDesignLogisticgetDesignMeanDiffgetDesignMeanDiffCarryovergetDesignMeanDiffEquivgetDesignMeanDiffMMRMgetDesignMeanDiffXOgetDesignMeanDiffXOEquivgetDesignMeanRatiogetDesignMeanRatioEquivgetDesignMeanRatioXOgetDesignMeanRatioXOEquivgetDesignOddsRatiogetDesignOddsRatioEquivgetDesignOneMeangetDesignOneMultinomgetDesignOneProportiongetDesignOneRateExactgetDesignOneSlopegetDesignOrderedBinomgetDesignPairedMeanDiffgetDesignPairedMeanDiffEquivgetDesignPairedMeanRatiogetDesignPairedMeanRatioEquivgetDesignPairedPropMcNemargetDesignRepeatedANOVAgetDesignRepeatedANOVAContrastgetDesignRiskDiffgetDesignRiskDiffEquivgetDesignRiskDiffExactgetDesignRiskDiffExactEquivgetDesignRiskRatiogetDesignRiskRatioEquivgetDesignRiskRatioExactgetDesignRiskRatioExactEquivgetDesignRiskRatioFMgetDesignSlopeDiffgetDesignSlopeDiffMMRMgetDesignTwoMultinomgetDesignTwoOrdinalgetDesignTwoWayANOVAgetDesignUnorderedBinomgetDesignUnorderedMultinomgetDesignWilcoxongetDurationFromNeventsgetNeventsFromHazardRatiogetRCIhdhedgesgkmdiffkmestkmpowerkmpower1skmpowerequivkmsamplesizekmsamplesize1skmsamplesizeequivkmstatkmstat1liferegrlogisregrlrpowerlrpowerequivlrsamplesizelrsamplesizeequivlrsimlrsim2elrsim2e3alrsim3alrstatlrstat1lrtestmnOddsRatioCImnRateDiffCImnRateRatioCImnRiskDiffCImnRiskRatioCImTPI2Tablenatrisknbpowernbpower1snbpowerequivnbsamplesizenbsamplesize1snbsamplesizeequivnbstatnbstat1neventnevent2patriskpdpeventphregrpowerFisherExactpowerOnePropExactpowerOneRateExactpowerRiskDiffExactpowerRiskDiffExactEquivpowerRiskRatioExactpowerRiskRatioExactEquivptpwexppwexpcutspwexploglikqrcppqtpwexpremlOddsRatioremlRateDiffremlRateRatioremlRiskDiffremlRiskRatiorepeatedPValueresiduals_phregrriskDiffExactCIriskDiffExactPValueriskRatioExactCIriskRatioExactPValuermdiffrmestrmpowerrmpower1srmpowerequivrmsamplesizermsamplesize1srmsamplesizeequivrmstrmstatrmstat1rtpwexprunShinyAppsamplesizeFisherExactsamplesizeOnePropExactsamplesizeOneRateExactsamplesizeRiskDiffExactsamplesizeRiskDiffExactEquivsamplesizeRiskRatioExactsamplesizeRiskRatioExactEquivsimon2stagesimonBayesAnalysissimonBayesSimsurvfit_phregrsurvQuantileupdateGraphzstatOddsRatiozstatRateDiffzstatRateRatiozstatRiskDiffzstatRiskRatio

    Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlifecyclelpSolvemagrittrmemoisemimemvtnormpromisesR6rappdirsRcpprlangsassshinysourcetoolswithrxtable

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    Rendered fromdirect_approximation_vs_schoenfeld.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-05-07
    Started: 2022-08-04

    Multiplicity Adjustment for Group Sequential Designs

    Kaifeng Lu

    Rendered fromgroup_sequential_multiplicity.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-05-07
    Started: 2023-02-06

    Power Calculation Using Max-Combo Tests

    Kaifeng Lu

    Rendered frommaxcombo.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-05-07
    Started: 2022-07-25

    Power Calculation With Stratification Variables

    Kaifeng Lu

    Rendered fromstratified.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-05-07
    Started: 2022-07-25

    Sample Size Calculation Under Non-Proportional Hazards

    Kaifeng Lu

    Rendered fromnon-proportional_hazards.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-05-07
    Started: 2022-07-25

    Sample Size Calculation With Fixed Follow-up

    Kaifeng Lu

    Rendered fromfixed_follow-up.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-10-22
    Started: 2022-07-25

    Simulation for Group Sequential Trials

    Kaifeng Lu

    Rendered fromgroup_sequential_simulation.Rmdusingknitr::rmarkdownon Oct 22 2024.

    Last update: 2024-02-27
    Started: 2022-07-25

    Readme and manuals

    Help Manual

    Help pageTopics
    Power and Sample Size Calculation for Non-Proportional Hazards and Beyondlrstat-package
    Number of Enrolled Subjectsaccrual
    Adaptive Design at an Interim LookadaptDesign
    Calendar Times for Target Number of Eventscaltime
    Error SpendingerrorSpent
    Stagewise Exit Probabilitiesexitprob
    Adjusted p-Values for Bonferroni-Based Graphical Approachesfadjpbon
    Adjusted p-Values for Dunnett-Based Graphical Approachesfadjpdun
    Adjusted p-Values for Simes-Based Graphical Approachesfadjpsim
    Adjusted p-Values for Modified Mixture Gatekeeping Proceduresfmodmix
    Group Sequential Trials Using Bonferroni-Based Graphical Approachesfseqbon
    Adjusted p-Values for Standard Mixture Gatekeeping Proceduresfstdmix
    Adjusted p-Values for Stepwise Testing Procedures for Two Sequencesfstp2seq
    Weight Matrix for All Intersection Hypothesesfwgtmat
    Accrual Duration to Enroll Target Number of SubjectsgetAccrualDurationFromN
    Efficacy Boundaries for Group Sequential DesigngetBound
    Power and Sample Size for a Generic Group Sequential DesigngetDesign
    Range of Accrual Duration for Target Number of EventsgetDurationFromNevents
    Required Number of Events Given Hazard RatiogetNeventsFromHazardRatio
    Kaplan-Meier Estimates of Survival Curvekmest
    Log-Rank Test Powerlrpower
    Log-Rank Test Sample Sizelrsamplesize
    Log-Rank Test Simulationlrsim
    Log-Rank Test Simulation for Two Endpointslrsim2e
    Log-Rank Test Simulation for Two Endpoints and Three Armslrsim2e3a
    Log-Rank Test Simulation for Three Armslrsim3a
    Number of Subjects Having an Event and Log-Rank Statisticslrstat
    Quantile Function of Truncated Piecewise Exponential Distributionqtpwexp
    Repeated p-Values for Group Sequential DesignrepeatedPValue
    Update Graph for Graphical ApproachesupdateGraph