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lrstat

The goal of lrstat is to calculate power and sample size under non-proportional hazards using weighted log-rank tests both analytically and using simulations in a time-to-event group-sequential trial.

It has built-in capabilities to use error-spending functions and can calcualte power, accrual duration, follow-up duration, and absolute accrual rates for the Fleming-Harrington's class of weighting functions.

Example

This is a basic example which shows you how to solve a common problem:

library(lrstat)
## basic example code for a two-stage group sequential trial with interim
## analysis at 80% of total number of events using Lan-DeMets O'Brien-Fleming
## error-spending. The accrual has a ramp-up periof of 9 months before 
## reaching 26 patients per month. The survival distribution for the treatment
## group has a delay effect of 6 months and a hazard ratio 0.58 after the delay. 
## The annual dropout rate is 5%. The accrual duration is 22 months. 
## The follow-up duration is 18 months for the last randomized patients. 
## The FH(0,1) weighted log-rank test is used for power calculation. 

lrpower(kMax = 2, informationRates = c(0.8, 1),
        alpha = 0.025, typeAlphaSpending = "sfOF",
        allocationRatioPlanned = 1, accrualTime = seq(0, 9),
        accrualIntensity = c(26/9*seq(1, 9), 26),
        piecewiseSurvivalTime = c(0, 6),
        lambda1 = c(0.0533, 0.0309),
        lambda2 = c(0.0533, 0.0533),
        gamma1 = -log(1-0.05)/12,
        gamma2 = -log(1-0.05)/12, 
        accrualDuration = 22,
        followupTime = 18, fixedFollowup = FALSE, 
        rho1 = 0, rho2 = 1,
        numSubintervals = 2000)

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Version

Install

install.packages('lrstat')

Monthly Downloads

731

Version

0.2.15

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/kaifenglu/lrstat

Maintainer

Kaifeng Lu

Last Published

July 14th, 2025

Functions in lrstat (0.2.15)

ClopperPearsonCI

Clopper-Pearson Confidence Interval for One-Sample Proportion

Calendar Times for Target Number of Events

Number of Enrolled Subjects

Simulation for a Binary and a Time-to-Event Endpoint in Group Sequential Trials

Adaptive Design at an Interim Look

Number of Patients Enrolled During an Interval and Having an Event by Specified Calendar Times

BOIN Decision Table for Dose-Finding Trials

Covariance Between Restricted Mean Survival Times

Adjusted p-Values for Standard Mixture Gatekeeping Procedures

Adjusted p-Values for Modified Mixture Gatekeeping Procedures

The Quantiles of a Survival Distribution

Group Sequential Trials Using Bonferroni-Based Graphical Approaches

Adjusted p-Values for Dunnett-Based Graphical Approaches

Adjusted p-Values for Simes-Based Graphical Approaches

Acute myelogenous leukemia survival data from the survival package

Repeated Confidence Interval After Adaptation

Adjusted p-Values for Bonferroni-Based Graphical Approaches

Stagewise Exit Probabilities

float_to_fraction

Converting a decimal to a fraction

Find Interval Numbers of Indices

getAccrualDurationFromN

Accrual Duration to Enroll Target Number of Subjects

Conditional Power Allowing for Varying Parameter Values

Adjusted p-Values for Holm, Hochberg, and Hommel Procedures

Adjusted p-Values for Stepwise Testing Procedures for Two Sequences

Power and Sample Size for a Generic Group Sequential Design

getDesignMeanDiff

Group Sequential Design for Two-Sample Mean Difference

getDesignMeanDiffCarryover

Power and Sample Size for Direct Treatment Effects in Crossover Trials

getDesignAgreement

Power and Sample Size for Cohen's kappa

Power and Sample Size for a Generic Group Sequential Equivalence Design

getDesignMeanDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Difference

Weight Matrix for All Intersection Hypotheses

getDesignMeanDiffCarryoverEquiv

Power and Sample Size for Equivalence in Direct Treatment Effects in Crossover Trials

Confidence Interval After Adaptation

getDesignLogistic

Power and Sample Size for Logistic Regression

Confidence Interval After Trial Termination

Efficacy Boundaries for Group Sequential Design

getDesignFisherExact

Power and Sample Size for Fisher's Exact Test for Two Proportions

Power and Sample Size for One-Way ANOVA

getDesignANOVAContrast

Power and Sample Size for One-Way ANOVA Contrast

getDesignMeanRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Ratio

getDesignMeanDiffXO

Group Sequential Design for Mean Difference in 2x2 Crossover

getDesignMeanDiffMMRM

Group Sequential Design for Two-Sample Mean Difference From the MMRM Model

getDesignMeanRatioXO

Group Sequential Design for Mean Ratio in 2x2 Crossover

getDesignMeanDiffXOEquiv

Group Sequential Design for Equivalence in Mean Difference in 2x2 Crossover

getDesignMeanRatioXOEquiv

Group Sequential Design for Equivalence in Mean Ratio in 2x2 Crossover

getDesignPairedMeanDiffEquiv

Group Sequential Design for Equivalence in Paired Mean Difference

getDesignOddsRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Odds Ratio

getDesignOneMean

Group Sequential Design for One-Sample Mean

getDesignOddsRatio

Group Sequential Design for Two-Sample Odds Ratio

getDesignRiskRatioExact

Power and Sample Size for Exact Unconditional Test for Risk Ratio

getDesignRiskRatioExactEquiv

Power and Sample Size for Exact Unconditional Test for Equivalence in Risk Ratio

getDesignOrderedBinom

Power and Sample Size for Cochran-Armitage Trend Test for Ordered Multi-Sample Binomial Response

getDesignOneRateExact

Power and Sample Size for One-Sample Poisson Rate Exact Test

getDesignPairedMeanDiff

Group Sequential Design for Paired Mean Difference

getDesignPairedMeanRatioEquiv

Group Sequential Design for Equivalence in Paired Mean Ratio

getDesignMeanRatio

Group Sequential Design for Two-Sample Mean Ratio

getDesignPairedMeanRatio

Group Sequential Design for Paired Mean Ratio

getDesignPairedPropMcNemar

Group Sequential Design for McNemar's Test for Paired Proportions

getDesignOneMultinom

Power and Sample Size for One-Sample Multinomial Response

getDesignSlopeDiffMMRM

Group Sequential Design for Two-Sample Slope Difference From the MMRM Model

getDesignTwoMultinom

Power and Sample Size for Difference in Two-Sample Multinomial Responses

getDesignRiskDiffExact

Power and Sample Size for Exact Unconditional Test for Risk Difference

getDesignRepeatedANOVAContrast

Power and Sample Size for One-Way Repeated Measures ANOVA Contrast

getDesignRepeatedANOVA

Power and Sample Size for Repeated-Measures ANOVA

getDesignOneSlope

Group Sequential Design for One-Sample Slope

getDesignRiskDiffExactEquiv

Power and Sample Size for Exact Unconditional Test for Equivalence in Risk Difference

getDesignSlopeDiff

Group Sequential Design for Two-Sample Slope Difference

getDesignRiskRatioFM

Group Sequential Design for Two-Sample Risk Ratio Based on the Farrington-Manning Score Test

Hedges' g Effect Size

Simulated CONCORDE trial data from the rpsftm package

getDesignRiskRatio

Group Sequential Design for Two-Sample Risk Ratio

getDesignOneProportion

Group Sequential Design for One-Sample Proportion

The binary data from Cox and Snell (1989, pp. 10-11).

Power for Equivalence in Milestone Survival Probability Difference

Power for One-Sample Milestone Survival Probability

Repeated Confidence Interval for Group Sequential Design

getNeventsFromHazardRatio

Required Number of Events Given Hazard Ratio

getDesignWilcoxon

Group Sequential Design for Two-Sample Wilcoxon Test

getDurationFromNevents

Range of Accrual Duration for Target Number of Events

getDesignRiskRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Ratio

getDesignTwoWayANOVA

Power and Sample Size for Two-Way ANOVA

getDesignTwoOrdinal

Power and Sample Size for the Wilcoxon Test for Two-Sample Ordinal Response

getDesignRiskDiff

Group Sequential Design for Two-Sample Risk Difference

getDesignUnorderedBinom

Power and Sample Size for Unordered Multi-Sample Binomial Response

getDesignRiskDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Difference

Log-Rank Test Simulation

Schoenfeld Method for Log-Rank Test Sample Size Calculation

Sample Size for Difference in Milestone Survival Probabilities

Hazard Function for Progressive Disease (PD)

Hazard Function for Sub Population

Estimate of Milestone Survival Difference

Sample Size for One-Sample Milestone Survival Probability

Number of Subjects Having an Event and Log-Rank Statistic for a hypothesized hazard ratio at a given calendar time

Kaplan-Meier Estimates of Survival Curve

Log-Rank Test of Survival Curve Difference

Power for Difference in Milestone Survival Probabilities

kmsamplesizeequiv

Sample Size for Equivalence in Milestone Survival Probability Difference

Stratified Difference in Milestone Survival Probabilities

Power for Equivalence in Hazard Ratio

Log-Rank Test Power

getDesignUnorderedMultinom

Power and Sample Size for Unordered Multi-Sample Multinomial Response

Integrated Event Probability Over an Interval With Constant Hazard

Log-Rank Test Sample Size

lrsamplesizeequiv

Sample Size for Equivalence in Hazard Ratio

Stanford heart transplant data from the survival package

mTPI-2 Decision Table

param_accrualIntensity

Parameter Description: accrualIntensity

Miettinen-Nurminen Score Confidence Interval for Two-Sample Odds Ratio

param_lambda2_stratified

Parameter Description: lambda2_stratified

nbsamplesizeequiv

Sample Size for Equivalence in Negative Binomial Rate Ratio

Parameter Description: lambda2

param_accrualTime

Parameter Description: accrualTime

param_fixedFollowup

Parameter Description: fixedFollowup

param_estimateHazardRatio

Parameter Description: estimateHazardRatio

Log-Rank Test Simulation for Three Arms

Log-Rank Test Simulation for Enrichment Design

Logistic Regression Models for Binary Data

Parametric Regression Models for Failure Time Data

Milestone Survival Probability by Stratum

Log-Rank Test Simulation for Two Endpoints

Miettinen-Nurminen Score Confidence Interval for Two-Sample Risk Difference

Miettinen-Nurminen Score Confidence Interval for Two-Sample Risk Ratio

Log-Rank Test Simulation for Two Endpoints and Three Arms

param_criticalValues

Parameter Description: criticalValues

Kaplan-Meier Survival Probability Based on Pooled Sample

param_efficacyStopping

Parameter Description: efficacyStopping

param_futilityBounds

Parameter Description: futilityBounds

param_followupTime

Parameter Description: followupTime

Negative Binomial Rate Ratio

Parameter Description: rho1

param_piecewiseSurvivalTime

Parameter Description: piecewiseSurvivalTime

powerFisherExact

Power for Fisher's Exact Test for Two Proportions

powerOnePropExact

Power for Binomial One-Sample Exact Test

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

Negative Binomial Rate Ratio by Stratum

Sample Size for One-Sample Negative Binomial Rate

Number of Subjects Having an Event

Sample Size for Negative Binomial Rate Ratio

Parameter Description: gamma1

param_gamma1_stratified

Parameter Description: gamma1_stratified

param_minFollowupTime

Parameter Description: minFollowupTime

Parameter Description: gamma2

param_typeOfComputation

Parameter Description: typeOfComputation

Probability of Having an Event

param_gamma2_stratified

Parameter Description: gamma2_stratified

param_userAlphaSpending

Parameter Description: userAlphaSpending

param_maxFollowupTime

Parameter Description: maxFollowupTime

Miettinen-Nurminen Score Confidence Interval for Two-Sample Rate Difference

print.designANOVA

Print Power and Sample Size Results for One-Way ANOVA

Miettinen-Nurminen Score Confidence Interval for Two-Sample Rate Ratio

print.designANOVAContrast

Print Power and Sample Size Results for a Single Contrast in One-Way ANOVA

Number of Subjects Having an Event and Log-Rank Statistics

param_typeBetaSpending

Parameter Description: typeBetaSpending

Parameter Description: lambda1

param_lambda1_stratified

Parameter Description: lambda1_stratified

param_typeAlphaSpending

Parameter Description: typeAlphaSpending

Number of Subjects Having an Event by Calendar Time

Power for One-Sample Negative Binomial Rate

Power for Equivalence in Negative Binomial Rate Ratio

Proportional Hazards Regression Models

param_accrualDuration

Parameter Description: accrualDuration

Distribution Function of the Standard Bivariate Normal

Integrated Event Probability Over an Interval

powerRiskRatioExact

Power for Exact Unconditional Test of Risk Ratio

powerRiskDiffExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Difference

print.designMeanDiffMMRM

Print Power and Sample Size Results for Two-Sample Mean Difference at the Last Time Point From the MMRM Model

print.designMeanDiffEquiv

Print Power and Sample Size Results for Equivalence in Two-Sample Mean Difference

powerOneRateExact

Power for Poisson One-Sample Exact Test

powerRiskDiffExact

Power for Exact Unconditional Test of Risk Difference

print.designOneSlope

Print Power and Sample Size Results for One-Sample Slope

Power for Negative Binomial Rate Ratio

Number of Subjects at Risk

print.designOneProportion

Print Power and Sample Size Results for One-Sample Proportion

print.designPairedMeanDiff

Print Power and Sample Size Results for Paired Mean Difference

print.designPairedMeanRatioEquiv

Print Power and Sample Size Results for Equivalence in Paired Mean Ratio

print.designMeanRatioXOEquiv

Print Power and Sample Size Results for Equivalence in Mean Ratio in 2x2 Crossover

print.designOrderedBinom

Print Power and Sample Size Results for Cochran-Armitage Trend Test for Ordered Multi-Sample Binomial Response

print.designMeanDiffCarryoverEquiv

Print Power and Sample Size Results for Equivalence in Direct Treatment Effects in Crossover Trials With or Without Accounting for Carryover Effects

print.designMeanRatioXO

Print Power and Sample Size Results for Mean Ratio in 2x2 Crossover

print.designMeanDiffCarryover

Print Power and Sample Size Results for Direct Treatment Effects in Crossover Trials With or Without Accounting for Carryover Effects

print.designPairedPropMcNemar

Print Power and Sample Size Results for McNemar's Test for Paired Proportions

powerRiskRatioExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Ratio

print.designWilcoxon

Print Power and Sample Size Results for Two-Sample Wilcoxon Test

print.estimateCI

Print the Point Estimate and Confidence Interval

Parameter Description: alpha

param_allocationRatioPlanned

Parameter Description: allocationRatioPlanned

print.designRiskRatio

Print Power and Sample Size Results for Two-Sample Risk Ratio

Parameter Description: gamma

param_futilityStopping

Parameter Description: futilityStopping

print.BOINTable

Print the Decision Table for the BOIN Design

print.designMeanRatioEquiv

Print Power and Sample Size Results for Equivalence in Two-Sample Mean Ratio

print.designMeanRatio

Print Power and Sample Size Results for Two-Sample Mean Ratio

param_informationRates

Parameter Description: informationRates

param_hazardRatioH0

Parameter Description: hazardRatioH0

Parameter Description: lambda

Parameter Description: kMax

Parameter Description: rho2

param_stratumFraction

Parameter Description: stratumFraction

param_parameterAlphaSpending

Parameter Description: parameterAlphaSpending

param_parameterBetaSpending

Parameter Description: parameterBetaSpending

Distribution Function of Truncated Piecewise Exponential Distribution

print.designRiskRatioEquiv

Print Power and Sample Size Results for Equivalence in Two-Sample Risk Ratio

Probability of Being at Risk

param_userBetaSpending

Parameter Description: userBetaSpending

print.designAgreement

Print Power and Sample Size Results for Cohen's kappa.

print.designUnorderedBinom

Print Power and Sample Size Results for Unordered Multi-Sample Binomial Response

print.designUnorderedMultinom

Print Power and Sample Size Results for Unordered Multi-Sample Multinomial Response

print.designEquiv

Print Group Sequential Equivalence Design

print.designRepeatedANOVA

Print Power and Sample Size Results for One-Way Repeated Measures ANOVA

print.designRiskDiff

Print Power and Sample Size Results for Two-Sample Risk Difference

print.designRiskDiffEquiv

Print Power and Sample Size Results for Equivalence in Two-Sample Risk Difference

residuals_liferegr

Residuals for Parametric Regression Models for Failure Time Data

print.mTPI2Table

Print the Decision Table for the mTPI-2 Design

Print Power and Sample Size Results for Negative Binomial Rate Ratio

REML Estimates of Individual Proportions With Specified Risk Ratio

Piecewise Exponential Approximation to a Survival Distribution

Repeated p-Values for Group Sequential Design

print.designMeanDiff

Print Power and Sample Size Results for Two-Sample Mean Difference

print.designLogistic

Print Power and Sample Size Results for Logistic Regression

print.designRepeatedANOVAContrast

Print Power and Sample Size Results for a Single Contrast in One-Way Repeated Measures ANOVA

residuals_phregr

Residuals for Proportional Hazards Regression Models

Simon's Two-Stage Design

Miettinen-Nurminen Score Test Statistic for Two-Sample Rate Ratio

Print Power and Sample Size Results for Log-Rank Tests

print.logisregr

Print logisregr Object

The randomized clinical trial SHIVA data in long format from the ipcwswitch package

print.rmpower1s

Print Power and Sample Size Results for One-Sample Restricted Mean Survival Time

Miettinen-Nurminen Score Test Statistic for Two-Sample Rate Difference

print.adaptDesign

Print Adaptive Group Sequential Design

Print Group Sequential Design

REML Estimates of Individual Rates With Specified Rate Ratio

REML Estimates of Individual Proportions With Specified Risk difference

print.rmpowerequiv

Print Power and Sample Size Results for Equivalence in Restricted Mean Survival Time Difference

print.designSlopeDiffMMRM

Print Power and Sample Size Results for Two-Sample Slope Difference at the Last Time Point From the MMRM Model

print.designOddsRatioEquiv

Print Power and Sample Size Results for Equivalence in Two-Sample Odds Ratio

print.designMeanDiffXOEquiv

Print Power and Sample Size Results for Equivalence in Mean Difference in 2x2 Crossover

print.designMeanDiffXO

Print Power and Sample Size Results for Mean Difference in 2x2 Crossover

Estimate of Restricted Mean Survival Time Difference

Simulation of Simon's Bayesian Basket Trials

print.designOddsRatio

Print Power and Sample Size Results for Two-Sample Odds Ratio

print.designTwoMultinom

Print Power and Sample Size Results for Difference in Two-Sample Multinomial Response

Print Power and Sample Size Results for Milestone Survival Difference

Estimate of Restricted Mean Survival Time

Sample Size for One-Sample Restricted Mean Survival Time

print.kmpower1s

Print Power and Sample Size Results for One-Sample Milestone Survival Probability

Print phregr Object

print.designPairedMeanDiffEquiv

Print Power and Sample Size Results for Equivalence in Paired Mean Difference

print.designPairedMeanRatio

Print Power and Sample Size Results for Paired Mean Ratio

Print Power and Sample Size Results for Restricted Mean Survival Time Difference

print.designOneMultinom

Print Power and Sample Size Results for One-Sample Multinomial Response

print.designOneMean

Print Power and Sample Size Results for One-Sample Mean

rmsamplesizeequiv

Sample Size for Equivalence in Restricted Mean Survival Time Difference

print.designTwoOrdinal

Print Power and Sample Size Results for Wilcoxon Test for Two-Sample Ordinal Response.

print.designTwoWayANOVA

Print Power and Sample Size Results for Two-Way ANOVA

simonBayesAnalysis

Analysis of Simon's Bayesian Basket Trials

Miettinen-Nurminen Score Test Statistic for Two-Sample Risk difference

Miettinen-Nurminen Score Test Statistic for Two-Sample Risk Ratio

Restricted Mean Survival Time

Singular Value Decomposition of a Matrix

Power for Difference in Restricted Mean Survival Times

Power for Equivalence in Restricted Mean Survival Time Difference

Sample Size for Difference in Restricted Mean Survival Times

print.designSlopeDiff

Print Power and Sample Size Results for Two-Sample Slope Difference

print.designRiskRatioFM

Print Power and Sample Size Results for Two-Sample Risk Ratio Based on the Farrington-Manning Score Test

Print Simulation Results for Log-Rank Tests

samplesizeRiskDiffExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Difference

samplesizeFisherExact

Sample Size for Fisher's Exact Test for Two Proportions

print.lrpowerequiv

Print Power and Sample Size Results for Equivalence in Hazard Ratio

Profile Log-Likelihood Function for Change Points in Piecewise Exponential Approximation

QR Decomposition of a Matrix

Quantile Function of Truncated Piecewise Exponential Distribution

A simulated time-to-event data set with 10 replications

samplesizeOnePropExact

Sample Size for Binomial One-Sample Exact Test

Power for One-Sample Restricted Mean Survival Time

print.kmpowerequiv

Print Power and Sample Size Results for Equivalence in Milestone Survival Probability Difference

samplesizeRiskRatioExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Ratio

Stratified Difference in Restricted Mean Survival Times

Print liferegr Object

Urinary tract infection data from the logistf package

print.nbpower1s

Print Power and Sample Size Results for One-Sample Negative Binomial Rate

samplesizeRiskRatioExact

Sample Size for Exact Unconditional Test of Risk Ratio

The repeated measures data from the "Six Cities" study of the health effects of air pollution (Ware et al. 1984).

Tobin's tobit data from the survival package

print.nbpowerequiv

Print Power and Sample Size Results for Equivalence in Negative Binomial Rate Ratio

REML Estimates of Individual Proportions With Specified Odds Ratio

REML Estimates of Individual Rates With Specified Rate Difference

riskDiffExactCI

Exact Unconditional Confidence Interval for Risk Difference

riskDiffExactPValue

P-Value for Exact Unconditional Test of Risk Difference

Restricted Mean Survival Time by Stratum

Brookmeyer-Crowley Confidence Interval for Quantiles of Right-Censored Time-to-Event Data

Random Multivariate Normal Generation

riskRatioExactCI

Exact Unconditional Confidence Interval for Risk Ratio

riskRatioExactPValue

P-Value for Exact Unconditional Test of Risk Ratio

runShinyApp_lrstat

Split a survival data set at specified cut points

Random Number Generation Function of Truncated Piecewise Exponential Distribution

Survival Curve for Proportional Hazards Regression Models

samplesizeOneRateExact

Sample Size for Poisson One-Sample Exact Test

samplesizeRiskDiffExact

Sample Size for Exact Unconditional Test of Risk Difference

Update Graph for Graphical Approaches

Miettinen-Nurminen Score Test Statistic for Two-Sample Odds Ratio