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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

723

Version

0.2.13

License

GPL (>= 2)

Maintainer

Kaifeng Lu

Last Published

March 20th, 2025

Functions in lrstat (0.2.13)

BOIN Decision Table

Number of Enrolled Subjects

ClopperPearsonCI

Clopper-Pearson Confidence Interval for One-Sample Proportion

Acute myelogenous leukemia survival data from the survival package

Calendar Times for Target Number of Events

Adaptive Design at an Interim Look

Covariance Between Restricted Mean Survival Times

Simulation for a Binary Endpoint and a Time-to-Event Endpoint

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

Stagewise Exit Probabilities

Adjusted p-Values for Standard Mixture Gatekeeping Procedures

Group Sequential Trials Using Bonferroni-Based Graphical Approaches

Adjusted p-Values for Bonferroni-Based Graphical Approaches

The Quantiles of a Survival Distribution

Adjusted p-Values for Modified Mixture Gatekeeping Procedures

Find Interval Numbers of Indices

float_to_fraction

Converting a decimal to a fraction

Repeated Confidence Interval After Adaptation

getAccrualDurationFromN

Accrual Duration to Enroll Target Number of Subjects

Weight Matrix for All Intersection Hypotheses

Confidence Interval After Adaptation

Adjusted p-Values for Dunnett-Based Graphical Approaches

Adjusted p-Values for Simes-Based Graphical Approaches

Efficacy Boundaries for Group Sequential Design

Adjusted p-Values for Stepwise Testing Procedures for Two Sequences

Confidence Interval After Trial Termination

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

Conditional Power Allowing for Varying Parameter Values

Power and Sample Size for a Generic Group Sequential Design

getDesignANOVAContrast

Power and Sample Size for One-Way ANOVA Contrast

Power and Sample Size for One-Way ANOVA

getDesignAgreement

Power and Sample Size for Cohen's kappa

Power and Sample Size for a Generic Group Sequential Equivalence Design

getDesignMeanDiffCarryoverEquiv

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

getDesignMeanDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Difference

getDesignFisherExact

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

getDesignLogistic

Power and Sample Size for Logistic Regression

getDesignMeanDiffCarryover

Power and Sample Size for Direct Treatment Effects in Crossover Trials

getDesignMeanDiff

Group Sequential Design for Two-Sample Mean Difference

getDesignOddsRatio

Group Sequential Design for Two-Sample Odds Ratio

getDesignMeanRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Ratio

getDesignMeanRatioXOEquiv

Group Sequential Design for Equivalence in Mean Ratio 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

getDesignMeanDiffXO

Group Sequential Design for Mean Difference in 2x2 Crossover

getDesignOddsRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Odds Ratio

getDesignOneMean

Group Sequential Design for One-Sample Mean

getDesignMeanDiffXOEquiv

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

getDesignMeanRatio

Group Sequential Design for Two-Sample Mean Ratio

getDesignOneRateExact

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

getDesignPairedMeanDiff

Group Sequential Design for Paired Mean Difference

getDesignOneProportion

Group Sequential Design for One-Sample Proportion

getDesignOrderedBinom

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

getDesignOneSlope

Group Sequential Design for One-Sample Slope

getDesignPairedMeanDiffEquiv

Group Sequential Design for Equivalence in Paired Mean Difference

getDesignPairedPropMcNemar

Group Sequential Design for McNemar's Test for Paired Proportions

getDesignOneMultinom

Power and Sample Size for One-Sample Multinomial Response

getDesignPairedMeanRatioEquiv

Group Sequential Design for Equivalence in Paired Mean Ratio

getDesignPairedMeanRatio

Group Sequential Design for Paired Mean Ratio

getDesignRiskRatio

Group Sequential Design for Two-Sample Risk Ratio

getDesignRiskRatioExact

Power and Sample Size for Exact Unconditional Test for Risk Ratio

getDesignRiskDiff

Group Sequential Design for Two-Sample Risk Difference

getDesignRiskDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Difference

getDesignRiskRatioExactEquiv

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

getDesignRiskDiffExactEquiv

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

getDesignRiskDiffExact

Power and Sample Size for Exact Unconditional Test for Risk Difference

getDesignRepeatedANOVA

Power and Sample Size for Repeated-Measures ANOVA

getDesignRepeatedANOVAContrast

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

getDesignRiskRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Ratio

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

getDurationFromNevents

Range of Accrual Duration for Target Number of Events

getDesignWilcoxon

Group Sequential Design for Two-Sample Wilcoxon Test

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

getDesignTwoOrdinal

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

getDesignTwoWayANOVA

Power and Sample Size for Two-Way ANOVA

getDesignUnorderedMultinom

Power and Sample Size for Unordered Multi-Sample Multinomial Response

getDesignUnorderedBinom

Power and Sample Size for Unordered Multi-Sample Binomial Response

Hedges' g Effect Size

Simulated CONCORDE trial data from the rpsftm package

Estimate of Milestone Survival Difference

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

Kaplan-Meier Estimates of Survival Curve

Power for Difference in Milestone Survival Probabilities

Integrated Event Probability Over an Interval With Constant Hazard

Stanford heart transplant data from the survival package

getNeventsFromHazardRatio

Required Number of Events Given Hazard Ratio

Repeated Confidence Interval for Group Sequential Design

Power for Equivalence in Hazard Ratio

Log-Rank Test Power

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

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

Parametric Regression Models for Failure Time Data

Sample Size for Difference in Milestone Survival Probabilities

Logistic Regression Models for Binary Data

Sample Size for One-Sample Milestone Survival Probability

Milestone Survival Probability by Stratum

Kaplan-Meier Survival Probability Based on Pooled Sample

Stratified Difference in Milestone Survival Probabilities

kmsamplesizeequiv

Sample Size for Equivalence in Milestone Survival Probability Difference

Power for Negative Binomial Rate Ratio

Power for One-Sample Negative Binomial Rate

Log-Rank Test Sample Size

Log-Rank Test Simulation for Two Endpoints and Three Arms

Number of Subjects Having an Event

Log-Rank Test Simulation for Two Endpoints

mTPI-2 Decision Table

Log-Rank Test of Survival Curve Difference

param_efficacyStopping

Parameter Description: efficacyStopping

Number of Subjects Having an Event by Calendar Time

param_estimateHazardRatio

Parameter Description: estimateHazardRatio

param_gamma2_stratified

Parameter Description: gamma2_stratified

param_parameterBetaSpending

Parameter Description: parameterBetaSpending

param_hazardRatioH0

Parameter Description: hazardRatioH0

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

lrsamplesizeequiv

Sample Size for Equivalence in Hazard Ratio

Number of Subjects at Risk

print.designLogistic

Print Power and Sample Size Results for Logistic Regression

powerRiskRatioExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Ratio

param_piecewiseSurvivalTime

Parameter Description: piecewiseSurvivalTime

Parameter Description: alpha

param_criticalValues

Parameter Description: criticalValues

print.BOINTable

Print the Decision Table for the BOIN Design

print.designMeanDiff

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

Power for Equivalence in Milestone Survival Probability Difference

Power for One-Sample Milestone Survival Probability

Parameter Description: gamma2

print.designOddsRatio

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

Negative Binomial Rate Ratio by Stratum

param_gamma1_stratified

Parameter Description: gamma1_stratified

Negative Binomial Rate Ratio

Log-Rank Test Simulation for Three Arms

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

print.designSlopeDiffMMRM

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

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

print.designPairedPropMcNemar

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

print.designMeanRatioXO

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

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

print.designMeanRatioXOEquiv

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

print.designAgreement

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

param_minFollowupTime

Parameter Description: minFollowupTime

param_parameterAlphaSpending

Parameter Description: parameterAlphaSpending

param_typeBetaSpending

Parameter Description: typeBetaSpending

print.designTwoOrdinal

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

param_typeOfComputation

Parameter Description: typeOfComputation

print.rmpowerequiv

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

param_accrualTime

Parameter Description: accrualTime

param_accrualDuration

Parameter Description: accrualDuration

param_userAlphaSpending

Parameter Description: userAlphaSpending

param_stratumFraction

Parameter Description: stratumFraction

param_allocationRatioPlanned

Parameter Description: allocationRatioPlanned

param_accrualIntensity

Parameter Description: accrualIntensity

param_informationRates

Parameter Description: informationRates

param_futilityBounds

Parameter Description: futilityBounds

param_typeAlphaSpending

Parameter Description: typeAlphaSpending

print.designPairedMeanRatioEquiv

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

powerOnePropExact

Power for Binomial One-Sample Exact Test

print.designRiskRatioEquiv

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

param_futilityStopping

Parameter Description: futilityStopping

Power for Equivalence in Negative Binomial Rate Ratio

Sample Size for Negative Binomial Rate Ratio

print.estimateCI

Print the Point Estimate and Confidence Interval

residuals_phregr

Residuals for Proportional Hazards Regression Models

print.designEquiv

Print Group Sequential Equivalence Design

print.designRiskRatioFM

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

Print Power and Sample Size Results for Log-Rank Tests

powerFisherExact

Power for Fisher's Exact Test for Two Proportions

print.designRepeatedANOVAContrast

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

print.designMeanDiffEquiv

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

Parameter Description: kMax

Parameter Description: lambda

print.designMeanDiffMMRM

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

print.designPairedMeanRatio

Print Power and Sample Size Results for Paired Mean Ratio

print.designPairedMeanDiffEquiv

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

print.designRiskRatio

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

Parameter Description: lambda1

print.designMeanDiffCarryoverEquiv

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

riskDiffExactCI

Exact Unconditional Confidence Interval for Risk Difference

REML Estimates of Individual Proportions With Specified Odds Ratio

REML Estimates of Individual Rates With Specified Rate Difference

Update Graph for Graphical Approaches

Proportional Hazards Regression Models

Parameter Description: lambda2

print.nbpowerequiv

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

print.designOneMean

Print Power and Sample Size Results for One-Sample Mean

param_lambda1_stratified

Parameter Description: lambda1_stratified

print.adaptDesign

Print Adaptive Group Sequential Design

print.logisregr

Print logisregr Object

powerRiskDiffExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Difference

print.designSlopeDiff

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

print.designTwoWayANOVA

Print Power and Sample Size Results for Two-Way ANOVA

Log-Rank Test Simulation

Number of Subjects Having an Event and Log-Rank Statistics

Schoenfeld Method for Log-Rank Test Sample Size Calculation

samplesizeRiskDiffExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Difference

riskRatioExactPValue

P-Value for Exact Unconditional Test of Risk Ratio

param_userBetaSpending

Parameter Description: userBetaSpending

Power for One-Sample Restricted Mean Survival Time

powerOneRateExact

Power for Poisson One-Sample Exact Test

Random Number Generation Function of Truncated Piecewise Exponential Distribution

rmsamplesizeequiv

Sample Size for Equivalence in Restricted Mean Survival Time Difference

print.rmpower1s

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

Estimate of Restricted Mean Survival Time Difference

Restricted Mean Survival Time

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

Probability of Having an Event

print.kmpower1s

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

print.designMeanDiffCarryover

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

Power for Equivalence in Restricted Mean Survival Time Difference

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

print.designOddsRatioEquiv

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

powerRiskDiffExact

Power for Exact Unconditional Test of Risk Difference

print.designMeanRatio

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

print.designOneProportion

Print Power and Sample Size Results for One-Sample Proportion

print.designOneSlope

Print Power and Sample Size Results for One-Sample Slope

print.designRepeatedANOVA

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

Stratified Difference in Restricted Mean Survival Times

Parameter Description: gamma1

Print Group Sequential Design

print.designMeanRatioEquiv

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

print.designOneMultinom

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

samplesizeRiskRatioExact

Sample Size for Exact Unconditional Test of Risk Ratio

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

print.designWilcoxon

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

Survival Curve for Proportional Hazards Regression Models

Sample Size for One-Sample Negative Binomial Rate

samplesizeFisherExact

Sample Size for Fisher's Exact Test for Two Proportions

Print phregr Object

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

nbsamplesizeequiv

Sample Size for Equivalence in Negative Binomial Rate Ratio

powerRiskRatioExact

Power for Exact Unconditional Test of Risk Ratio

Parameter Description: rho1

param_fixedFollowup

Parameter Description: fixedFollowup

print.designRiskDiff

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

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

Simon's Two-Stage Design

QR Decomposition of a Matrix

print.nbpower1s

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

Parameter Description: rho2

print.designPairedMeanDiff

Print Power and Sample Size Results for Paired Mean Difference

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

print.designOrderedBinom

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

Print Power and Sample Size Results for Milestone Survival Difference

print.mTPI2Table

Print the Decision Table for the mTPI-2 Design

samplesizeOnePropExact

Sample Size for Binomial One-Sample Exact Test

Quantile Function of Truncated Piecewise Exponential Distribution

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

Estimate of Restricted Mean Survival Time

runShinyApp_lrstat

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

Repeated p-Values for Group Sequential Design

print.designUnorderedBinom

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

REML Estimates of Individual Proportions With Specified Risk Ratio

Probability of Being at Risk

print.designUnorderedMultinom

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

Piecewise Exponential Approximation to a Survival Distribution

print.designTwoMultinom

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

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

print.designANOVA

Print Power and Sample Size Results for One-Way ANOVA

param_lambda2_stratified

Parameter Description: lambda2_stratified

param_followupTime

Parameter Description: followupTime

Parameter Description: gamma

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

Sample Size for Difference in Restricted Mean Survival Times

Distribution Function of Truncated Piecewise Exponential Distribution

Tobin's tobit data from the survival package

Urinary tract infection data from the logistf package

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

Print Power and Sample Size Results for Negative Binomial Rate Ratio

Restricted Mean Survival Time by Stratum

REML Estimates of Individual Proportions With Specified Risk difference

REML Estimates of Individual Rates With Specified Rate Ratio

Sample Size for One-Sample Restricted Mean Survival Time

print.designANOVAContrast

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

print.designMeanDiffXO

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

print.kmpowerequiv

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

Split a survival data set at specified cut points

Integrated Event Probability Over an Interval

samplesizeRiskRatioExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Ratio

param_maxFollowupTime

Parameter Description: maxFollowupTime

print.designRiskDiffEquiv

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

riskDiffExactPValue

P-Value for Exact Unconditional Test of Risk Difference

print.designMeanDiffXOEquiv

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

print.lrpowerequiv

Print Power and Sample Size Results for Equivalence in Hazard Ratio

riskRatioExactCI

Exact Unconditional Confidence Interval for Risk Ratio

Print liferegr Object

Print Simulation Results for Log-Rank Tests

samplesizeRiskDiffExact

Sample Size for Exact Unconditional Test of Risk Difference

Power for Difference in Restricted Mean Survival Times

simonBayesAnalysis

Analysis of Simon's Bayesian Basket Trials

samplesizeOneRateExact

Sample Size for Poisson One-Sample Exact Test

Simulation of Simon's Bayesian Basket Trials

Singular Value Decomposition of a Matrix

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