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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

0.2.12

License

GPL (>= 2)

Maintainer

Kaifeng Lu

Last Published

January 17th, 2025

Functions in lrstat (0.2.12)

Group Sequential Trials Using Bonferroni-Based Graphical Approaches

Adjusted p-Values for Standard Mixture Gatekeeping Procedures

Adjusted p-Values for Bonferroni-Based Graphical Approaches

Stagewise Exit Probabilities

Covariance Between Restricted Mean Survival Times

Weight Matrix for All Intersection Hypotheses

Adaptive Design at an Interim Look

Acute myelogenous leukemia survival data from the survival package

Find Interval Numbers of Indices

float_to_fraction

Converting a decimal to a fraction

Adjusted p-Values for Modified Mixture Gatekeeping Procedures

The Quantiles of a Survival Distribution

Confidence Interval After Adaptation

getDesignMeanDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Difference

getDesignMeanDiffMMRM

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

Power and Sample Size for One-Way ANOVA

getDesignANOVAContrast

Power and Sample Size for One-Way ANOVA Contrast

getDesignMeanDiffCarryover

Power and Sample Size for Direct Treatment Effects in Crossover Trials Accounting for Carryover Effects

Repeated Confidence Interval After Adaptation

getAccrualDurationFromN

Accrual Duration to Enroll Target Number of Subjects

getDesignMeanDiff

Group Sequential Design for Two-Sample Mean Difference

getDesignOddsRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Odds Ratio

Power and Sample Size for a Generic Group Sequential Design

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

getDesignOddsRatio

Group Sequential Design for Two-Sample Odds Ratio

Calendar Times for Target Number of Events

Conditional Power Allowing for Varying Parameter Values

getDesignFisherExact

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

getDesignMeanDiffXO

Group Sequential Design for Mean Difference in 2x2 Crossover

getDesignMeanDiffXOEquiv

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

getDesignLogistic

Power and Sample Size for Logistic Regression

getDesignOneMean

Group Sequential Design for One-Sample Mean

getDesignPairedPropMcNemar

Group Sequential Design for McNemar's Test for Paired Proportions

getDesignRepeatedANOVA

Power and Sample Size for Repeated-Measures ANOVA

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

Adjusted p-Values for Stepwise Testing Procedures for Two Sequences

getDesignPairedMeanRatio

Group Sequential Design for Paired Mean Ratio

getDesignPairedMeanRatioEquiv

Group Sequential Design for Equivalence in Paired Mean Ratio

getDesignRiskDiffExact

Power and Sample Size for Exact Unconditional Test for Risk Difference

getDesignRiskDiffEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Difference

BOIN Decision Table

ClopperPearsonCI

Clopper-Pearson Confidence Interval for One-Sample Proportion

getDesignOneMultinom

Power and Sample Size for One-Sample Multinomial Response

getDesignRiskRatioExactEquiv

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

getDesignPairedMeanDiff

Group Sequential Design for Paired Mean Difference

getDesignRiskRatioFM

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

getDesignPairedMeanDiffEquiv

Group Sequential Design for Equivalence in Paired Mean Difference

getDesignMeanRatio

Group Sequential Design for Two-Sample Mean Ratio

getDesignMeanRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Mean Ratio

getNeventsFromHazardRatio

Required Number of Events Given Hazard Ratio

getDurationFromNevents

Range of Accrual Duration for Target Number of Events

getDesignOneProportion

Group Sequential Design for One-Sample Proportion

getDesignSlopeDiff

Group Sequential Design for Two-Sample Slope Difference

getDesignSlopeDiffMMRM

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

getDesignUnorderedBinom

Power and Sample Size for Unordered Multi-Sample Binomial Response

getDesignTwoWayANOVA

Power and Sample Size for Two-Way ANOVA

getDesignRepeatedANOVAContrast

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

getDesignTwoOrdinal

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

getDesignTwoMultinom

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

getDesignRiskDiff

Group Sequential Design for Two-Sample Risk Difference

getDesignOneRateExact

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

Integrated Event Probability Over an Interval With Constant Hazard

Repeated Confidence Interval for Group Sequential Design

Simulated CONCORDE trial data from the rpsftm package

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

getDesignUnorderedMultinom

Power and Sample Size for Unordered Multi-Sample Multinomial Response

Estimate of Milestone Survival Difference

getDesignRiskRatioExact

Power and Sample Size for Exact Unconditional Test for Risk Ratio

getDesignRiskRatioEquiv

Group Sequential Design for Equivalence in Two-Sample Risk Ratio

getDesignWilcoxon

Group Sequential Design for Two-Sample Wilcoxon Test

Kaplan-Meier Estimates of Survival Curve

Hedges' g Effect Size

Stanford heart transplant data from the survival package

Adjusted p-Values for Dunnett-Based Graphical Approaches

Adjusted p-Values for Simes-Based Graphical Approaches

Efficacy Boundaries for Group Sequential Design

Confidence Interval After Trial Termination

getDesignAgreement

Power and Sample Size for Cohen's kappa

Power and Sample Size for a Generic Group Sequential Equivalence Design

getDesignMeanRatioXO

Group Sequential Design for Mean Ratio in 2x2 Crossover

getDesignMeanRatioXOEquiv

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

getDesignOneSlope

Group Sequential Design for One-Sample Slope

Logistic Regression Models for Binary Data

Milestone Survival Probability by Stratum

Stratified Difference in Milestone Survival Probabilities

Log-Rank Test Power

Sample Size for One-Sample Milestone Survival Probability

getDesignOrderedBinom

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

Power for Difference in Milestone Survival Probabilities

getDesignRiskRatio

Group Sequential Design for Two-Sample Risk Ratio

Power for One-Sample Milestone Survival Probability

getDesignRiskDiffExactEquiv

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

Kaplan-Meier Survival Probability Based on Pooled Sample

kmsamplesizeequiv

Sample Size for Equivalence in Milestone Survival Probability Difference

Parametric Regression Models for Failure Time Data

Sample Size for Difference in Milestone Survival Probabilities

Power for Equivalence in Milestone Survival Probability Difference

lrsamplesizeequiv

Sample Size for Equivalence in Hazard Ratio

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

Power for Equivalence in Hazard Ratio

Log-Rank Test Sample Size

Log-Rank Test Simulation

Schoenfeld Method for Log-Rank Test Sample Size Calculation

Log-Rank Test Simulation for Two Endpoints and Three Arms

Log-Rank Test Simulation for Three Arms

Number of Subjects Having an Event and Log-Rank Statistics

Log-Rank Test Simulation for Two Endpoints

mTPI-2 Decision Table

Number of Subjects at Risk

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

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

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

Log-Rank Test of Survival Curve Difference

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

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

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

Power for Negative Binomial Rate Ratio

Number of Subjects Having an Event

nbsamplesizeequiv

Sample Size for Equivalence in Negative Binomial Rate Ratio

Sample Size for One-Sample Negative Binomial Rate

param_accrualDuration

Parameter Description: accrualDuration

Number of Subjects Having an Event by Calendar Time

Negative Binomial Rate Ratio

Sample Size for Negative Binomial Rate Ratio

Power for Equivalence in Negative Binomial Rate Ratio

Power for One-Sample Negative Binomial Rate

Parameter Description: alpha

Negative Binomial Rate Ratio by Stratum

param_accrualTime

Parameter Description: accrualTime

param_allocationRatioPlanned

Parameter Description: allocationRatioPlanned

param_accrualIntensity

Parameter Description: accrualIntensity

param_estimateHazardRatio

Parameter Description: estimateHazardRatio

param_criticalValues

Parameter Description: criticalValues

param_efficacyStopping

Parameter Description: efficacyStopping

param_followupTime

Parameter Description: followupTime

Parameter Description: gamma2

param_futilityBounds

Parameter Description: futilityBounds

param_hazardRatioH0

Parameter Description: hazardRatioH0

param_fixedFollowup

Parameter Description: fixedFollowup

param_minFollowupTime

Parameter Description: minFollowupTime

Parameter Description: gamma1

param_maxFollowupTime

Parameter Description: maxFollowupTime

param_informationRates

Parameter Description: informationRates

Probability of Being at Risk

param_futilityStopping

Parameter Description: futilityStopping

Parameter Description: gamma

param_piecewiseSurvivalTime

Parameter Description: piecewiseSurvivalTime

param_userBetaSpending

Parameter Description: userBetaSpending

Probability of Having an Event

Parameter Description: rho1

Integrated Event Probability Over an Interval

Proportional Hazards Regression Models

print.BOINTable

Print the Decision Table for the BOIN Design

param_lambda1_stratified

Parameter Description: lambda1_stratified

Parameter Description: lambda1

param_gamma1_stratified

Parameter Description: gamma1_stratified

powerOnePropExact

Power for Binomial One-Sample Exact Test

param_typeAlphaSpending

Parameter Description: typeAlphaSpending

param_typeBetaSpending

Parameter Description: typeBetaSpending

param_gamma2_stratified

Parameter Description: gamma2_stratified

print.adaptDesign

Print Adaptive Group Sequential Design

powerOneRateExact

Power for Poisson One-Sample Exact Test

param_userAlphaSpending

Parameter Description: userAlphaSpending

param_typeOfComputation

Parameter Description: typeOfComputation

print.designAgreement

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

Parameter Description: lambda2

print.designANOVAContrast

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

print.designMeanRatio

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

print.designMeanDiffEquiv

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

powerFisherExact

Power for Fisher's Exact Test for Two Proportions

Parameter Description: lambda

Parameter Description: kMax

print.designEquiv

Print Group Sequential Equivalence Design

print.designPairedMeanDiffEquiv

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

print.designMeanDiffMMRM

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

print.designOddsRatio

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

print.designMeanRatioEquiv

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

param_stratumFraction

Parameter Description: stratumFraction

Print Group Sequential Design

print.designLogistic

Print Power and Sample Size Results for Logistic Regression

param_lambda2_stratified

Parameter Description: lambda2_stratified

print.designMeanDiffXOEquiv

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

Parameter Description: rho2

powerRiskRatioExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Ratio

print.designOrderedBinom

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

print.designOneProportion

Print Power and Sample Size Results for One-Sample Proportion

print.designMeanDiffXO

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

powerRiskRatioExact

Power for Exact Unconditional Test of Risk Ratio

print.designOddsRatioEquiv

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

param_parameterAlphaSpending

Parameter Description: parameterAlphaSpending

print.designRiskRatioFM

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

print.designOneSlope

Print Power and Sample Size Results for One-Sample Slope

print.designOneMultinom

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

print.designANOVA

Print Power and Sample Size Results for One-Way ANOVA

print.designTwoOrdinal

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

print.designRiskDiff

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

print.nbpower1s

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

Print Power and Sample Size Results for Negative Binomial Rate Ratio

param_parameterBetaSpending

Parameter Description: parameterBetaSpending

print.designRiskDiffEquiv

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

print.mTPI2Table

Print the Decision Table for the mTPI-2 Design

Print liferegr Object

print.designOneMean

Print Power and Sample Size Results for One-Sample Mean

print.nbpowerequiv

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

print.kmpowerequiv

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

print.designSlopeDiff

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

print.designWilcoxon

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

print.estimateCI

Print the Point Estimate and Confidence Interval

print.designPairedMeanDiff

Print Power and Sample Size Results for Paired Mean Difference

powerRiskDiffExact

Power for Exact Unconditional Test of Risk Difference

print.designTwoWayANOVA

Print Power and Sample Size Results for Two-Way ANOVA

print.designRepeatedANOVA

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

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

riskRatioExactCI

Exact Unconditional Confidence Interval for Risk Ratio

riskDiffExactPValue

P-Value for Exact Unconditional Test of Risk Difference

print.designRepeatedANOVAContrast

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

print.logisregr

Print logisregr Object

Print Power and Sample Size Results for Log-Rank Tests

print.rmpower1s

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

QR Decomposition of a Matrix

riskRatioExactPValue

P-Value for Exact Unconditional Test of Risk Ratio

Piecewise Exponential Approximation to a Survival Distribution

Distribution Function of Truncated Piecewise Exponential Distribution

REML Estimates of Individual Rates With Specified Rate Ratio

riskDiffExactCI

Exact Unconditional Confidence Interval for Risk Difference

REML Estimates of Individual Proportions With Specified Risk difference

print.designUnorderedBinom

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

print.designPairedMeanRatio

Print Power and Sample Size Results for Paired Mean Ratio

print.rmpowerequiv

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

print.designRiskRatioEquiv

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

print.designUnorderedMultinom

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

Print Simulation Results for Log-Rank Tests

print.lrpowerequiv

Print Power and Sample Size Results for Equivalence in Hazard Ratio

print.designRiskRatio

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

Estimate of Restricted Mean Survival Time

Sample Size for Difference in Restricted Mean Survival Times

Estimate of Restricted Mean Survival Time Difference

rmsamplesizeequiv

Sample Size for Equivalence in Restricted Mean Survival Time Difference

Sample Size for One-Sample Restricted Mean Survival Time

Power for Difference in Restricted Mean Survival Times

Restricted Mean Survival Time

Stratified Difference in Restricted Mean Survival Times

Restricted Mean Survival Time by Stratum

samplesizeRiskDiffExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Difference

samplesizeRiskRatioExactEquiv

Sample Size for Exact Unconditional Test of Equivalence in Risk Ratio

Urinary tract infection data from the logistf package

Quantile Function of Truncated Piecewise Exponential Distribution

Random Number Generation Function of Truncated Piecewise Exponential Distribution

residuals_phregr

Residuals for Proportional Hazards Regression Models

samplesizeFisherExact

Sample Size for Fisher's Exact Test for Two Proportions

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

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

Simon's Two-Stage Design

samplesizeRiskDiffExact

Sample Size for Exact Unconditional Test of Risk Difference

Singular Value Decomposition of a Matrix

Survival Curve for Proportional Hazards Regression Models

Tobin's tobit data from the survival package

samplesizeOneRateExact

Sample Size for Poisson One-Sample Exact Test

simonBayesAnalysis

Analysis of Simon's Bayesian Basket Trials

Update Graph for Graphical Approaches

Simulation of Simon's Bayesian Basket Trials

samplesizeRiskRatioExact

Sample Size for Exact Unconditional Test of Risk Ratio

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

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

samplesizeOnePropExact

Sample Size for Binomial One-Sample Exact Test

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

powerRiskDiffExactEquiv

Power for Exact Unconditional Test of Equivalence in Risk Difference

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

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

print.designMeanRatioXO

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

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

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

Print Power and Sample Size Results for Milestone Survival Difference

print.designMeanDiff

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

print.designMeanDiffCarryover

Print Power and Sample Size Results for Direct Treatment Effects in Crossover Trials Accounting for Carryover Effects

Power for Equivalence in Restricted Mean Survival Time Difference

REML Estimates of Individual Proportions With Specified Risk Ratio

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.designSlopeDiffMMRM

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

print.designPairedPropMcNemar

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

print.kmpower1s

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

print.designTwoMultinom

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

REML Estimates of Individual Rates With Specified Rate Difference

Repeated p-Values for Group Sequential Design

REML Estimates of Individual Proportions With Specified Odds Ratio

Power for One-Sample Restricted Mean Survival Time

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

Print phregr Object

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

Number of Enrolled Subjects