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

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

## Documentation for package ‘lrstat’ version 0.3.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M N P Q R S T U Z

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

## -- A --

accrual | Number of Enrolled Subjects
adaptDesign | Adaptive Design at an Interim Look
adaptDesign_multiarm | Adaptive Multi-Arm Multi-Stage Design
adaptDesign_seamless | Adaptive Phase 2/3 Seamless Design
aml | Acute myelogenous leukemia survival data from the survival package
assess_phregr | Assess Proportional Hazards Assumption Based on Supremum Test

## -- B --

binary_tte_sim | Simulation for a Binary and a Time-to-Event Endpoint in Group Sequential Trials
BOINTable | BOIN Decision Table for Dose-Finding Trials

## -- C --

caltime | Calendar Times for Target Number of Events
ClopperPearsonCI | Clopper-Pearson Confidence Interval for One-Sample Proportion
corr_pfs_os | Correlation Between PFS and OS Given Correlation Between PD and OS
covrmst | Covariance Between Restricted Mean Survival Times

## -- D --

dtpwexp | Density Function of Truncated Piecewise Exponential Distribution

## -- E --

errorSpent | Error Spending
exitprob | Stagewise Exit Probabilities
exitprob_multiarm | Exit Probabilities for Multi-Arm Multi-Stage Design
exitprob_seamless | Exit Probabilities for Phase 2/3 Seamless Design

## -- F --

fadjpbon | Adjusted p-Values for Bonferroni-Based Graphical Approaches
fadjpdun | Adjusted p-Values for Dunnett-Based Graphical Approaches
fadjpsim | Adjusted p-Values for Simes-Based Graphical Approaches
fCERCer | Compute conditional error rates
fCERNewBound | Compute new stage-wise bounds after adaptation
fCERRej | Determine stage 2 rejections from conditional error rates
fCERStageBound | Compute stage-wise bounds for multiple testing
fDefaultWgtmat | Default Weight Matrix for All Intersection Hypotheses
finthyp | Indicator Matrix for All Intersection Hypotheses
float_to_fraction | Converting a decimal to a fraction
fmodmix | Adjusted p-Values for Modified Mixture Gatekeeping Procedures
fPCRej | Determine stage 2 rejections using p-value combination
fPCStage1 | Determine stage 1 rejections for adaptive multiple testing
fPCStagewise | Compute stage-wise local p-values
fquantile | The Quantiles of a Survival Distribution
fseqbon | Group Sequential Trials Using Bonferroni-Based Graphical Approaches
fstdmix | Adjusted p-Values for Standard Mixture Gatekeeping Procedures
fstp2seq | Adjusted p-Values for Stepwise Testing Procedures for Two Sequences
ftrunc | Adjusted p-Values for Holm, Hochberg, and Hommel Procedures
fwgtmat | Weight Matrix for All Intersection Hypotheses

## -- G --

getAccrualDurationFromN | Accrual Duration to Enroll Target Number of Subjects
getADCI | Confidence Interval After Adaptation
getADCI_multiarm | Confidence Interval After Adaptation for Multi-Arm Multi-Stage Design
getADCI_seamless | Confidence Interval After Adaptation for Phase 2/3 Seamless Design
getADRCI | Repeated Confidence Interval After Adaptation
getBound | Efficacy Boundaries for Group Sequential Design
getBound_multiarm | Efficacy Boundaries for Multi-Arm Multi-Stage Design
getBound_seamless | Efficacy Boundaries for Phase 2/3 Seamless Design
getCI | Confidence Interval After Trial Termination
getCI_multiarm | Confidence Interval After Trial Termination for Multi-Arm Multi-Stage Design
getCI_seamless | Confidence Interval After Trial Termination for Phase 2/3 Seamless Design
getCP | Conditional Power for Generic Group Sequential Design
getCP_multiarm | Conditional Power for Multi-Arm Multi-Stage Design
getCP_seamless | Conditional Power for Phase 2/3 Seamless Design
getDesign | Power and Sample Size for Generic Group Sequential Design
getDesign2 | Power and Sample Size for Group Sequential Design With Futility Stopping Under Null Hypothesis
getDesignAgreement | Power and Sample Size for Cohen's kappa
getDesignANOVA | Power and Sample Size for One-Way ANOVA
getDesignANOVAContrast | Power and Sample Size for One-Way ANOVA Contrast
getDesignEquiv | Power and Sample Size for Generic Group Sequential Equivalence Design
getDesignFisherExact | Power and Sample Size for Fisher's Exact Test for Two Proportions
getDesignLogistic | Power and Sample Size for Logistic Regression
getDesignMeanDiff | Group Sequential Design for Two-Sample Mean Difference
getDesignMeanDiffCarryover | Power and Sample Size for Direct Treatment Effects in Crossover Trials
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
getDesignMeanDiffMMRM | Group Sequential Design for Two-Sample Mean Difference From the MMRM Model
getDesignMeanDiffXO | Group Sequential Design for Mean Difference in 2x2 Crossover
getDesignMeanDiffXOEquiv | Group Sequential Design for Equivalence in Mean Difference in 2x2 Crossover
getDesignMeanRatio | Group Sequential Design for Two-Sample Mean Ratio
getDesignMeanRatioEquiv | Group Sequential Design for Equivalence in Two-Sample Mean Ratio
getDesignMeanRatioXO | Group Sequential Design for Mean Ratio in 2x2 Crossover
getDesignMeanRatioXOEquiv | Group Sequential Design for Equivalence in Mean Ratio in 2x2 Crossover
getDesignOddsRatio | Group Sequential Design for Two-Sample Odds Ratio
getDesignOddsRatioEquiv | Group Sequential Design for Equivalence in Two-Sample Odds Ratio
getDesignOneMean | Group Sequential Design for One-Sample Mean
getDesignOneMultinom | Power and Sample Size for One-Sample Multinomial Response
getDesignOneProportion | Group Sequential Design for One-Sample Proportion
getDesignOneRateExact | Power and Sample Size for One-Sample Poisson Rate Exact Test
getDesignOneSlope | Group Sequential Design for One-Sample Slope
getDesignOrderedBinom | Power and Sample Size for Cochran-Armitage Trend Test for Ordered Multi-Sample Binomial Response
getDesignPairedMeanDiff | Group Sequential Design for Paired Mean Difference
getDesignPairedMeanDiffEquiv | Group Sequential Design for Equivalence in Paired Mean Difference
getDesignPairedMeanRatio | Group Sequential Design for Paired Mean Ratio
getDesignPairedMeanRatioEquiv | Group Sequential Design for Equivalence in Paired Mean Ratio
getDesignPairedPropMcNemar | Group Sequential Design for McNemar's Test for Paired Proportions
getDesignRepeatedANOVA | Power and Sample Size for Repeated-Measures ANOVA
getDesignRepeatedANOVAContrast | Power and Sample Size for One-Way Repeated Measures ANOVA Contrast
getDesignRiskDiff | Group Sequential Design for Two-Sample Risk Difference
getDesignRiskDiffEquiv | Group Sequential Design for Equivalence in Two-Sample Risk Difference
getDesignRiskDiffExact | Power and Sample Size for Exact Unconditional Test for Risk Difference
getDesignRiskDiffExactEquiv | Power and Sample Size for Exact Unconditional Test for Equivalence in Risk Difference
getDesignRiskRatio | Group Sequential Design for Two-Sample Risk Ratio
getDesignRiskRatioEquiv | Group Sequential Design for Equivalence in Two-Sample Risk 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
getDesignRiskRatioFM | Group Sequential Design for Two-Sample Risk Ratio Based on the Farrington-Manning Score Test
getDesignSlopeDiff | Group Sequential Design for Two-Sample Slope Difference
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
getDesignTwoOrdinal | Power and Sample Size for the Wilcoxon Test for Two-Sample Ordinal Response
getDesignTwoWayANOVA | Power and Sample Size for Two-Way ANOVA
getDesignUnorderedBinom | Power and Sample Size for Unordered Multi-Sample Binomial Response
getDesignUnorderedMultinom | Power and Sample Size for Unordered Multi-Sample Multinomial Response
getDesignWilcoxon | Group Sequential Design for Two-Sample Wilcoxon Test
getDesign_multiarm | Power and Sample Size for Multi-Arm Multi-Stage Design
getDesign_seamless | Power and Sample Size for Phase 2/3 Seamless Design
getDurationFromNevents | Range of Accrual Duration for Target Number of Events
getNeventsFromHazardRatio | Required Number of Events Given Hazard Ratio
getRCI | Repeated Confidence Interval for Group Sequential Design

## -- H --

hazard_pd | Hazard Function for Progressive Disease (PD) Given Correlation Between PD and OS
hazard_sub | Hazard Function for Sub Population
heart | Stanford heart transplant data from the survival package
hedgesg | Hedges' g Effect Size

## -- I --

immdef | Simulated CONCORDE trial data from the rpsftm package
ingots | The binary data from Cox and Snell (1989, pp. 10-11).

## -- K --

kmdiff | Estimate of Milestone Survival Difference
kmest | Kaplan-Meier Estimates of Survival Curve
kmpower | Power for Difference in Milestone Survival Probabilities
kmpower1s | Power for One-Sample Milestone Survival Probability
kmpowerequiv | Power for Equivalence in Milestone Survival Probability Difference
kmsamplesize | Sample Size for Difference in Milestone Survival Probabilities
kmsamplesize1s | Sample Size for One-Sample Milestone Survival Probability
kmsamplesizeequiv | Sample Size for Equivalence in Milestone Survival Probability Difference
kmstat | Stratified Difference in Milestone Survival Probabilities

## -- L --

liferegr | Parametric Regression Models for Failure Time Data
liver | The liver data used in SAS PROC PHREG documentation examples.
logisregr | Logistic Regression Models for Binary Data
lrpower | Log-Rank Test Power
lrpowerequiv | Power for Equivalence in Hazard Ratio
lrsamplesize | Log-Rank Test Sample Size
lrsamplesizeequiv | Sample Size for Equivalence in Hazard Ratio
lrschoenfeld | Schoenfeld Method for Log-Rank Test Sample Size Calculation
lrsim | Log-Rank Test Simulation
lrsim2e | Log-Rank Test Simulation for PFS and OS Endpoints
lrsim2e3a | Log-Rank Test Simulation for Two Endpoints (PFS and OS) and Three Arms
lrsim3a | Log-Rank Test Simulation for Three Arms
lrsimsub | Log-Rank Test Simulation for Enrichment Design
lrsim_bmTrtSel | Simulation of a seamless phase II/III design with treatment selection based on a short-term endpoint
lrsim_mcpmod | Log-Rank Test Simulation for MCPMod Design
lrsim_multiarm | Log-Rank Test Simulation for Multi-Arm Multi-Stage Design
lrsim_seamless | Log-Rank Test Simulation for Phase 2/3 Seamless Design
lrstat | Number of Subjects Having an Event and Log-Rank Statistics
lrtest | Log-Rank Test of Survival Curve Difference

## -- M --

mnOddsRatioCI | Miettinen-Nurminen Score Confidence Interval for Two-Sample Odds Ratio
mnRateDiffCI | Miettinen-Nurminen Score Confidence Interval for Two-Sample Rate Difference
mnRateRatioCI | Miettinen-Nurminen Score Confidence Interval for Two-Sample Rate Ratio
mnRiskDiffCI | Miettinen-Nurminen Score Confidence Interval for Two-Sample Risk Difference
mnRiskRatioCI | Miettinen-Nurminen Score Confidence Interval for Two-Sample Risk Ratio
mTPI2Table | mTPI-2 Decision Table
mtpwexp | Mean and Variance of Truncated Piecewise Exponential Distribution

## -- N --

natrisk | Number of Subjects at Risk
nbpower | Power for Negative Binomial Rate Ratio
nbpower1s | Power for One-Sample Negative Binomial Rate
nbpowerequiv | Power for Equivalence in Negative Binomial Rate Ratio
nbsamplesize | Sample Size for Negative Binomial Rate Ratio
nbsamplesize1s | Sample Size for One-Sample Negative Binomial Rate
nbsamplesizeequiv | Sample Size for Equivalence in Negative Binomial Rate Ratio
nbstat | Negative Binomial Rate Ratio
nevent | Number of Subjects Having an Event by Calendar Time

## -- P --

patrisk | Probability of Being at Risk
pbvnorm | Distribution Function of the Standard Bivariate Normal
pevent | Probability of Having an Event
phregr | Proportional Hazards Regression Models
pmvnormr | Multivariate Normal Probabilities over a Hyperrectangle
ptpwexp | Distribution Function of Truncated Piecewise Exponential Distribution
pwexpcuts | Piecewise Exponential Approximation to a Survival Distribution
pwexploglik | Profile Log-Likelihood Function for Change Points in Piecewise Exponential Approximation

## -- Q --

qmvnormr | Equicoordinate Quantiles of the Multivariate Normal Distribution
qtpwexp | Quantile Function of Truncated Piecewise Exponential Distribution

## -- R --

rawdata | A simulated time-to-event data set with 10 replications
rdsim_multiarm | Risk Difference Simulation for Multi-Arm Multi-Stage Design
rdsim_seamless | Risk Difference Simulation for Phase 2/3 Seamless Design
remlOddsRatio | REML Estimates of Individual Proportions With Specified Odds Ratio
remlRateDiff | REML Estimates of Individual Rates With Specified Rate Difference
remlRateRatio | REML Estimates of Individual Rates With Specified Rate Ratio
remlRiskDiff | REML Estimates of Individual Proportions With Specified Risk difference
remlRiskRatio | REML Estimates of Individual Proportions With Specified Risk Ratio
repeatedPValue | Repeated p-Values for Group Sequential Design
residuals_liferegr | Residuals for Parametric Regression Models for Failure Time Data
residuals_phregr | Residuals for Proportional Hazards Regression Models
riskDiffExactCI | Exact Unconditional Confidence Interval for Risk Difference
riskDiffExactPValue | P-Value for Exact Unconditional Test of Risk Difference
riskRatioExactCI | Exact Unconditional Confidence Interval for Risk Ratio
riskRatioExactPValue | P-Value for Exact Unconditional Test of Risk Ratio
rmdiff | Estimate of Restricted Mean Survival Time Difference
rmest | Estimate of Restricted Mean Survival Time
rmpower | Power for Difference in Restricted Mean Survival Times
rmpower1s | Power for One-Sample Restricted Mean Survival Time
rmpowerequiv | Power for Equivalence in Restricted Mean Survival Time Difference
rmsamplesize | Sample Size for Difference in Restricted Mean Survival Times
rmsamplesize1s | Sample Size for One-Sample Restricted Mean Survival Time
rmsamplesizeequiv | Sample Size for Equivalence in Restricted Mean Survival Time Difference
rmst | Restricted Mean Survival Time
rmstat | Stratified Difference in Restricted Mean Survival Times
rtpwexp | Random Number Generation Function of Truncated Piecewise Exponential Distribution
runShinyApp_lrstat | Run Shiny App

## -- S --

sexagg | Urinary tract infection data from the logistf package
shilong | The randomized clinical trial SHIVA data in long format from the ipcwswitch package
simon2stage | Simon's Two-Stage Design
simonBayesAnalysis | Analysis of Simon's Bayesian Basket Trials
simonBayesSim | Simulation of Simon's Bayesian Basket Trials
six | The repeated measures data from the "Six Cities" study of the health effects of air pollution (Ware et al. 1984).
survfit_phregr | Survival Curve for Proportional Hazards Regression Models
survQuantile | Brookmeyer-Crowley Confidence Interval for Quantiles of Right-Censored Time-to-Event Data
svdcpp | Singular Value Decomposition of a Matrix

## -- T --

tobin | Tobin's tobit data from the survival package

## -- U --

updateGraph | Update Graph for Graphical Approaches

## -- Z --

zph_phregr | Assess Proportional Hazards Assumption Based on Scaled Schoenfeld Residuals
zstatOddsRatio | Miettinen-Nurminen Score Test Statistic for Two-Sample Odds Ratio
zstatRateDiff | Miettinen-Nurminen Score Test Statistic for Two-Sample Rate Difference
zstatRateRatio | Miettinen-Nurminen Score Test Statistic for Two-Sample Rate Ratio
zstatRiskDiff | Miettinen-Nurminen Score Test Statistic for Two-Sample Risk difference
zstatRiskRatio | Miettinen-Nurminen Score Test Statistic for Two-Sample Risk Ratio