R Observatory: Metrics for lrstat version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lrstat

0.3.4

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

2packages dependsuggested by 1

10.2Kdownloads / year

57.0%test coverage

13/13flavors OK

Overview

About

Maintained by Kaifeng LuCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.3.4

removed the rankp0 argument and output from the seamless design functions and simulators, which now always select the most promising treatment at the end of phase 2
added bm_rank and pe_rank methods to lrsim_bmTrtSel for rank-based Dunnett adjustment for dose selection in stage 1 in seamless phase 2/3 designs
added getNFromNeventsAndFollowup and its C++ backend in lrstat.cpp for accrual duration calculations under target-event and follow-up constraints
corrected the minimum weighted p-value ratio initialization in fadjpduncpp (used by fadjpdun) from 1.0 to positive infinity so that ratios exceeding 1 are properly accounted for when computing intersection p-values
added the simulate parameter to the lrschoenfeld function, and added a half-count correction for extreme simulated powers

Show all changes in 0.3.4Hide the rest of the changes in 0.3.4

added the Bonferroni p-value combination method ctbonferroni to lrsim_bmTrtSel
added the familywise error rate fwer to the output of lrsim_bmTrtSel
added disjunctive and conjunctive power to each byMethod result from lrsim_bmTrtSel and to the run_scenario output data frame
added event-driven phase III analyses to lrsim_bmTrtSel through the totalNumberOfEvents target, while retaining studyDurationPhase3 for fixed-duration analyses
changed long-term time-to-event endpoint generation in lrsim_bmTrtSel from response-status-stratified hazards to a copula-based approach, with the latent biomarker response variable correlated directly with the TTE endpoint
optimized the CE variants in lrsim_bmTrtSel by precalculating the sample size based nominal time stage boundaries once before data generation
optimized selection-boundary calculations by making use of no efficacy stopping in stage 1.
optimized exitprob_seamless under equal treatment effects by evaluating the phase-2 selected-arm probabilities once and using arm symmetry for the remaining arms
renamed the fPCStagewise input parameters stg1_inthyp_nr and stg2_elemhyp to stg1_inthyp_nr_idx and stg2_elemhyp_idx, respectively, to make their index semantics explicit and align them with the output names and related adaptive-testing interfaces
standardized lrsim_bmTrtSel testing method identifiers to lowercase, including inputs, returned methods and byMethod names, and sumdataTTE rejection indicator columns
added sumdataBIN and sumdataTTE summary datasets to lrsim_bmTrtSel, including zBiomarker in sumdataBIN and all individual and pooled stage 1 log-rank Z statistics in sumdataTTE to allow derivation of rejection decisions for all methods, along with optional subject-level rawdataBIN and rawdataTTE datasets controlled by maxNumberOfRawDatasets
added rmvnorm and related multivariate-normal sampling helpers for drawing correlated random vectors from a covariance matrix via Cholesky-based generation and seeded overloads
added pordmvnormr to compute lower- and upper-tail probabilities for order statistics of multivariate normal random variables, with analytic shortcuts for nonnegative compound-symmetry covariance structures and inclusion-exclusion over reduced-dimensional orthant probabilities for general covariance matrices
removed mvtnorm from Suggests
changed the default value of corrEfficacyToxicity in lrsim_bmTrtSel_cpp() from 0.5 to 0
corrected a collapse argument typo in print.nbpower
consolidated alpha- and beta-spending function formatting across print methods through the shared .format_spending() helper, preserving the existing printed output

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("lrstat", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("kaifenglu/lrstat")

Development version from kaifenglu/lrstat. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-lrstat

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-lrstat

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-lrstat

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 24.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.4

READMEYes · 378 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 0.3.4Citation fileNoWebsiteYes · pkgdown

Help pages: 340 (126 internal)includes a package overview page
Examples that run: 100%217 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 17%

Vignettes (6)

How these are measured

Downloads

10.2K

CRAN downloads in the past year

Rank #3,837 · ~28/day · ~853/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

2.4K90 days

10.2K1 year

Compare downloads with other packages →

Also on507 r2u6 autocran

How downloads are counted

Repository

kaifenglu/lrstat ↗Account: kaifenglu

5Stars

1Forks

0Open issues

0Open PRs

0Releases

803Commits

4Commit identities

803 commits · Last activity 2026-09-29 · 0% stars, 30d · Default branch at 0.3.5, ahead of CRAN 0.3.4 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 83
Median days to close, 50 most recently updated closed PRs: 74

Stars over time

2025-06-05 · 32026-08-20 · 5

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/kaifenglu/lrstat on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-29 · The repository has a site deploy workflow

pkgdown site last built 2026-08-12, before release 0.3.4 (2026-09-15)

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-24
Named in .Rbuildignore: .claude
GitHub Copilotfirst seen 2026-05-13
Pull request: opened by its own account
Commits: 3 by its own account

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing lrstat adds 72 packages (40 with compiled code, 83 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (8)

Rcpp RcppParallelparallelrlang ggplot2 plotly shinystats

LinkingTo (4)

Rcpp RcppParallel RcppThread BH

Suggests (11)

testthat dplyr tidyr knitr rmarkdownsurvivalshinyjs shinyFeedback shinyMatrix (>= 0.8.0)prompter pkgdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

eventPred survSampleSize

Suggests, most downloaded first

graphicalMCP

How these are counted

Code & Tests

Datasets

People & History

People (1)

Kaifeng Lu

Author, Maintainer since 0.1.0 (2021)

Releases (37)

Pick two releases to compare their code metrics.

0.3.4Latest
record
2026-09-15 · current release · diff ↗ ·
added 2 exports
getNFromNeventsAndFollowup, pordmvnormr
0.3.3
record
2026-08-25 · diff ↗ ·
removed 8 exports
adaptDesign_mams, exitprob_mams, getADCI_mams, getBound_mams, getCI_mams, getCP_mams, getDesign_mams, lrsim_mams

added 22 exports
adaptDesign_multiarm, exitprob_multiarm, fCERCer, fCERNewBound, fCERRej, fCERStageBound, fDefaultWgtmat, fPCRej, fPCStage1, fPCStagewise, finthyp, getADCI_multiarm, getBound_multiarm, getCI_multiarm, getCP_multiarm, getDesign2, getDesign_multiarm, lrsim_bmTrtSel, lrsim_mcpmod, lrsim_multiarm, rdsim_multiarm, rdsim_seamless
0.3.2
record
2026-05-13 · diff ↗ ·
removed 4 exports
exitprob_tsssd, getBound_tsssd, getDesign_tsssd, lrsim_tsssd

added 16 exports
adaptDesign_mams, adaptDesign_seamless, exitprob_mams, exitprob_seamless, getADCI_mams, getADCI_seamless, getBound_mams, getBound_seamless, getCI_mams, getCI_seamless, getCP_mams, getCP_seamless, getDesign_mams, getDesign_seamless, lrsim_mams, lrsim_seamless
R
R 4.6.0 released · 2026-04-24
0.3.1
record
2026-04-08 · diff ↗ ·
added 6 exports
exitprob_tsssd, getBound_tsssd, getDesign_tsssd, lrsim_tsssd, pmvnormr, qmvnormr
0.3.0
record
2026-03-07 · diff ↗ ·
removed 12 exports
ad, findInterval3, hd, kmstat1, lrstat1, nbstat1, nevent2, pd, qrcpp, rmstat1, rmvnorm, survsplit

added 5 exports
assess_phregr, corr_pfs_os, dtpwexp, mtpwexp, zph_phregr
0.2.15
record
2025-07-14 · diff ↗ ·
added 5 exports
hazard_pd, hazard_sub, lrsimsub, pbvnorm, rmvnorm
0.2.14
record
2025-06-09 · diff ↗ ·
added 1 export
residuals_liferegr
R
R 4.5.0 released · 2025-04-11
0.2.13
record
2025-03-20 · diff ↗ ·
removed 1 export
runShinyApp

added 3 exports
getDesignMeanDiffCarryoverEquiv, runShinyApp_lrstat, survsplit
0.2.12
record
2025-01-17 · diff ↗ ·
added 3 exports
float_to_fraction, lrschoenfeld, svdcpp
0.2.11
record
2024-12-04 · diff ↗ ·
added 1 export
kmsurv
0.2.10
record
2024-10-18 · diff ↗ ·
removed 1 export
rpsft

added 4 exports
logisregr, qrcpp, residuals_phregr, survfit_phregr
0.2.9
record
2024-06-23 · diff ↗ ·
added 2 exports
binary_tte_sim, rpsft
0.2.8
record
2024-06-19 · diff ↗
0.2.7
record
2024-06-13 · diff ↗ ·
added 4 exports
liferegr, phregr, simonBayesAnalysis, simonBayesSim

Show 35 earlier eventsHide 35 earlier events

unarchivedReturned to CRAN
2024-05-11
0.2.6
record
2024-05-11 · diff ↗ ·
removed 2 exports
simonBayesAnalysis, simonBayesSim
archivedRemoved from CRAN
2024-05-07
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
0.2.5
record
2024-04-22 · diff ↗ ·
removed 1 export
findInterval2

added 20 exports
findInterval3, fquantile, kmdiff, kmest, lrtest, pwexpcuts, pwexploglik, riskDiffExactCI, riskDiffExactPValue, riskRatioExactCI, riskRatioExactPValue, rmdiff, rmest, simonBayesAnalysis, simonBayesSim, zstatOddsRatio, zstatRateDiff, zstatRateRatio, zstatRiskDiff, zstatRiskRatio
unarchivedReturned to CRAN
2024-03-19
0.2.4
record
2024-03-19 · diff ↗ ·
removed 2 exports
kmest, kmest1

added 21 exports
covrmst, kmpower, kmpower1s, kmpowerequiv, kmsamplesize, kmsamplesize1s, kmsamplesizeequiv, kmstat, kmstat1, lrpowerequiv, lrsamplesizeequiv, nbstat1, rmpower, rmpower1s, rmpowerequiv, rmsamplesize, rmsamplesize1s, rmsamplesizeequiv, rmst, rmstat, rmstat1
archivedRemoved from CRAN
2024-03-13
issues were not corrected in time
0.2.3
record
2024-02-27 · diff ↗ ·
added 88 exports
BOINTable, ClopperPearsonCI, getDesignANOVA, getDesignANOVAContrast, getDesignAgreement, getDesignEquiv, getDesignFisherExact, getDesignLogistic, getDesignMeanDiff, getDesignMeanDiffCarryover, getDesignMeanDiffEquiv, getDesignMeanDiffMMRM, getDesignMeanDiffXO, getDesignMeanDiffXOEquiv, getDesignMeanRatio, getDesignMeanRatioEquiv, getDesignMeanRatioXO, getDesignMeanRatioXOEquiv, getDesignOddsRatio, getDesignOddsRatioEquiv, getDesignOneMean, getDesignOneMultinom, getDesignOneProportion, getDesignOneRateExact, getDesignOneSlope, getDesignOrderedBinom, getDesignPairedMeanDiff, getDesignPairedMeanDiffEquiv, getDesignPairedMeanRatio, getDesignPairedMeanRatioEquiv and 58 more
0.2.2
record
2023-12-22 · diff ↗ ·
added 1 export
ftrunc
0.2.1
record
2023-11-28 · diff ↗ ·
removed 1 export
getAccrualDuration

added 7 exports
adaptDesign, getADCI, getADRCI, getAccrualDurationFromN, getCI, getCP, getRCI
0.2.0
record
2023-10-01 · diff ↗ ·
added 1 export
fadjpdun
0.1.15
record
2023-08-17 · diff ↗ ·
added 3 exports
fmodmix, fstdmix, fstp2seq
0.1.14
record
2023-06-09 · diff ↗ ·
added 3 exports
getAccrualDuration, getDurationFromNevents, getNeventsFromHazardRatio
0.1.13
record
2023-05-21 · diff ↗
0.1.12
record
2023-04-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.11
record
2023-02-09 · diff ↗ ·
added 2 exports
kmest, kmest1
0.1.10
record
2022-10-25 · diff ↗
0.1.9
record
2022-10-09 · diff ↗ ·
added 2 exports
fadjpsim, fwgtmat
0.1.8
record
2022-09-11 · diff ↗ ·
removed 2 exports
set_seed, stl_sort

added 8 exports
fadjpbon, fseqbon, getBound, lrsim2e, lrsim2e3a, lrsim3a, repeatedPValue, updateGraph
unarchivedReturned to CRAN
2022-08-29
0.1.7
record
2022-08-29 · diff ↗ ·
added 1 export
getDesign
archivedRemoved from CRAN
2022-08-24
issues were not corrected in time
unarchivedReturned to CRAN
2022-08-09
0.1.6
record
2022-08-09 · diff ↗
archivedRemoved from CRAN
2022-06-25
check problems were not corrected in time
0.1.5
record
2022-06-09 · diff ↗
0.1.4
record
2022-06-07 · diff ↗ ·
added 1 export
lrstat1
R
R 4.2.0 released · 2022-04-22
0.1.3
record
2022-02-09 · diff ↗
0.1.2
record
2022-02-02 · diff ↗ ·
added 1 export
errorSpent
0.1.1
record
2021-12-23 · diff ↗ ·
removed 1 export
qtpwexp1
0.1.0
record
2021-12-17
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-17
Total releases: 37 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 106 KB / 10 files
Download size: 1.2 MB

Appears in task views

Clinical Trial Design, Monitoring, Analysis and Reporting

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("lrstat")

Format

Lu, K. (2026). lrstat: Power and Sample Size Calculation for Non-Proportional Hazards and Beyond (Version 0.3.4) [Computer software]. https://doi.org/10.32614/CRAN.package.lrstat

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for lrstat version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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