Package: stepp 3.2.7

stepp: Subpopulation Treatment Effect Pattern Plot (STEPP)

A method to explore the treatment-covariate interactions in survival or generalized linear model (GLM) for continuous, binomial and count data arising from two or more treatment arms of a clinical trial. A permutation distribution approach to inference is implemented, based on permuting the covariate values within each treatment group.

Authors:Wai-ki Yip [aut, cre], Ann Lazar [ctb], David Zahrieh [ctb], Chip Cole [ctb], Ann Lazar [ctb], Marco Bonetti [ctb], Victoria Wang [ctb], William Barcella [ctb], Sergio Venturini [aut] Richard Gelber [ctb]

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stepp.pdf |stepp.html✨
stepp/json (API)

# Install 'stepp' in R:
install.packages('stepp', repos = c('https://steppdev.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/steppdev/stepp/issues

Datasets:
  • aspirin - The aspirin data set.
  • balance_example - Sample data to use with the 'balance_patients()' function.
  • bigCI - The BIG 1-98 trial dataset for cumulative incidence STEPP.
  • bigKM - The BIG 1-98 trial dataset for Kaplan-Meier STEPP.
  • simdataKM - Simulated data for Kaplan-Meier STEPP analysis.

On CRAN:

22 exports 1.31 score 60 dependencies 1 mentions 25 scripts 927 downloads

Last updated 1 months agofrom:6cd2114d0c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 10 2024
R-4.5-win-x86_64OKSep 10 2024
R-4.5-linux-x86_64OKSep 10 2024
R-4.4-win-x86_64OKSep 10 2024
R-4.4-mac-x86_64OKSep 10 2024
R-4.4-mac-aarch64OKSep 10 2024
R-4.3-win-x86_64OKSep 10 2024
R-4.3-mac-x86_64OKSep 10 2024
R-4.3-mac-aarch64OKSep 10 2024

Exports:analyze.CumInc.steppanalyze.KM.steppbalance_patientsestimategen.tailwingenerateplotprintsteppstepp_plotstepp_printstepp_summarystepp.CIstepp.edgestepp.GLMstepp.KMstepp.rnotestepp.subpopstepp.teststepp.winsummarytest

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecowplotcpp11DerivdoBydplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrquantregR6RColorBrewerRcppRcppEigenrlangrstudioapiscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Analyze competing risks data using Cumulative Incidence methodanalyze.CumInc.stepp
Analyze survival data using Kaplan-Meier methodanalyze.KM.stepp
The aspirin data set.aspirin
Sample data to use with the 'balance_patients()' function.balance_example
Utility function for determining the optimal values for generating the subpopulations.balance_patients
The BIG 1-98 trial dataset for cumulative incidence STEPP.bigCI
The BIG 1-98 trial dataset for Kaplan-Meier STEPP.bigKM
The standard generic function for all estimate methodsestimate
Utility function to generate tail-oriented windowgen.tailwin
The standard generic function for the generate method in stsubpop classgenerate
Simulated data for Kaplan-Meier STEPP analysis.simdataKM
Analyze survival or competing risks datastepp
A function to generate the stepp plotsstepp_plot
The function to print the estimate, covariance matrices and test statistics.stepp_print
The function to produce a summary of the size and various attributes of each subpopulationstepp_summary
The constructor to create the stmodelCI objectstepp.CI
The method performs an edge analysis on the STEPP GLM model estimate objects.stepp.edge
The constructor to create the stmodelGLM objectstepp.GLM
The constructor to create the stmodelKM objectstepp.KM
The method to print the release note for STEPP.stepp.rnote
The constructor to create the stsubpop object and generate the subpopulations based on the specified stepp window and covariate of intereststepp.subpop
The constructor to generate a complete steppes object with effect estimates and test statisticsstepp.test
The constructor to create the stepp window objectstepp.win
Class '"steppes"'estimate,steppes-method plot,steppes-method print,steppes-method steppes-class summary,steppes-method test,steppes-method
Class '"stmodel"'stmodel-class
Class '"stmodelCI"'estimate,stmodelCI-method print,stmodelCI-method stmodelCI-class test,stmodelCI-method
Class '"stmodelGLM"'estimate,stmodelGLM-method print,stmodelGLM-method stmodelGLM-class test,stmodelGLM-method
Class '"stmodelKM"'estimate,stmodelKM-method print,stmodelKM-method stmodelKM-class test,stmodelKM-method
Class '"stsubpop"'generate,stsubpop-method stsubpop-class summary,stsubpop-method
Class '"stwin"'stwin-class summary,stwin-method
the standard generic function for all test methodstest