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Changelog

Source: NEWS.md

gsDesign 3.6.5 (November, 2024)

CRAN release: 2024-11-14

Improvements

  • toInteger() (introduced in gsDesign 3.5.0) is updated to match broader, non-gsDesign conventions for deriving integer sample size and event counts (@keaven, #172).

    This update may result in different outputs compared to previous versions. Users who use this function should review the updated function documentation (?toInteger) and vignette("toInteger") for details.

Testing

Documentation

  • Add the cph role to the Authors@R field following best practices (@nanxstats, #166).

gsDesign 3.6.4 (July, 2024)

CRAN release: 2024-07-26

Improvements

We have made the spending function summary output more readable and informative.

  • Text summaries for spending functions with multiple parameters are now properly formatted. For instance, a b = 0.5 1.5 is now displayed as a = 0.5, b = 1.5 (@jdblischak, #162).
  • The summary() method for sfLDOF() no longer includes the redundant none = 1 in its output (@jdblischak, #159).

Documentation

  • Added a note about using a positive scalar for sfupar in sfLDOF() to create a generalized O’Brien-Fleming spending function (@keaven, 52cc711, 99996b).
  • Improved math rendering in our pkgdown site vignettes by switching to KaTeX, which is now supported in pkgdown 2.1.0 (@nanxstats, #161).
  • Standardized vignette titles and headings by using h2 as the base level and adopting sentence case throughout (@nanxstats, #158).

gsDesign 3.6.3 (July, 2024)

CRAN release: 2024-07-09

New features

Improvements

Testing

gsDesign 3.6.2 (April, 2024)

CRAN release: 2024-04-09

Documentation

Testing

  • Move independently programmed functions for validation as standard test helper files (#130).

gsDesign 3.6.1 (February, 2024)

CRAN release: 2024-02-13

New features

Improvements

  • The plotting functions now use dplyr::reframe() to replace dplyr::summarize() when performing grouped cumsum() (@jdblischak, #114).
  • The plotting functions are updated to use the .data pronoun from rlang with ggplot2::aes(). This simplifies the code and follows the recommended practice when using ggplot2 in packages (@jdblischak, #124).
  • hGraph() now uses named guide argument in the scale_fill_manual() call to be compatible with ggplot2 3.5.0 (@teunbrand, #115). Note: this function has been deprecated and moved to gMCPLite since gsDesign 3.4.0. It will be removed from gsDesign in a future version. Please use gMCPLite::hGraph() instead.

Documentation

  • vignettes("SurvivalOverview") is updated with more details and minor corrections (@keaven, #126).
  • Fix equation syntax in plotting function documentation to render math symbols properly (@keaven, #118).

gsDesign 3.6.0 (November, 2023)

CRAN release: 2023-11-12

Breaking changes

  • gsSurv() and nSurv() have updated default values for T and minfup so that function calls with no arguments will run. Legacy code with T or minfup not explicitly specified could break (#105).

New features

  • gsSurvCalendar() function added to enable group sequential design for time-to-event outcomes using calendar timing of interim analysis specification (#105).
  • as_rtf() method for gsBinomialExact() objects added, enable RTF table outputs for standard word processing software (#102).

Improvements

  • toBinomialExact() and gsBinomialExact(): fix error checking in bound computations, improve documentation and error messages (#105).
  • print.gsSurv(): Improve the display of targeted events (very minor). The boundary crossing probability computations did not change. The need is made evident by the addition of the toInteger() function (#105).
  • toInteger(): Fix the documentation and execution based on the ratio argument (#105).
  • Update the vaccine efficacy, Poisson mixture model, and toInteger vignettes (#105).
  • Standardize and improve roxygen2 documentation (#104).

gsDesign 3.5.0 (July, 2023)

CRAN release: 2023-07-19

  • sfPower() now allows a wider parameter range (0, 15].
  • toInteger() function added to convert gsDesign or gsSurv classes to integer sample size and event counts.
  • toBinomialExact() function added to convert time-to-event bounds to exact binomial for low event rate studies.
  • Added “A Gentle Introduction to Group Sequential Design” vignette for an introduction to asymptotics for group sequential design.
  • as_table() and as_gt() methods for gsBinomialExact objects added, as described in the new “Binomial SPRT” vignette.
  • In plot.ssrCP(), the hat syntax in the mathematical expression is revised, resolving labeling issues.
  • ggplot2::qplot() usage replaced due to its deprecation in ggplot2 3.4.0.
  • Link update for the gsDesign manual in the documentation, now directly pointing to the gsDesign technical manual bookdown project.
  • Introduced a new hex sticker logo.

gsDesign 3.4.0 (October, 2022)

CRAN release: 2022-10-12

  • Removed restriction on gsCP() interim test statistic zi (#63).
  • Removed gMCP dependency. Updated vignettes and linked to vignettes in gMCPLite (#69).
  • Added deprecation warning to hGraph() and suggested using gMCPLite::hGraph() instead (#70).
  • Moved ggplot2 from Depends to Imports (#56).

gsDesign 3.3.0 (May, 2022)

CRAN release: 2022-05-27

  • Addition of vignettes
    • Demonstrate cure model and calendar-based analysis timing for time-to-event endpoint design
    • Vaccine efficacy design using spending bounds and exact binomial boundary crossing probabilities
  • Minor fix to labeling in print.gsProbability
  • Fixed error in sfStep
  • Updates to reduce R CMD check and other minor issues

gsDesign 3.2.2 (January, 2022)

CRAN release: 2022-02-02

  • Use inherits() instead of is() to determine if an object is an instance of a class, when appropriate
  • Correctly close graphics device in unit tests to avoid plot output file not found issues
  • Minor fixes to hGraph() for multiplicity graphs
  • Minor fix to nBinomial() when odds-ratio scale specified to resolve user issue
  • Minor changes to vignettes

gsDesign 3.2.1 (July, 2021)

CRAN release: 2021-07-12

  • Changed gt package usage in a vignette due to deprecated gt function
  • Replied to minor comments from CRAN reviewer (no functionality impact)
  • Minor update to DESCRIPTION citing Jennison and Turnbull reference

gsDesign 3.2.0 (January, 2021)

CRAN release: 2021-03-13

  • Substantially updated unit testing to increase code coverage above 80%
  • Updated error checking messages to print function where check fails
  • Removed dependencies on plyr packages
  • Updated github actions

gsDesign 3.1.1 (May, 2020)

CRAN release: 2020-05-07

  • Vignettes updated
  • Added hGraph() to support ggplot2 versions of multiplicity graphs
  • Eliminated unnecessary check from sequentialPValue
  • Targeted release to CRAN
  • Removed dependencies on reshape2, plyr
  • Updated continuous integration
  • Updated license

gsDesign 3.1.0 (April, 2019)

  • Addition of pkgdown web site
  • Updated unit testing to from RUnit to testthat
  • Converted to roxygen2 generation of help files
  • Converted vignettes to R Markdown
  • Added Travis-CI and Appveyor support
  • Added sequentialPValue function
  • Backwards compatible addition of spending time capabilities to gsDesign and gsSurv

gsDesign 3.0-5 (January, 2018)

  • Registered C routines
  • Fixed “gsbound”
  • Replaced “array” by “rep” calls to avoid R CMD check warnings

gsDesign 3.0-4 (September, 2017)

  • First Github-based release
  • Cleaned up documentation for nBinomial1Sample()
  • Updated documentation and code (including one default value for an argument) for nBinomial1Sample() to improve error handling and clarity
  • Updated sfLDOF() to generalize with rho parameter; still backwards compatible for Lan-DeMets O’Brien-Fleming

gsDesign 3.0-3

  • Introduced spending time as a separate concept from information time to enable concepts such as calendar-based spending functions. The only user function changed is the gsDesign() function and the change is the addition of the parameters usTime and lsTime; default behavior is backwards compatible.

gsDesign 3.0-2 (February, 2016)

  • Simplified conditional power section of gsDesignManual.pdf in doc directory
  • Corrected basic calculation in gsCP()
  • Eliminated deprecated ggplot2 function opts()

gsDesign 3.0-1 (January, 2016)

CRAN release: 2016-02-01

  • More changes to comply with R standards (in NAMESPACE - importFrom statements - and DESCRIPTION - adding plyr to imports) ensuring appropriate references.
  • Deleted link in documentation that no longer exists (gsBinomialExact.Rd).
  • Last planned RForge-based release; moving to Github.

gsDesign 3.0-0 (December, 2015)

  • Updated xtable extension to meet R standards for extensions.
  • Fixed xtable.gsSurv and print.gsSurv to work with 1-sided designs
  • Update to calls to ggplot to replace show_guide (deprecated) with show.legend arguments where used in ggplot2::geom_text calls; no user impact
  • Minor typo fixed in sfLogistic help file
  • Cleaned up “imports” and “depends” in an effort to be an R “good citizen”
  • Registered S3 methods in NAMESPACE

gsDesign 2.9-4

  • Minor edit to package description to comply with R standards

gsDesign 2.9-3 (November, 2014)

CRAN release: 2014-11-10

  • Added sfTrimmed as likely preferred spending function approach to skipping early or all interim efficacy analyses; this also can adjust bound when final analysis is performed with less than maximum planned information. Updated help(sfTrimmed) to demonstrate these capabilities.
  • Added sfGapped, which is primarily intended to eliminate futility analyses later in a study; see help(sfGapped) for an example
  • Added summary.spendfn() to provide textual summary of spending functions; this simplified the print function for gsDesign objects
  • Added sfStep() which can be used to set an interim spend when the exact amount of information is unknown; an example of how this can be misused is provided in the help file
  • Fixed rounding so that gsBoundSummary, xtable.gsSurv and summary.gsDesign are consistent for gsSurv objects