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Changelog

Source: NEWS.md

TrialSimulator 1.0.0

Update

  • Fix issues to meet CRAN submission conditions.

TrialSimulator 0.97.0

Bug Fix

  • Fix a bug in function event_plot() for plot of cumulative events number when endpoint name is "ep". This is due to data masking in dplyr.
  • Fix issues in unit tests caused by new dropout mechanisum.
  • use Bonferroni method in unit test of update_sample_ratio. This test is probably broken by randomness (it is okay).

TrialSimulator 0.96.0

Update

  • Update mechanism of simulating dropout time. Switching from trial level to patient level, i.e. dropout time is now the time from a patient is enrolled until leaving a trial. This aligns with common practice and popular softwares.

TrialSimulator 0.95.0

Update

  • Add vignette of action function.

TrialSimulator 0.94.0

New Feature

  • Add function summarizeMilestoneTime and its plot method to summarize triggering time of milestones.

TrialSimulator 0.93.0

New Feature

  • update_sample_ratio() now supports updating multiple arms simultaneously. When ratio is not a whole number, sample() is used to replace the permuted block algorithm to randomize patients to arms. This enable response-adaptive design.
  • Add a vignette of response-adaptive design using update_sample_ratio().

TrialSimulator 0.92.0

Update

-Add vignette of fixed design. -Add vignette of wrapper functions of commom statistical tests.

TrialSimulator 0.91.0

New Feature

  • Add function that maps medians of PFS and OS, and their correlation to the hazard parameters. The induced hazard parameters can be used with PFS-OS generator .

Update

  • Add vignette of simulating PFS and OS.

TrialSimulator 0.90.0

New Feature

  • Save event counts per arm in simulation output.
  • No long stop the program when all planned patients are already randomized into the trial when calling the function enroll_patients. This is useful when a milestone is triggered after all patients are recruited.

Bug Fix

  • Fix a bug that affects functions and when patient recruitment is completed fast thus no sample increment between some milestones. This bug can substantially reduce testing powers.

TrialSimulator 0.89.0

New Feature

  • Support ... in eventNumber to count event in subset of trial data. This is useful in enrichment design when milestone is defined based on biomarker.

TrialSimulator 0.88.0

New Feature

  • Add function get as alias of get_custom_data in the Trials class.

Bug Fix

  • Fix a bug that no results is returned to controller when an error is triggered.

Update

  • Print informative message when trial$dunnettTest(..., planned_info = "default") triggers an error.

TrialSimulator 0.87.0

Bug Fix

  • Revise Trials$dunnettTest to be compatible to one-sided logrank test.

TrialSimulator 0.86.0

Bug Fix

  • Fix a bug in the fourth-state model.

TrialSimulator 0.85.0

New Feature

  • Add data generators of time to response, progression and death.

TrialSimulator 0.84.0

New Feature

  • The function fitLogrank now supports formula. strata(...) can be in formula. No covariate is accepted.
  • Add unit tests for fitLogistic.

TrialSimulator 0.83.0

New Feature

  • The function fitLogistic now supports scale = "coefficient" to compute regression coefficient as main effect of arm in the presence of covariates. It is also equivalent to scale = "log odds ratio" in the absence of covariates.
  • Add unit tests for fitLogistic.

TrialSimulator 0.82.0

New Feature

  • The function fitCoxph now supports formula to compute log hazard ratio or hazard ratio as main effect of arm. It will detect whether arm’s main effect is specified in formula. It allows covariates and interaction between covariates and arm. However, only the main effect of arm is tested and returned.
  • Add unit tests for fitCoxph.

TrialSimulator 0.81.0

New Feature

  • The function fitLogistic now supports computing log odds ratio, odds ratio, risk ratio, and risk difference using emmeans contrast, in the presence of covariates.
  • Add unit tests for fitLogistic and fitLinear.

TrialSimulator 0.80.0

New Feature

  • The function fitLogistic now supports formula with covariates, and uses emmeans contrast to compute average treatment effect (ATE) on the logit scale.

TrialSimulator 0.79.0

New Feature

  • The function fitLinear now supports formula with covariates, and uses emmeans contrast to compute average treatment effect (ATE) on the mean scale.

TrialSimulator 0.78.0

Updates

  • The trigger_condition in the function milestone is deprecated and is replaced with when. Note that trigger_condition is still supported in the R6 class Milestones.

TrialSimulator 0.77.0

Updates

  • Add case for unit test.

TrialSimulator 0.76.0

Bug Fixes

  • Fix a bug that trial$get_custom_data throws an error when n > 1 in controller$run(n) because custom data is wiped out in trial$reset.

TrialSimulator 0.75.0

Update

  • Add vignette of defining arms.

TrialSimulator 0.74.0

New Feature

  • Support inclusion criteria in arm through the ... argument.

TrialSimulator 0.73.0

New Feature

  • Print summary report of arms when printing an arm object in console or rmarkdown.

TrialSimulator 0.72.0

New Feature

  • Print summary report of endpoints when printing an endpoint object in console or rmarkdown.

TrialSimulator 0.70.0

Updates

  • Add vignette for longitudinal endpoints.

TrialSimulator 0.68.0

Updates

  • Rename trial event as milestone. This a major update. Relevant codes and documents are updated accordingly.
  • Add executable examples for controller() as per suggestion from CRAN team.

TrialSimulator 0.67.0

Updates

  • Print event counts at trial events using message() so that Shiny app can display it properly.

TrialSimulator 0.66.0

Updates

  • Add cases for unit test.

TrialSimulator 0.65.0

New Features

  • Add function solveMixtureExponentialDistribution to compute median of exponential endpoint of subgroup or the overall population.

TrialSimulator 0.63.0

New Features

  • Add wrapper functions endpoints, arm, trial, event, listener and controller for Endpoint$new, Arm$new, Trial$new, Event$new, Listener$new and Controller$new.

TrialSimulator 0.62.0

New Features

  • Allow extending trial duration with Trial$set_duration.

TrialSimulator 0.61.0

Updates

  • Deprecate function enroll_a_patient. Use enroll_patients only.

TrialSimulator 0.58.0

Updates

  • Update vignette of adaptive seamless design.

Bug Fixes

  • Fix a bug to use n > 1 in Controller$run when an arm can possibly be removed adaptively during a trial.

New Features

  • Allow specifying arms in enrollment. This is useful to count randomized patients of all arms even if some are removed adaptively.

TrialSimulator 0.57.0

Updates

TrialSimulator 0.56.0

New Features

  • Controller$run now can specify number of simulation replicates by newly added argument n. If n is greater than 1, simulation results can be accessed in Controller$get_output().

TrialSimulator 0.55.0

Bug Fixes

  • Fix a bug in StaggeredRecruiter to force the enrollment time of the first patient is zero. This is an known issue but I was too lazy to fix it. Earlier version may have overestimated time of events.

New Features

  • add function fitFarringtonManning of Farrington-Manning test for rate difference.

TrialSimulator 0.54.0

New Features

  • Add function Trial$bind to row bind data frame in action functions. It is useful to prepare inputs of group sequential or graphical test.

TrialSimulator 0.53.0

New Features

  • Add vignette of condition system.

TrialSimulator 0.52.0

Bug Fixes

  • Fix a bug that data is not censored correctly at events. This bug does not affect a trial without interims.

TrialSimulator 0.51.0

New Features

  • Add vignette of non-time-to-event endpoints.
  • Add function weibullDropout to compute parameters of Weibull distribution when using it for dropout distribution.

TrialSimulator 0.49.0

New Features

  • Add vignette of time-to-event endpoints.

TrialSimulator 0.48.0

Bug Fixes

  • Fix a bug when alpha of a node in graph is set to rounding error bound 1e-5 while no alpha should have been propagated.

TrialSimulator 0.47.0

New Features

  • Support new condition system for event triggering. Built-in functions enrollment, eventNumber and calendarTime can be combined with & and |. Nested combination is supported by using parentheses.
  • TriggerByEventNumbers and TriggerByCalendarTime are therefore deprecated.

TrialSimulator 0.44.0

Bug Fixes

  • Fix a bug when adding an arm that is already in the trial.

TrialSimulator 0.43.0

New Features

  • Add function fitLogistic to fit logistic regression model.
  • Support model fitting for multiple treatment arms in logistic regression, Cox PH model, and logrank test.

TrialSimulator 0.42.0

Minor Updates

  • Add a logo.

TrialSimulator 0.40.0

Bug Fixes

  • Revise examples for CRAN submission.

TrialSimulator 0.39.0

Bug Fixes

  • Remove space in class name to eliminate R CMD check note.

TrialSimulator 0.38.2

Bug Fixes

  • Throw error message when none of the hypotheses at test has non-zero alpha in graphical test.
  • Update vignette.

TrialSimulator 0.38.1

New Features

  • Plot stacked area chart for accumulative event numbers of endpoints.

Bug Fixes

  • Fix a bug when small weight (epsilon) is used in graph in graphical testing. Small weight can be conflict with integral tolerance error.

TrialSimulator 0.37.0

New Features

  • Return more informative error message when custom random number generators are used to define endpoints. Specifically, it guides users to return columns for time-to-event endpoints properly.
  • Update manual for generator in Endpoint.

TrialSimulator 0.36.0

Bug Fixes

  • Fix a bug in GraphicalTesting when a hypothesis is tested multiple times at the same stage because more alpha is passed from other rejected hypothesis.

TrialSimulator 0.35.0

New Features

  • Warn when incremental information is too low that can affect normality approximation of combination test.

Bug Fixes

  • Minor bugs fixed.

TrialSimulator 0.33.0

New Features

  • Add README.

TrialSimulator 0.33.0

New Features

  • Provide a default action function do_nothing() if users have no intent to do anything at a triggered event. This function can be passed to the argument action when creating a new event, e.g., Event$new(name = 'interim', trigger_condition = TriggerByCalendarTime, action = do_nothing, calendar_time = 64).

TrialSimulator 0.30.0

New Features

  • Capture error inside Controller$run() and insert error message into output (see Trial$get_output()$error_message). It helps to integrate TrialSimulator with targets.

TrialSimulator 0.29.0

New Features

  • Support closed test based on inverse normal combination test.
  • Seed can be accessed by Trial$get_seed().

TrialSimulator 0.28.0

New Features

  • Support inverse normal combination test when multiple treatment arms present. Dunnett’s test is used for comparison.
  • Specify random seed if user dose not pick one. Seed is saved into Trial’s output for reproducibility.

TrialSimulator 0.27.0

New Features

  • Support dry run for fixed design.

TrialSimulator 0.26.0

New Features

  • Adjust boundary at final analysis for over- or under-running trials.
  • Support custom alpha spending function in graphical testing procedure.

TrialSimulator 0.25.0

New Features

  • Support inverse normal combination test for logrank statistics.

TrialSimulator 0.24.0

New Features

  • Update GraphicalTesting based on simplified interface of GroupSequentialTest.