High-Performance Open-Source Archive
Fix the calculation of intersection hypothesis pvalue when family weights is null for all gatekeeping procedures.
Revise the error fraction function to avoid floating point issue
Fix the images in the Case studies vignette
Revise the specification of serial and parallel parameters in MixtureGatekeepingAdj (matrix instead of list)
Revise the Outcome table generation function used for reporting
ReporteRs R package is not available on the CRAN
anymore, the report generation feature has been revised using the
officer and flextable R packages. These
packages are now required to use the GenerateReport
function.Addition of the multinomial distribution
(MultinomialDist, see Analysis
model).
Addition of the ordinal logistic regression test
(OrdinalLogisticRegTest, see Analysis
model).
Addition of the Proportion statistic (PropStat, see
Analysis
model).
Addition of the Fallback procedure (FallbackAdj, see
Analysis
model).
Addition of a function to get the analysis results generated in
the CSE using the AnalysisStack function (see Analysis
stack).
Addition of the ExtractAnalysisStack function to
extract a specific set of results in an AnalysisStack
object (see Analysis
stack).
Creation of a vignette to describe the functions implementing the
adjusted p-values (AdjustPvalues) and one-sided
simultaneous confidence intervals (AdjustCIs).
Minor revisions of the generated report
It is now possible to use an option to specify the desirable
direction of the treatment effect in a test, e.g.,
larger = TRUE means that numerically larger values are
expected in the second sample compared to the first sample and
larger = FALSE otherwise. This is an optional argument for
all two-sample statistical tests to be included in the Test object. By
default, if this argument is not specified, it is expected that a
numerically larger value is expected in the second sample (i.e., by
default larger = TRUE).
Due to difficulties for several users to install the Mediana R
package because of java issue, the ReporteRs R package is
not required anymore (remove from Imports). However, to be able to
generate the report, the user will require to have the
ReporteRs R package installed.
Minor revision to the two-sample non-inferiority test for proportions to ensure that the number of successes is not greater than the sample size
Addition of the AdjustPvalues function which can be
used to get adjusted p-values from a Multiple Testing Procedure. This
function cannot be used within the CSE framework but it is an add-on
function to compute adjusted p-values.
Addition of the AdjustCIs function which can be used
to get simultaneous confidence intervals from a Multiple Testing
Procedure. This function cannot be used within the CSE framework but it
is an add-on function to simultaneous confidence intervals.
Creation of vignettes
Addition of the Fixed-sequence procedure
(FixedSeqAdj, see Analysis
model).
Addition of the Cox method to calculate the HR, effect size and
ratio of effect size for time-to-event endpoint. This can be
accomplished by setting the method argument in the
parameter list to set-up the calculation based on the Cox method.
(par = parameters(method = "Cox"), see Analysis
model).
Addition of the package version information in the report.
Revision of one-sided p-value computation for Log-Rank test.
Revision of the call for Statistic in the core function (not visible).
Revision of the function to calculate the Hazard Ratio Statistic
(HazardRatioStat method). By default, this calculation is now based on
the log-rank statistic ((O2/E2)/(O1/E1) where O and E are Observed and
Expected event in sample 2 and sample 1. A parameter can be added using
the method argument in the parameter list to set-up the
calculation based on the Cox method
(par = parameters(method = "Cox"), see Analysis
model).
Revision of the function to calculate the effect size for
time-to-event endpoint (EffectSizeEventStat method, based
on the HazardRatioStat method)
Revision of the functions to calculate the ratio of effect size
for continuous (RatioEffectSizeContStat method), binary
(RatioEffectSizePropStat method) and event
(RatioEffectSizeEventStat method) endpoint.
Revision of the function to generate the Test, Statistic, Design and result tables in the report.
Addition of the Beta distribution (BetaDist, see Data
model).
Addition of the Truncated exponential distribution, which could
be used as enrollment distribution (TruncatedExpoDist, see
Data
model).
Addition of the Non-inferiority test for proportion
(PropTestNI, see Analysis
model).
Addition of the mixture-based gatekeeping procedure
(MixtureGatekeepingAdj see Analysis
model).
Addition of a function to get the data generated in the CSE using
the DataStack function (see Data
stack).
Addition of a function to extract a specific set of data in a
DataStack object (see Data
stack).
Addition of the “Evaluation Model” section in the generated report describing the criteria and their parameters (see Simulation report).
Revision of the generation of dropout time.
Correction of the NormalParamAdj function.
Correction of the FisherTest function.
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