NEWS

---

incubate 1.3.0 (2024-08-16)

• implement different maximum-likelihood based estimation methods (naive ML, weighed ML, corrected ML), with option to profile out Weibull's scale-parameter
• use some log-transformed parameters internally for more stable and less constrained optimization
• test_diff: allow for likelihood-ratio test
• include restricted mean survival time function for delayed exponential and Weibull
• [experimental] implement two delay phases for exponential and for Weibull
• update simulation R-scripts (in inst/scripts/) to also use ML-based estimation and LR-tests

incubate 1.2.1 (2023-08-21)

• fix package help: due to changes in roxygen

incubate 1.2.0 (2022-07-25)

• check for minimal number of observations and fail early if not enough observations
• test_diff:
  • test-statistic gets lower bound of 0 enforced (a restricted model can not have better fit than unrestricted model)
  • deactivate Anderson-Darling (AD) GOF-test as its performance in simulations under two-group setting was unsatisfactory
• include simulation R-scripts in package under inst/scripts/ folder. When the package is installed the scripts are found at in the -directory scripts/ within the package.
• rename methods:
  • 'MSE' => 'MPSE' (as the term MSE has already other meanings)
  • 'MLE' => 'MLE0' (to indicate that this is the standard MLE that is not appropriate for delay models)
• rework implementation of objective-function: do not rely on attributes but use the environment of the objective function instead. This means fewer copies of information are made.

incubate 1.1.9

• New implementation of delay smoothing: use objective function along candidate delay values to guide in smoothing
  • define an interval for delay candidate values
  • sample from this interval according to the objective function: the better the value of the objective function the more likely it is to sample a value. For speed of computation, we vary only delay and keep the other parameters at their estimate.
  • use smd_factor to either concentrate or flatten around the best delay estimate
• Better implementation for MLE-fitting:
  • Support MLE-fitting also for Weibull (one group setting only)
  • Move MLE-objective function into a general objective function factory method

incubate 1.1.8 (2022-05-04)

• correct URL for bug reports in DESCRIPTION

incubate 1.1.7

• more robust test that passes also on Apple-silicon
• doc: add homepage in DESCRIPTION

incubate 1.1.6 (2022-04-28)

• use LGPL-licence

incubate 1.1.5

• doc: further improvements (document all return values)

incubate 1.1.4

• doc: small improvements

incubate 1.1.3

• README: better intro text and more text for example

incubate 1.1.2

• small changes for CRAN-warnings
• test: bigger data set for delay estimation

incubate 1.1.1

• Fix errors/warnings from check
  • document every function parameter
  • S3-methods have right parameters
  • specify package name for external functions (e.g., from stats)
  • global variables (use .data and aes_)
• add cran-comments.md file

incubate 1.1.0

• confint: use better default values
• confint: when using bootstrap smoothing for delay, make sure the smoothing keeps limited for tiny estimated rates lambda (see SMD_MINRATE)
• bug fix: plot.incubate_fit has legible colour legend title

incubate 1.0.0

• data: add experimental data stankovic from a publication Stankovic et al EGFL7 enhances surface expression of integrin doi:10.15252/emmm.201708420 (2018) as example data set
• This version of package is also published at https://zenodo.org/record/6462382

incubate 0.9.9

• power_diff: improve heuristics in iterative search for sample size, given power

incubate 0.9.8

• test_diff: change name of P-values (within object)
• power_diff: allow to specify power and do iterative computation

incubate 0.9.7

• confint: smooth delay for parametric bootstrap & delayed exponential model via rectified Gaussian (instead of normal Gaussian)

incubate 0.9.6

• confint: add option to smooth delay for parametric bootstrap & delayed exponential model

incubate 0.9.5

• confint: redefine logshift to mean what is added to the argument of log, before it was subtracted. This meaning seems more natural.

incubate 0.9.4

• confint: logshift accepts also NA and NULL. Useful for simulation studies with optional logshift-setting.

incubate 0.9.3

• confint: parameterized logshift for delay, new default is 0.01

incubate 0.9.2

• confint: log-transformation revisited: shift mainly for delay (and hardly a shift for the other parameters)
• confint: extend test coverage to confint routines

incubate 0.9.1

• confint: allow for log-transformation of bootstrapped coefficients

incubate 0.9

• confint: separate bootstrap data generation and inference step. This allows for more efficient confint-simulations.

incubate 0.8

• enhance test-coverage for package
• reorganize tests to better match the R-script

incubate 0.7.6

• test_diff: do GOF-tests also for unrestricted model (e.g. gof_pearson1) besides for the restricted null model (renamed to gof_pearson0)

incubate 0.7.5

• remove dependency on dplyr

incubate 0.7.4

• add bs_infer = 't0'
• add +3 to degrees of freedom for t-quantiles in bs_infer='t' and ='t0'
• version bump belated: these features were temporarily also released as 0.7.3

incubate 0.7.3

• fixed mapping of bootstrap inference names for boot-package

incubate 0.7.2

• allow to use boot package to calculate confidence interval

incubate 0.7.1

• allow to choose which tests to perform in test_diff (helpful when calculation of AD GOF-tests fails on older R-installations)

incubate 0.7

• change of S3-classes:
  • for delay model fitting the new class is incubate_fit
  • for tests the new class is incubate_test
• confidence intervals supports now simple data generation to draw from the data with replacement (besides parametric bootstrap)
• preliminary support for MLE-fitting: this allows to compare confidence intervals based on MSE vs MLE

incubate 0.6.1

• make handling of ties in calculation of spacings within the objective function more robust

incubate 0.6

• implement AD-GOF test within test_GOF

incubate 0.5

• add separate function test_GOF for goodness of fit (GOF) tests based on a fitted model
• add Moran's GOF-test

incubate 0.4

• bug fix in MSE-criterion
• bug fix in tie-handling
• function estimRoundingError to estimate rounding error (for tie handling)

incubate 0.3

• simplified power function (dropped stuff and conventions from sscn-package)

incubate 0.2

• ties='equidist' is default method to handle ties

incubate 0.1

• more choice in handling of ties: equidist and random
• rename function test_delay_diff to test_diff

incubate 0.0.5

• add confidence intervals (based on basic bootstrap) for model parameters

incubate 0.0.4

• Weibull: bind= is implemented for all possible parameter combinations
• internal clean up

incubate 0.0.3

• more warnings when MSE-optimization fails
• bug fix for power simulation
• bug fix in testing

incubate 0.0.2

• initial start as a move out from package sscn (git history is not moved along, though)
• code robustness: add try code at lower level, directly at where optim is called.