Changes in version 1.4.0.9000 - current development version Changes in version 1.4.0 (2026-03-22) - allow for random right-censoring in the response variable - allow for delayed normal distribution as new statistical model - weighted MLE (MLEw) - bugfix in weight approximation (relevant for W3) - weight functions as non-exported functions (and not as internal data) - use MLEc as standard criterion for MLEw method (as it has no own likelihood function) - objective function has criterion= as character option - implement S3-function logLik - delay_test: use name LRT (instead of LR) for likelihood ratio tests - new data sets: - data set long2017 from melanoma clinical trial - historic data set measles_sailer with serial interval times of measles outbreak on the sailer HMS America from England to Australia in 1829 Changes in version 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 distribution functions - update simulation R-scripts (in inst/scripts/) to also use ML-based estimation and LR-tests (LRT), with and without censoring Changes in version 1.2.1 (2023-08-21) - fix package help after changes in roxygen Changes in version 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 in the scripts/ sub-directory of the package installation. - 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. Changes in version 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 Changes in version 1.1.8 (2022-05-04) - correct URL for bug reports in DESCRIPTION Changes in version 1.1.7 - more robust test that passes also on Apple-silicon - doc: add homepage in DESCRIPTION Changes in version 1.1.6 (2022-04-28) - use LGPL-licence Changes in version 1.1.5 - doc: further improvements (document all return values) Changes in version 1.1.4 - doc: small improvements Changes in version 1.1.3 - README: better intro text and more text for example Changes in version 1.1.2 - small changes for CRAN-warnings - test: bigger data set for delay estimation Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 0.9.9 - power_diff: improve heuristics in iterative search for sample size, given power Changes in version 0.9.8 - test_diff: change name of P-values (within object) - power_diff: allow to specify power and do iterative computation Changes in version 0.9.7 - confint: smooth delay for parametric bootstrap & delayed exponential model via rectified Gaussian (instead of normal Gaussian) Changes in version 0.9.6 - confint: add option to smooth delay for parametric bootstrap & delayed exponential model Changes in version 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. Changes in version 0.9.4 - confint: logshift accepts also NA and NULL. Useful for simulation studies with optional logshift-setting. Changes in version 0.9.3 - confint: parameterized logshift for delay, new default is 0.01 Changes in version 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 Changes in version 0.9.1 - confint: allow for log-transformation of bootstrapped coefficients Changes in version 0.9 - confint: separate bootstrap data generation and inference step. This allows for more efficient confint-simulations. Changes in version 0.8 - enhance test-coverage for package - reorganize tests to better match the R-script Changes in version 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) Changes in version 0.7.5 - remove dependency on dplyr Changes in version 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 Changes in version 0.7.3 - fixed mapping of bootstrap inference names for boot-package Changes in version 0.7.2 - allow to use boot package to calculate confidence interval Changes in version 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) Changes in version 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 Changes in version 0.6.1 - make handling of ties in calculation of spacings within the objective function more robust Changes in version 0.6 - implement AD-GOF test within test_GOF Changes in version 0.5 - add separate function test_GOF for goodness of fit (GOF) tests based on a fitted model - add Moran's GOF-test Changes in version 0.4 - bug fix in MSE-criterion - bug fix in tie-handling - function estimRoundingError to estimate rounding error (for tie handling) Changes in version 0.3 - simplified power function (dropped stuff and conventions from sscn-package) Changes in version 0.2 - ties='equidist' is default method to handle ties Changes in version 0.1 - more choice in handling of ties: equidist and random - rename function test_delay_diff to test_diff Changes in version 0.0.5 - add confidence intervals (based on basic bootstrap) for model parameters Changes in version 0.0.4 - Weibull: bind= is implemented for all possible parameter combinations - internal clean up Changes in version 0.0.3 - more warnings when MSE-optimization fails - bug fix for power simulation - bug fix in testing Changes in version 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.