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incubate 1.3.0
- 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
- fix package help: due to changes in roxygen
incubate 1.2.0
- 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
- 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
incubate 1.1.5
- doc: further improvements (document all return values)
incubate 1.1.4
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.
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