measles_sailer data: generation numbering now starts at
0 (not 1)
fixed uniform censoring in rexp_delayed and
rweib_delayed: Lambert W function (implemented in C++)
useful for exponential, uniroot approach for Weibull
enhance documentation
incubate 1.4.0
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
incubate 1.3.0
implement different maximum-likelihood based estimation methods with
option to profile out Weibull’s scale-parameter
MLEn: naive ML
MLEw: weighted ML
MLEc: corrected ML
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
incubate 1.2.1
fix package help after 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 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.
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
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 due to 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
add data set stankovic: experimental data on tumour
growth in mice (Stankovic et al, EGFL7 enhances surface expression of
integrin (2018))