replicate with
realization, including in names of arguments and output. As
a result, the argument included.replicates.BMA is now
deprecated and will be removed in version 1.0.0. Use
included.realizations.BMA instead.ecdfplot() now has an argument show.mean
(default TRUE) to toggle whether to plot curves for the
distribution of the mean doses across realizations and individuals.Shortened column names CI.lowerbound and
CI.upperbound in the summary() output to
CI.lower and CI.upper, respectively.
Substantially increased ERC computation speed for the
clogit and prophaz families.
Confidence intervals are no longer computed inside
ameras(). The arguments CI,
params.profCI, maxit.profCI, and
tol.profCI are deprecated and will be removed in version
1.0.0. Use the new confint() method instead. See
?confint.amerasfit for details.
The direct argument interface to ameras() is
deprecated and will be removed in version 1.0.0. The arguments
Y, dosevars, doseRRmod,
deg, M, X, offset,
entry, exit, and setnr are
deprecated. Please use the new formula interface instead. See
?ameras for details.
Implemented a formula interface for ameras(). The
dose variable is specified using the special dose() term,
which supports tidyselect syntax for selecting dose columns and allows
specifying the dose-response model and effect modifiers directly in the
formula. See ?ameras for details and examples.
Added confint.amerasfit() for computing confidence
intervals separately from model fitting. See
?confint.amerasfit for details.
Added function ecdfplot() for exploratory
visualization of the dose realizations before model fitting.
Reduced memory usage for large datasets.
summary.amerasfit() now only includes confidence
interval columns after they have been computed via
confint(). Before calling confint(), a note is
printed directing the user to compute confidence intervals.
Profile likelihood confidence interval bounds now include p-values in the summary table, making it easier to assess the accuracy of the root-finding algorithm.
Removed memoization of the profile likelihood function as it was causing issues and likely not providing much benefit.
keep.data added to ameras() (default
TRUE). When TRUE, the data are stored on the
returned amerasfit object, which is required for profile
likelihood confidence interval computation via confint()
without re-supplying the data. Set to FALSE to reduce
memory usage for large datasets, in which case the data must be supplied
to confint() explicitly. See ?ameras and
?confint.amerasfit for details.