This is a minor release implementing new functionality, updating documentation, and fixing multiple minor issues, mostly in validation of supplied arguments.
Simulate follow-up (and data collection) lag: added option to
have different numbers of simulated patients with outcome data available
compared to the total number of simulated patients randomised at each
adaptive analysis (randomised_at_looks argument in
setup_trial() family of functions). Defaults to same
behaviour as previously (i.e., assuming that outcome data are
immediately available following randomisation). As a consequence,
run_trial() now always conducts a final analysis after the
last adaptive analysis (including both final posterior and ‘raw’
estimates), including the outcome data of all patients randomised to all
arms, regardless of how many had outcome data available at the last
conducted adaptive analysis. Both sets of results are saved and printed
for individual simulations; extract_results(), the
summary() and the print() methods for multiple
simulations have gained the additional argument final_ests
that controls whether the results from this final analysis or from the
last relevant adaptive analysis including each arm are used when
calculating some performance metrics (defaults are set to ensure
backwards compatibility and otherwise use the final estimates in
situations where not all patients are included in the final adaptive
analysis). An example has been added to the Basic examples
vignette illustrating the use of this argument.
Updated plot_history() and
plot_status() to add the possibility to plot different
metrics according to the number of patients randomised as specified by
the the new randomised_at_looks argument to the
setup_trial() functions as described above.
Added the update_saved_trials() function, which
‘updates’ multiple trial simulation objects saved by
run_trials() using previous versions of
adaptr. This reformats the objects to work with the updated
functions. Not all values can be added to previously saved simulation
results without re-running; these values will be replaced with
NAs, and - if used - may lead to printing or plotting of
missing values. However, the function allows re-use of the same data
from previous simulations without having to re-run them (mostly relevant
for time-consuming simulations). Important: please
notice that other objects (i.e., objects returned from the
setup_trial() family of functions and single simulations
returned by run_trial()) may create problems or errors with
some functions if created by previous versions of the package and
manually reloaded; these objects will have to be updated by re-running
the code using the newest version of the package. Similarly, manually
reloaded results from run_trials() that are not updated
using this function may cause errors/problems when used.
Added the check_performance() function (and a
corresponding print() method) which calculates performance
metrics and can be used to calculate uncertainty measures using
non-parametric bootstrapping. This function is now used internally by
the summary() method for multiple trial objects.
Added the plot_convergence() function which plots
performance metrics according to the number of simulations conducted for
multiple simulated trials (possibly after splitting the simulations into
batches), used to assess stability of performance metrics.
Added the possibility to define different probability thresholds
for different adaptive analyses to the setup_trials()
family of functions (for inferiority, superiority, equivalence, and
futility probability thresholds), with according updates in
run_trial() and the print() method for trial
specifications.
Updated plot_status(); multiple arms may now
simultaneously be plotted by specifying more than one valid arm or
NA (which lead to statuses for all arms being plotted) in
the arm argument. In addition, arm name(s) are
now always included on the plots.
Added reference to open access article describing key methodological considerations in adaptive clinical trials using adaptive stopping, arm dropping, and randomisation to the package documentation (https://doi.org/10.1016/j.jclinepi.2022.11.002).
The proportion of conclusive trials when restricting the trials
summarised (in extract_results()) may now be calculated by
the summary() method for multiple trial simulations and by
the new check_performance() function, even if this measure
may be difficult to interpret when the trials summarised is
restricted.
Minor fixes, updates, and added clarification to the documentation in multiple places, including in vignettes, which have also been updated to illustrate some of the new functions added.
Minor fix to print() method for individual trial
results, which did not correctly print additional information about
trials.
Fixed a bug where the same number of patients included could be
used for subsequent data_looks in the
setup_trial() family of functions; this now produces an
error.
Added internal vapply_lgl() helper function; the
internal vapply() helper functions are now used
consistently to simplify the code.
Added multiple internal (non-exported) helper functions to
simplify code throughout the package: stop0(),
warning0(), %f|%, and
summarise_num().
Added names = FALSE argument to
quantile() calls in the summary() method for
trial_results objects to avoid unnecessary naming of some
components if they are subsequently extracted from the returned
object.
Ideal design percentages may be calculated as NaN,
Inf or -Inf in scenarios with no differences;
these are now all converted to NA before being returned by
the various functions.
Minor edits/clarifications to several errors/warnings/messages.
Minor fix to internal verify_int() function; when
supplied with, e.g., a character vector, execution was stopped with an
error instead of returning FALSE, as needed to print the
proper error messages after checks.
Minor fix to plot_status(), where the upper area
(representing trials/arms still recruiting) was sometimes erroneously
not plotted due to a floating point issue where the summed proportions
could sometimes slightly exceed 1.
Added additional tests to test increase coverage of existing and new functions.
Minor fix in internal reallocate_probs() function,
when "match"-ing control arm allocation to the highest
probability in a non-control arm and if all probabilities were initially
0, the returned vector lacked names, which have now been added.
Minor fixes to internal validate_trial() function in
order to: not give an error when multiple values were supplied to the
control_prob_fixed argument; and to give the correct error
when multiple values were provided to equivalence_diff or
futility_diff; and to give an error when NA
was supplied to futility_only_first; and to add some
tolerance to the checks of data_looks and
randomised_at_looks to avoid errors due to floating point
imprecision when specified using multiplication or similar; and correct
errors if decimal numbers for patient count arguments were supplied; and
additional minor updates to errors/messages.
This is a patch release triggered by a CRAN request for updates.
Minor formatting changes to the adaptr-package help
page to comply with CRAN request to only use HTML5 (as used by R
>=4.2.0).
Minor bug fixes in print() methods for trial
specifications and summaries of multiple trial results.
Minor updates in messages in setup_trial().
Minor release:
Updates to the run_trials() function to allow
exporting objects to clusters when running simulations on multiple
cores.
Updates to internal function verify_int() due to
updates in R >= 4.2.0, to avoid incorrect error messages in future
versions due to changed behaviour with the &&
function when used with arguments with length > 1 (https://stat.ethz.ch/pipermail/r-announce/2022/000683.html).
Minor documentation edits and updated citation info (reference to software paper published in Journal of Open Source Software, https://doi.org/10.21105/joss.04284).