emulator_from_data changed to avoid overfitting in edge caseshit_by_wave when number of waves exceeded the number of targetsemulator_from_data now safely terminates if users supply width-zero ranges, or if regression is a ‘perfect fit’ for data; behaviour of check.ranges = TRUE modified to ensure consistent ranges are calculated.slice_sample now stable against strange edge case behaviour.exp_sq).seek_good and importance_sample to more efficiently propose points where the plausible set is already large.hit_by_wave now accepts an n.sig parameter to allow user determination of what constitutes a match to observational data.plot_lattice now accepts parameter subset plotting, aiding visualisation for large dimensional parameter spaces.emulator_plot a small (between 2 and 4) list of emulators using the include_legend argument.Proto_emulator, generate_new_design can be forced to maintain emulator ordering rather than order for efficiency.purrr); documentation updates.diagnostic_pass for automated diagnostics and modifications of emulators; hit_by_wave for visualisation of history matching progress.simulator_plot et al. where some combinations of wave_numbers and zero_in caused out-of-index errors.emulator_type = "variance" or emulator_type = "covariance".xx_emulator_from_data functions are now a single function; variance_emulator_from_data and bimodal_emulator_from_data are now called using emulator_from_data with argument emulator_type = 'variance' and emulator_type = 'multistate' respectively. To avoid confusion about the output of the function, generate_new_runs has been renamed to generate_new_design. Older functions have been deprecated and will be removed in a subsequent version.Changes to generate_new_design to avoid implausibility asymptoting in edge cases.
Explicit checks included to ensure that ordering of parameter ranges matches with data.frames provided for training
Fixes to ensure that 1d systems behave as expected.
Fix to avoid singular correlation matrices in some situations where corr_type = 'exp_sq'.
Fixes for edge-case multistate emulator training problems, and for situations where model.matrix behaviour fails (due to deparse truncation issues in core R functions).
Modifications to emulator design via emulator_from_data: in particular hyperparameter estimation has been made more robust; emulator regression surfaces now support cubic terms; variance and multistate emulators now more robust to different numbers of repetitions at different input sites.
Covariance emulation introduced (via emulator_from_data(..., emulator_type = 'covariance')), allowing a full covariance matrix to be robustly emulated. Results are presented using a prototype emulator matrix EmulatedMatrix to efficiently make predictions, including checks to ensure that predicted matrices are semi-positive definite. In the future, covariance matrices will be supported in implausibility measures and point proposals.
Multiple fixes to deal with singletons: ensuring 1d examples work with generate_new_runs; single output systems behave appropriately under clustering, diagnostics, and implausibility for bimodal_emulator_from_data; modifications to simulator_plot for single output systems; bug-fix in generate_new_runs for user-provided single-element plausible sets.
Small fixes to guarantee compatibility with new functionality.
Fixed scoping issue with variance emulators where emulator would not get the correct s_diag function when initialised within a collection of emulators in variance_emulator_from_data
Beeswarm plots added as alternative to simulator_plot (credit to T.J. McKinley)
Custom multi-emulator implausibility now supported within generate_new_runs: multiple conditions can be supplied as part of the point-screening process via accept_measure. Structure of optional arguments for generate_new_runs has been modified (with backwards-compatibility for older code) - see help file for details.
Added check to emulator_from_data to handle mismatched input names and ranges
Proto_emulator introduced: the hmer framework of diagnostics, visualisation, and point proposal can be used with entirely custom objects.Fix to implausibility for variance emulators to take account of ensemble size
Functions full_wave, variance_emulator_from_data, bimodal_emulator_from_data all accept an na.rm argument to handle missing data
Fixed edge cases where generate_new_runs could get stuck at a particular implausibility cutoff, and increased stability of termination for points generation from variance/bimodal emulators
Other small fixes, including modification to ggplot functions to handle deprecation of size aesthetic
Optimisation of emulator calculations, particularly within correlation matrices
Optimised point generation to leverage Latin Hypercube Designs, where useful
Modification to standard_errors to highlight points of interest
Modifications made to facilitate support for custom emulators and implausibility measures (to come in a later update).
Implemented more error catching/handling for correlation functions, including explicit stop calls if hyperparameters are not provided/ill-specified and automatic coercion to data.matrix to ensure compatibility with derivative functions
Internal functions collect_emulators, scale_input, convertRanges and multiply_function modified to handle various edge case usages and issues with multiple waves of stochastic or bimodal emulators
Modified lhs_gen_cluster so that if emulators cannot/need not be clustered, default lhs_gen behaviour is used
Fixed Emulator code to address calculation issues with derivatives that meant that partial derivatives did not commute
Various other small fixes
Unit testing framework implemented and tracked; unit tests for all relevant functions are now in place
Functions generate_new_runs and nth_implausible will try to determine a sensible value of n or nth when calculating nth-maximum implausibility if none is supplied by the user.
Badges and sticker added to readme
NEWS.md file to track changes to the package.