├── .Rbuildignore ├── .covrignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── check-standard.yaml │ ├── rhub.yaml │ └── test-coverage.yaml ├── .gitignore ├── .travis.yml ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── CorrelatorDocumentation.R ├── Emulator.R ├── EmulatorDocumentation.R ├── HierarchicalEmulatorDocumentation.R ├── ProtoEmulatorDocumentation.R ├── Proto_emulator.R ├── VarianceEmulator.R ├── correlations.R ├── covariancehelpers.R ├── data.R ├── derivative_functions.R ├── diagnosticplots.R ├── diagnostics.R ├── fullwave.R ├── genpoints.R ├── idemc.R ├── implausibility.R ├── modelbuilding.R ├── multiwaveplot.R ├── plotting.R ├── sysdata.rda └── utils.R ├── README.Rmd ├── README.md ├── codecov.yml ├── cran-comments.md ├── data ├── BirthDeath.rda ├── SIREmulators.rda ├── SIRImplausibility.rda ├── SIRMultiWaveData.rda ├── SIRMultiWaveEmulators.rda ├── SIRSample.rda ├── bimodalData.rda └── problemData.rda ├── hmer.Rproj ├── inst └── CITATION ├── man ├── BirthDeath.Rd ├── Correlator.Rd ├── Emulator.Rd ├── HierarchicalEmulator.Rd ├── Proto_emulator.Rd ├── SIREmulators.Rd ├── SIRImplausibility.Rd ├── SIRMultiWaveData.Rd ├── SIRMultiWaveEmulators.Rd ├── SIRSample.Rd ├── SIR_stochastic.Rd ├── analyze_diagnostic.Rd ├── behaviour_plot.Rd ├── bimodal_emulator_from_data.Rd ├── classification_diag.Rd ├── collect_emulators.Rd ├── comparison_diag.Rd ├── diagnostic_pass.Rd ├── diagnostic_wrap.Rd ├── directional_deriv.Rd ├── directional_proposal.Rd ├── effect_strength.Rd ├── emulator_from_data.Rd ├── emulator_plot.Rd ├── exp_sq.Rd ├── export_emulator_to_json.Rd ├── figures │ ├── logo.png │ └── logo.svg ├── full_wave.Rd ├── gamma_exp.Rd ├── generate_new_design.Rd ├── generate_new_runs.Rd ├── get_diagnostic.Rd ├── hit_by_wave.Rd ├── idemc.Rd ├── import_emulator_from_json.Rd ├── individual_errors.Rd ├── matern.Rd ├── maximin_sample.Rd ├── nth_implausible.Rd ├── orn_uhl.Rd ├── output_plot.Rd ├── plot_actives.Rd ├── plot_lattice.Rd ├── plot_wrap.Rd ├── prin_vars.Rd ├── problem_data.Rd ├── rat_quad.Rd ├── residual_diag.Rd ├── simulator_plot.Rd ├── space_removal.Rd ├── space_removed.Rd ├── standard_errors.Rd ├── subset_emulators.Rd ├── summary_diag.Rd ├── validation_diagnostics.Rd ├── validation_pairs.Rd ├── variance_emulator_from_data.Rd ├── wave_dependencies.Rd ├── wave_points.Rd └── wave_values.Rd ├── tests ├── testthat.R └── testthat │ ├── .gitignore │ ├── test-cluster.R │ ├── test-correlator.R │ ├── test-custom_functionality.R │ ├── test-derivative_functions.R │ ├── test-em_building.R │ ├── test-emulator.R │ ├── test-emulator_admin.R │ ├── test-exp_sq.R │ ├── test-gamma_exp.R │ ├── test-get_dist.R │ ├── test-implausibility.R │ ├── test-kurtosis.R │ ├── test-matern.R │ ├── test-orn_uhl.R │ ├── test-plotting.R │ ├── test-point_gen.R │ ├── test-proto_em.R │ ├── test-rat_quad.R │ ├── test-scale_eval.R │ ├── test-validation_diag.R │ └── test-variance_ems.R └── 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