Package: hmer 1.6.0

Andrew Iskauskas

hmer: History Matching and Emulation Package

A set of objects and functions for Bayes Linear emulation and history matching. Core functionality includes automated training of emulators to data, diagnostic functions to ensure suitability, and a variety of proposal methods for generating 'waves' of points. For details on the mathematical background, there are many papers available on the topic (see references attached to function help files or the below references); for details of the functions in this package, consult the manual or help files. Iskauskas, A, et al. (2024) <doi:10.18637/jss.v109.i10>. Bower, R.G., Goldstein, M., and Vernon, I. (2010) <doi:10.1214/10-BA524>. Craig, P.S., Goldstein, M., Seheult, A.H., and Smith, J.A. (1997) <doi:10.1007/978-1-4612-2290-3_2>.

Authors:Andrew Iskauskas [aut, cre], TJ McKinley [aut]

hmer_1.6.0.tar.gz
hmer_1.6.0.zip(r-4.5)hmer_1.6.0.zip(r-4.4)hmer_1.6.0.zip(r-4.3)
hmer_1.6.0.tgz(r-4.4-any)hmer_1.6.0.tgz(r-4.3-any)
hmer_1.6.0.tar.gz(r-4.5-noble)hmer_1.6.0.tar.gz(r-4.4-noble)
hmer_1.6.0.tgz(r-4.4-emscripten)hmer_1.6.0.tgz(r-4.3-emscripten)
hmer.pdf |hmer.html
hmer/json (API)
NEWS

# Install 'hmer' in R:
install.packages('hmer', repos = c('https://andy-iskauskas.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/andy-iskauskas/hmer/issues

Datasets:

On CRAN:

50 exports 16 stars 2.53 score 68 dependencies 34 scripts 885 downloads

Last updated 8 days agofrom:cd346e06c6. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 10 2024
R-4.5-winOKSep 10 2024
R-4.5-linuxOKSep 10 2024
R-4.4-winOKSep 10 2024
R-4.4-macOKSep 10 2024
R-4.3-winOKSep 10 2024
R-4.3-macOKSep 10 2024

Exports:analyze_diagnosticbehaviour_plotbimodal_emulator_from_dataclassification_diagcollect_emulatorscomparison_diagCorrelatordiagnostic_passdiagnostic_wrapdirectional_derivdirectional_proposaleffect_strengthEmulatoremulator_from_dataemulator_plotexp_sqexport_emulator_to_jsonfull_wavegamma_expgenerate_new_designgenerate_new_runsget_diagnosticHierarchicalEmulatorhit_by_waveidemcimport_emulator_from_jsonindividual_errorsmaternmaximin_samplenth_implausibleorn_uhloutput_plotplot_activesplot_latticeplot_wrapProto_emulatorrat_quadresidual_diagsimulator_plotspace_removalspace_removedstandard_errorssubset_emulatorssummary_diagvalidation_diagnosticsvalidation_pairsvariance_emulator_from_datawave_dependencieswave_pointswave_values

Dependencies:backportsbeeswarmbitbit64broombroom.helperscardsclicliprclustercolorspacecpp11crayondplyrfansifarverforcatsgenericsGGallyggbeeswarmggplot2ggstatsgluegridExtragtablehavenhmsisobandjsonlitelabelinglabelledlatticelhslifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepatchworkpdistpillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangscalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviporviridisviridisLitevroomwithr

Demonstrating the hmer Package

Rendered fromdemonstrating-the-hmer-package.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2023-12-14
Started: 2021-08-05

Emulation and History Matching Handbook

Rendered fromemulationhandbook.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2023-12-14
Started: 2022-03-28

Low Dimensional Examples

Rendered fromlow-dimensional-examples.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2024-05-14
Started: 2021-05-14

Stochastic Emulation

Rendered fromstochasticandbimodalemulation.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2024-05-15
Started: 2022-02-16

Readme and manuals

Help Manual

Help pageTopics
Diagnostic Analysis for Emulatorsanalyze_diagnostic
Output Plottingbehaviour_plot
Bimodal Emulationbimodal_emulator_from_data
Birth-Death Model ResultsBirthDeath
Classification Diagnosticsclassification_diag
Collect and order emulatorscollect_emulators
Comparison Diagnosticscomparison_diag
Correlation StructureCorrelator
Automated Diagnostics and Modificationsdiagnostic_pass
Diagnostic plots for wave outputsdiagnostic_wrap
Derivative inner productdirectional_deriv
Emulated Derivative Point Proposaldirectional_proposal
Find Effect Strength of Active Variableseffect_strength
Bayes Linear EmulatorEmulator
Generate Emulators from Dataemulator_from_data
Plot Emulator Outputsemulator_plot
Exponential squared correlation functionexp_sq
Export Emulatorsexport_emulator_to_json
Automatic Wave Calculationfull_wave
Gamma-exponential correlation functiongamma_exp
Generate Proposal Pointsgenerate_new_design
Generate Proposal Pointsgenerate_new_runs
Diagnostic Tests for Emulatorsget_diagnostic
Hierarchical Bayes Linear EmulatorHierarchicalEmulator
Output Hit Summaryhit_by_wave
IDEMC Point Generationidemc
Import JSON Emulator Dataimport_emulator_from_json
Predictive Error Plotsindividual_errors
Matern correlation functionmatern
Generate Maximin Sample of Pointsmaximin_sample
nth Maximum Implausibilitynth_implausible
Ornstein-Uhlenbeck correlation functionorn_uhl
Emulator Expectation Against Target Outputsoutput_plot
Active variable plottingplot_actives
Plot Lattice of Emulator Implausibilitiesplot_lattice
Plot proposed pointsplot_wrap
Data for an interesting emulation problemproblem_data
Prototype Class for Emulator-like ObjectsProto_emulator
Rational Quadratic correlation functionrat_quad
Emulator Regression Residualsresidual_diag
Plot simulator outputs for multiple wavessimulator_plot
Stochastic SIR DataSIR_stochastic
Sample EmulatorsSIREmulators
Sample Implausibility DataSIRImplausibility
Sample Multi-wave ResultsSIRMultiWaveData
Sample Multi-wave EmulatorsSIRMultiWaveEmulators
Sample SIR dataSIRSample
Percentage of Space Removedspace_removal
Space Removal Diagnosticsspace_removed
Standardized Error Diagnosticsstandard_errors
Subsetting for Bimodal/Variance Emulatorssubset_emulators
Summary Statistics for Emulatorssummary_diag
Emulator Diagnosticsvalidation_diagnostics
Validation Set Diagnostics and Implausibilityvalidation_pairs
Variance Emulator Creation (Deprecated)variance_emulator_from_data
Multiple Wave Inputs vs Outputswave_dependencies
Multiple Wave Point Plottingwave_points
Multiple Wave Output Plottingwave_values