├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── .lintr ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GUI.R ├── GUImini.R ├── RacViewer.R ├── Racmacs-package.R ├── RcppExports.R ├── acmacs_placeAbvs.R ├── map_blobs.R ├── map_diagnostics_bootstrap.R ├── map_diagnostics_bootstrap_blobs.R ├── map_diagnostics_dimtest.R ├── map_diagnostics_leverage.R ├── map_diagnostics_triangulation_blobs.R ├── map_edit_names.R ├── map_ggplot.R ├── map_info_long.R ├── map_legend.R ├── map_loadsave.R ├── map_merge.R ├── map_merge_report.R ├── map_methods.R ├── map_new.R ├── map_optimizations.R ├── map_optimize.R ├── map_optimize_reactivity.R ├── map_plot.R ├── map_plotspec.R ├── map_point_coords.R ├── map_point_matching.R ├── map_procrustes.R ├── map_props.R ├── map_props_diagnostics.R ├── map_props_optimizations.R ├── map_props_plotspec.R ├── map_props_points_antigens.R ├── map_props_points_sera.R ├── map_reactivity_adjusts.R ├── map_sequences.R ├── map_stress.R ├── map_subset.R ├── map_transformation.R ├── map_viewer.R ├── plot_diagnostics.R ├── rac_blobs.R ├── rac_normaliseNames.R ├── rac_process_titers.R ├── shiny_diagnostics.R ├── shiny_gadget.R ├── shiny_load.R ├── shiny_optimizations.R ├── shiny_optimize.R ├── shiny_relax.R ├── shiny_save.R ├── shiny_server.R ├── shiny_ui.R ├── shiny_utils.R ├── utils_blobs.R ├── utils_documentation.R ├── utils_geometry.R ├── utils_matrix_getters.R ├── utils_messages.R ├── utils_plotting.R ├── utils_progress.R ├── utils_r3js.R ├── utils_rotation.R ├── utils_tests.R └── utils_type_checking.R ├── README.md ├── Racmacs.Rproj ├── cran-comments.md ├── inst ├── WORDLIST ├── extdata │ ├── ferret_ag_dictionary.csv │ ├── h3map2004.ace │ ├── h3map2004_hitable.csv │ ├── h3map2004_sequences_ag.csv │ ├── h3map2004_sequences_sr.csv │ ├── h3map2004_subset.ace │ └── icons │ │ └── buttons │ │ ├── controls.svg │ │ ├── sequences.svg │ │ └── view-table.svg ├── htmlwidgets │ ├── .gitignore │ ├── RacViewer.js │ ├── RacViewer.yaml │ └── RacViewer │ │ ├── .gitignore │ │ └── lib │ │ ├── functions │ │ ├── agreactivity.js │ │ ├── agsr.js │ │ ├── animation.js │ │ ├── api.js │ │ ├── blobs.js │ │ ├── bootstrap.js │ │ ├── browser.js │ │ ├── buttons.js │ │ ├── connections.js │ │ ├── controls.js │ │ ├── data.js │ │ ├── diagnostics.js │ │ ├── dimensions.js │ │ ├── drag.js │ │ ├── elements.js │ │ ├── filters.js │ │ ├── graphics.js │ │ ├── grid.js │ │ ├── hemisphering.js │ │ ├── icons.js │ │ ├── legend.js │ │ ├── load.js │ │ ├── optimization.js │ │ ├── points.js │ │ ├── procrustes.js │ │ ├── projections.js │ │ ├── save.js │ │ ├── selections.js │ │ ├── sequences.js │ │ ├── shortcuts.js │ │ ├── stress.js │ │ ├── table.js │ │ └── utils.js │ │ ├── init.js │ │ ├── jscolor │ │ └── jscolor.min.js │ │ ├── optimization │ │ └── optimization.js │ │ ├── r3js │ │ └── lib │ │ │ ├── functions │ │ │ ├── api.js │ │ │ ├── buttons.js │ │ │ ├── camera.js │ │ │ ├── colors.js │ │ │ ├── dynamic.js │ │ │ ├── element.js │ │ │ ├── element_arrow.js │ │ │ ├── element_glarrow.js │ │ │ ├── element_gllines.js │ │ │ ├── element_glpoints.js │ │ │ ├── element_grid.js │ │ │ ├── element_light.js │ │ │ ├── element_lines.js │ │ │ ├── element_points.js │ │ │ ├── element_polygon.js │ │ │ ├── element_sphere.js │ │ │ ├── element_surface.js │ │ │ ├── element_text.js │ │ │ ├── element_triangles.js │ │ │ ├── events.js │ │ │ ├── highlight.js │ │ │ ├── icons.js │ │ │ ├── legend.js │ │ │ ├── load.js │ │ │ ├── navigation.js │ │ │ ├── plotting.js │ │ │ ├── raytrace.js │ │ │ ├── renderer.js │ │ │ ├── save_img.js │ │ │ ├── scene.js │ │ │ ├── selection.js │ │ │ ├── shaders.js │ │ │ ├── sprites.js │ │ │ ├── toggle.js │ │ │ ├── utils.js │ │ │ └── viewport.js │ │ │ ├── init.js │ │ │ ├── styles │ │ │ └── r3js.css │ │ │ └── threejs │ │ │ ├── LICENSE │ │ │ ├── fonts │ │ │ └── helvetiker_regular.typeface.js │ │ │ ├── lines │ │ │ ├── Line2.js │ │ │ ├── LineGeometry.js │ │ │ ├── LineMaterial.js │ │ │ ├── LineSegments2.js │ │ │ ├── LineSegmentsGeometry.js │ │ │ ├── Wireframe.js │ │ │ └── WireframeGeometry2.js │ │ │ ├── plugins │ │ │ ├── ColladaLoader.js │ │ │ ├── Detector.js │ │ │ ├── GLTFExporter.js │ │ │ ├── PLYExporter.js │ │ │ └── THREE.MeshLine.js │ │ │ ├── renderers │ │ │ ├── CSS2DRenderer.js │ │ │ ├── CSS2DRenderer_r3js.js │ │ │ ├── CSS2DRenderer_r3js_old.js │ │ │ ├── CSS3DRenderer.js │ │ │ ├── Projector.js │ │ │ └── SVGRenderer.js │ │ │ ├── three.min.js │ │ │ └── utils │ │ │ ├── BufferGeometryUtils.js │ │ │ └── SceneUtils.js │ │ ├── styles │ │ ├── blobs.css │ │ ├── browser.css │ │ ├── checkbox.css │ │ ├── controlpanel.css │ │ ├── diagnostics.css │ │ ├── drag.css │ │ ├── hitable.css │ │ ├── load.css │ │ ├── procrustes.css │ │ ├── projections.css │ │ └── racViewer.css │ │ └── textures │ │ └── sprites │ │ ├── ball.png │ │ ├── circle.png │ │ ├── circle2.png │ │ ├── disc.png │ │ ├── ring.png │ │ └── sprites.afdesign ├── shinyapps │ └── RacmacsGUI │ │ ├── app.R │ │ ├── tests │ │ ├── testdata │ │ │ └── testmap.ace │ │ ├── testthat.R │ │ └── testthat │ │ │ └── test-server.R │ │ └── www │ │ ├── acorg_logo.png │ │ ├── browser.css │ │ ├── filter.css │ │ ├── gui_title.png │ │ ├── racmacs.css │ │ └── racmacs.js └── templates │ └── diagnostics_page.Rmd ├── man ├── RacMerge.options.Rd ├── RacOptimizer.options.Rd ├── RacViewer-shiny.Rd ├── RacViewer.Rd ├── RacViewer.options.Rd ├── Racmacs-package.Rd ├── acmap.Rd ├── acmapAttributes.Rd ├── addOptimization.Rd ├── adjustedLogTiterTable.Rd ├── adjustedTiterTable.Rd ├── agAttributes.Rd ├── agGroups.Rd ├── agHomologousSr.Rd ├── agLabIDs.Rd ├── agReactivityAdjustments.Rd ├── agSequences.Rd ├── applyMapTransform.Rd ├── applyPlotspec.Rd ├── as.json.Rd ├── blob.Rd ├── blobsize.Rd ├── bootstrapBlobs.Rd ├── bootstrapMap.Rd ├── checkHemisphering.Rd ├── colBases.Rd ├── deprecated_functions.Rd ├── dilutionStepsize.Rd ├── dimensionTestMap.Rd ├── edit_agNames.Rd ├── edit_srNames.Rd ├── export_viewer.Rd ├── figures │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png ├── getOptimization.Rd ├── ggplot.acmap.Rd ├── htmlAdjustedTiterTable.Rd ├── htmlMergeReport.Rd ├── htmlTiterTable.Rd ├── keepBestOptimization.Rd ├── keepOptimizations.Rd ├── keepSingleOptimization.Rd ├── layerNames.Rd ├── listOptimizations.Rd ├── logtiterTable.Rd ├── logtiterTableLayers.Rd ├── make.acmap.Rd ├── map-table-distances.Rd ├── mapBootstrapCoords.Rd ├── mapCohesion.Rd ├── mapComment.Rd ├── mapDescription.Rd ├── mapDimensions.Rd ├── mapDistances.Rd ├── mapGadget.Rd ├── mapName.Rd ├── mapRelaxed.Rd ├── mapResiduals.Rd ├── mapStress.Rd ├── mapTransformation.Rd ├── matchStrains.Rd ├── mergeMaps.Rd ├── mergeReport.Rd ├── moveTrappedPoints.Rd ├── optimizationProperties.Rd ├── optimizeAgReactivity.Rd ├── optimizeMap.Rd ├── orderPoints.Rd ├── plot.acmap.Rd ├── pointStress.Rd ├── procrustesData.Rd ├── procrustesMap.Rd ├── ptAnnotations.Rd ├── ptBaseCoords.Rd ├── ptBootstrapBlob.Rd ├── ptBootstrapCoords.Rd ├── ptClades.Rd ├── ptCoords.Rd ├── ptDrawingOrder.Rd ├── ptLeverage.Rd ├── ptOpacity.Rd ├── ptStyles.Rd ├── ptTriangulationBlob.Rd ├── randomizeCoords.Rd ├── read.acmap.Rd ├── read.titerTable.Rd ├── realignMap.Rd ├── realignOptimizations.Rd ├── recalculateStress.Rd ├── reflectMap.Rd ├── relaxMap.Rd ├── relaxMapOneStep.Rd ├── removeOptimizations.Rd ├── removePoints.Rd ├── rotateMap.Rd ├── runGUI.Rd ├── save.acmap.Rd ├── save.coords.Rd ├── save.titerTable.Rd ├── setLegend.Rd ├── sortOptimizations.Rd ├── splitTiterLayers.Rd ├── srAttributes.Rd ├── srGroups.Rd ├── srHomologousAgs.Rd ├── srSequences.Rd ├── standardizeStrainNames.Rd ├── stressTable.Rd ├── subsetCommonPoints.Rd ├── subsetMap.Rd ├── tableColbases.Rd ├── tableDistances.Rd ├── titerTable.Rd ├── titerTableFlat.Rd ├── titerTableLayers.Rd ├── translateMap.Rd ├── triangulationBlobs.Rd ├── unstableMaps.Rd ├── update_ferret_seraNames.Rd ├── view.Rd ├── view.acmap.Rd └── view.default.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── src ├── .gitignore ├── Makevars ├── Makevars.win ├── Racmacs_types.h ├── Racmacs_wrappers.cpp ├── Racmacs_wrappers_antigens.cpp ├── Racmacs_wrappers_optimizations.cpp ├── Racmacs_wrappers_plotspec.cpp ├── Racmacs_wrappers_sera.cpp ├── RcppExports.cpp ├── ac_bootstrap.cpp ├── ac_bootstrap.h ├── ac_bootstrap_output.h ├── ac_coords_stress.h ├── ac_dimension_test.cpp ├── ac_dimension_test.h ├── ac_errorlines.cpp ├── ac_errorlines.h ├── ac_hemi_test.cpp ├── ac_hemi_test.h ├── ac_matching.cpp ├── ac_matching.h ├── ac_merge.cpp ├── ac_merge.h ├── ac_move_trapped_points.cpp ├── ac_optim_map_stress.cpp ├── ac_optim_map_stress.h ├── ac_optimization.cpp ├── ac_optimization.h ├── ac_optimize_ag_reactivity.cpp ├── ac_optimizer_options.h ├── ac_relax_coords.h ├── ac_stress.cpp ├── ac_stress.h ├── ac_stress_blobs.cpp ├── ac_stress_blobs.h ├── ac_titers.cpp ├── ac_titers.h ├── ac_utils.cpp ├── acmap_diagnostics.h ├── acmap_map.cpp ├── acmap_map.h ├── acmap_optimization.cpp ├── acmap_optimization.h ├── acmap_plotspec.h ├── acmap_point.cpp ├── acmap_point.h ├── acmap_sequences.h ├── acmap_titers.cpp ├── acmap_titers.h ├── json_assert.cpp ├── json_assert.h ├── json_read_to_acmap.cpp ├── json_read_to_acmap.h ├── json_write_from_acmap.cpp ├── json_write_from_acmap.h ├── procrustes.cpp ├── procrustes.h ├── utils.cpp ├── utils.h ├── utils_error.cpp ├── utils_error.h ├── utils_euc_dist.cpp ├── utils_geometry.cpp ├── utils_interpolation.cpp ├── utils_progress.h ├── utils_transformation.cpp └── utils_transformation.h ├── tests ├── testdata │ ├── test_mergemap1.ace │ ├── test_mergemap2.ace │ ├── test_mergemap3.ace │ ├── testmap.ace │ ├── testmap_h3subset.ace │ ├── testmap_h3subset3d.ace │ ├── testmap_h3subset3d_1000bootstraps.ace │ ├── testmap_h3subset_sequences.csv │ ├── testmap_h3subset_srsequences.csv │ ├── testmap_large.ace │ ├── testmap_merge.ace │ ├── testmap_small.ace │ └── titer_tables │ │ ├── titer_table1.RData │ │ ├── titer_table1.csv │ │ ├── titer_table1.xlsx │ │ ├── titer_table2.RData │ │ ├── titer_table2.txt │ │ ├── titer_table3.RData │ │ ├── titer_table3_asterisk.csv │ │ ├── titer_table4.RData │ │ ├── titer_table4_blank.csv │ │ └── titer_table5_underconstrained.csv ├── testthat.R └── testthat │ ├── .gitignore │ ├── test-ac_procrustes.R │ ├── test-colbases.R │ ├── test-diagnostic_plotting.R │ ├── test-diagnostics_bootstrap.R │ ├── test-diagnostics_dimTesting.R │ ├── test-diagnostics_stress.R │ ├── test-diagnostics_stressblobs.R │ ├── test-errors.R │ ├── test-gui.R │ ├── test-map_creation.R │ ├── test-map_editing.R │ ├── test-map_loading.R │ ├── test-map_merging.R │ ├── test-map_methods.R │ ├── test-map_optimization.R │ ├── test-map_optimizations.R │ ├── test-map_plotspec.R │ ├── test-map_procrustes.R │ ├── test-map_saving.R │ ├── test-map_sequences.R │ ├── test-map_strains.R │ ├── test-map_subset.R │ ├── test-map_transformation.R │ ├── test-map_viewer_settings.R │ ├── test-merging.R │ ├── test-methods.R │ ├── test-name_parser.R │ ├── test-plot_map.R │ ├── test-r3js.R │ ├── test-reading_HI_table.R │ ├── test-stability.R │ ├── test-underconstrained_positions.R │ ├── test-view_map.R │ └── test-view_procrustes.R └── vignettes ├── .gitignore ├── adding-sequences.Rmd ├── assessing_map_uncertainty.Rmd ├── comparing-maps.Rmd ├── customising-map-appearance.Rmd ├── figures ├── intro_fig1.png ├── intro_fig2.png ├── intro_fig3.png ├── intro_fig4.png ├── intro_fig5.png ├── intro_fig6.png ├── intro_fig7.png └── intro_h3n2map.png ├── 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