Global functions | |
---|---|
.onLoad | Source code |
RacMerge.options | Man page Source code |
RacOptimizer.options | Man page Source code |
RacViewer | Man page Source code |
RacViewer-shiny | Man page |
RacViewer.options | Man page Source code |
RacViewerOutput | Man page Source code |
Racmacs | Man page |
Racmacs-package | Man page |
`agAnnotations<-` | Source code |
`agClades<-` | Source code |
`agCoords<-` | Source code |
`agDiagnostics<-` | Source code |
`agFill<-` | Source code |
`agGroups<-` | Source code |
`agLabIDs<-` | Source code |
`agNucleotideSequences<-` | Source code |
`agOpacity<-` | Source code |
`agOutline<-` | Source code |
`agReactivityAdjustments<-` | Source code |
`agSequences<-` | Source code |
`dilutionStepsize<-` | Source code |
`layerNames<-` | Source code |
`mapDescription<-` | Source code |
`mapName<-` | Source code |
`ptCoords<-` | Source code |
`ptDrawingOrder<-` | Source code |
`srAnnotations<-` | Source code |
`srClades<-` | Source code |
`srCoords<-` | Source code |
`srDiagnostics<-` | Source code |
`srFill<-` | Source code |
`srGroups<-` | Source code |
`srHomologousAgs<-` | Source code |
`srNucleotideSequences<-` | Source code |
`srOpacity<-` | Source code |
`srOutline<-` | Source code |
`srSequences<-` | Source code |
`titerTable<-` | Source code |
`titerTableFlat<-` | Source code |
`titerTableLayers<-` | Source code |
ac_ag_get_annotations | Source code |
ac_ag_get_clade | Source code |
ac_ag_get_continent | Source code |
ac_ag_get_date | Source code |
ac_ag_get_extra | Source code |
ac_ag_get_group | Source code |
ac_ag_get_group_levels | Source code |
ac_ag_get_id | Source code |
ac_ag_get_labids | Source code |
ac_ag_get_lineage | Source code |
ac_ag_get_match_id | Source code |
ac_ag_get_name | Source code |
ac_ag_get_passage | Source code |
ac_ag_get_reassortant | Source code |
ac_ag_get_reference | Source code |
ac_ag_get_strings | Source code |
ac_ag_names | Source code |
ac_ag_set_annotations | Source code |
ac_ag_set_clade | Source code |
ac_ag_set_continent | Source code |
ac_ag_set_date | Source code |
ac_ag_set_extra | Source code |
ac_ag_set_group | Source code |
ac_ag_set_group_levels | Source code |
ac_ag_set_id | Source code |
ac_ag_set_labids | Source code |
ac_ag_set_lineage | Source code |
ac_ag_set_name | Source code |
ac_ag_set_passage | Source code |
ac_ag_set_reassortant | Source code |
ac_ag_set_reference | Source code |
ac_ag_set_strings | Source code |
ac_align_coords | Source code |
ac_align_map | Source code |
ac_align_optimization | Source code |
ac_align_optimizations | Source code |
ac_apply_optimization_transform | Source code |
ac_bootstrap_map | Source code |
ac_coordDistMatrix | Source code |
ac_coord_dists | Source code |
ac_coords_stress | Source code |
ac_dimension_test_map | Source code |
ac_errorline_data | Source code |
ac_get_ag_coords | Source code |
ac_get_sr_coords | Source code |
ac_hemi_test | Source code |
ac_match_map_ags | Source code |
ac_match_map_sr | Source code |
ac_merge_frozen_merge | Source code |
ac_merge_frozen_overlay | Source code |
ac_merge_incremental | Source code |
ac_merge_relaxed_overlay | Source code |
ac_merge_reoptimized | Source code |
ac_merge_tables | Source code |
ac_merge_titer_layers | Source code |
ac_merge_titers | Source code |
ac_move_trapped_points | Source code |
ac_newOptimization | Source code |
ac_new_antigen | Source code |
ac_new_serum | Source code |
ac_numeric_table_distances | Source code |
ac_opt_get_ag_base_coords | Source code |
ac_opt_get_agreactivityadjustments | Source code |
ac_opt_get_comment | Source code |
ac_opt_get_dimensions | Source code |
ac_opt_get_fixedcolbases | Source code |
ac_opt_get_mincolbasis | Source code |
ac_opt_get_sr_base_coords | Source code |
ac_opt_get_stress | Source code |
ac_opt_get_transformation | Source code |
ac_opt_get_translation | Source code |
ac_opt_set_ag_base_coords | Source code |
ac_opt_set_agreactivityadjustments | Source code |
ac_opt_set_comment | Source code |
ac_opt_set_fixedcolbases | Source code |
ac_opt_set_mincolbasis | Source code |
ac_opt_set_sr_base_coords | Source code |
ac_opt_set_stress | Source code |
ac_opt_set_transformation | Source code |
ac_opt_set_translation | Source code |
ac_optimize_map | Source code |
ac_plotspec_get_aspect | Source code |
ac_plotspec_get_fill | Source code |
ac_plotspec_get_outline | Source code |
ac_plotspec_get_outline_width | Source code |
ac_plotspec_get_rotation | Source code |
ac_plotspec_get_shape | Source code |
ac_plotspec_get_shown | Source code |
ac_plotspec_get_size | Source code |
ac_plotspec_set_aspect | Source code |
ac_plotspec_set_fill | Source code |
ac_plotspec_set_outline | Source code |
ac_plotspec_set_outline_width | Source code |
ac_plotspec_set_rotation | Source code |
ac_plotspec_set_shape | Source code |
ac_plotspec_set_shown | Source code |
ac_plotspec_set_size | Source code |
ac_point_residuals | Source code |
ac_point_stresses | Source code |
ac_procrustes | Source code |
ac_procrustes_map_coords | Source code |
ac_procrustes_map_data | Source code |
ac_progress_bar | Source code |
ac_reactivity_adjustment_stress | Source code |
ac_reflect_optimization | Source code |
ac_relaxOptimization | Source code |
ac_relax_coords | Source code |
ac_rotate_optimization | Source code |
ac_runOptimizations | Source code |
ac_set_ag_coords | Source code |
ac_set_sr_coords | Source code |
ac_sr_get_annotations | Source code |
ac_sr_get_clade | Source code |
ac_sr_get_continent | Source code |
ac_sr_get_date | Source code |
ac_sr_get_extra | Source code |
ac_sr_get_group | Source code |
ac_sr_get_group_levels | Source code |
ac_sr_get_homologous_ags | Source code |
ac_sr_get_id | Source code |
ac_sr_get_lineage | Source code |
ac_sr_get_match_id | Source code |
ac_sr_get_name | Source code |
ac_sr_get_passage | Source code |
ac_sr_get_reassortant | Source code |
ac_sr_get_reference | Source code |
ac_sr_get_species | Source code |
ac_sr_get_strings | Source code |
ac_sr_set_annotations | Source code |
ac_sr_set_clade | Source code |
ac_sr_set_continent | Source code |
ac_sr_set_date | Source code |
ac_sr_set_extra | Source code |
ac_sr_set_group | Source code |
ac_sr_set_group_levels | Source code |
ac_sr_set_homologous_ags | Source code |
ac_sr_set_id | Source code |
ac_sr_set_lineage | Source code |
ac_sr_set_name | Source code |
ac_sr_set_passage | Source code |
ac_sr_set_reassortant | Source code |
ac_sr_set_reference | Source code |
ac_sr_set_species | Source code |
ac_sr_set_strings | Source code |
ac_stress_blob_grid | Source code |
ac_subset_map | Source code |
ac_table_colbases | Source code |
ac_titer_layer_merge_types | Source code |
ac_titer_layer_sd | Source code |
ac_titer_merge_type | Source code |
ac_translate_optimization | Source code |
ac_update_progress | Source code |
acmap | Man page Source code |
acmap.new | Source code |
acmapAttributes | Man page |
acmap_to_json | Source code |
acpoint_grob | Source code |
addMapGrid | Source code |
addOptimization | Man page Source code |
adjustedLogTiterTable | Man page Source code |
adjustedTiterTable | Man page Source code |
agAnnotations | Man page Source code |
agAnnotations<- | Man page |
agAspect | Man page |
agAspect<- | Man page |
agAttributes | Man page |
agBaseBlob | Source code |
agBaseBootstrapBlobs | Source code |
agBaseCoords | Man page |
agBaseCoords<- | Man page |
agBaseTriangulationBlobs | Source code |
agBlob | Source code |
agBootstrapBlob | Man page Source code |
agBootstrapBlobs | Man page Source code |
agBootstrapCoords | Man page Source code |
agClades | Man page Source code |
agClades<- | Man page |
agCohesion | Man page Source code |
agContinent | Man page |
agContinent<- | Man page |
agCoords | Man page Source code |
agCoords<- | Man page |
agDates | Man page |
agDates<- | Man page |
agDiagnostics | Source code |
agExtra | Man page |
agExtra<- | Man page |
agExtraMatrix | Source code |
agFill | Man page |
agFill<- | Man page |
agGroupMatrix | Source code |
agGroups | Man page Source code |
agGroups<- | Man page |
agHemisphering | Source code |
agHomologousSr | Man page Source code |
agIDs | Man page |
agIDs<- | Man page |
agLabIDs | Man page Source code |
agLabIDs<- | Man page |
agLeverage | Man page Source code |
agLineage | Man page |
agLineage<- | Man page |
agMeanResiduals | Source code |
agNameMatrix | Source code |
agNames | Man page |
agNames<- | Man page |
agNucleotideSequences | Man page Source code |
agNucleotideSequences<- | Man page |
agNumMatrix | Source code |
agOpacity<- | Man page |
agOutline | Man page |
agOutline<- | Man page |
agOutlineWidth | Man page |
agOutlineWidth<- | Man page |
agPassage | Man page |
agPassage<- | Man page |
agReactivityAdjustments | Man page Source code |
agReactivityAdjustments<- | Man page |
agReassortant | Man page |
agReassortant<- | Man page |
agReference | Man page |
agReference<- | Man page |
agRotation | Man page |
agRotation<- | Man page |
agSequences | Man page Source code |
agSequences<- | Man page |
agShape | Man page |
agShape<- | Man page |
agShown | Man page |
agShown<- | Man page |
agSize | Man page |
agSize<- | Man page |
agStress | Man page Source code |
agStressPerTiter | Man page Source code |
agStrings | Man page |
agStrings<- | Man page |
agTriangulationBlob | Man page Source code |
agTriangulationBlobs | Man page Source code |
allMapDimensions | Man page Source code |
allMapProperties | Source code |
allMapStresses | Man page Source code |
antigens_getter | Source code |
antigens_setter | Source code |
applyMapTransform | Man page Source code |
applyPlotspec | Man page Source code |
as.json | Man page Source code |
as.plotly | Source code |
blob | Man page Source code |
blob_area | Source code |
blob_volume | Source code |
blobsize | Man page Source code |
bootstrapBlobs | Man page Source code |
bootstrapData | Source code |
bootstrapMap | Man page Source code |
btn_img | Source code |
calc_agLeverage | Source code |
calc_srLeverage | Source code |
calc_titerLeverage | Source code |
check.acmap | Source code |
check.charactermatrix | Source code |
check.charactervector | Source code |
check.dimensions | Source code |
check.integer | Source code |
check.integerlist | Source code |
check.logical | Source code |
check.logicalvector | Source code |
check.numeric | Source code |
check.numericmatrix | Source code |
check.numericvector | Source code |
check.optnum | Source code |
check.string | Source code |
check.validtiters | Source code |
checkHemisphering | Man page Source code |
clamp | Source code |
colBaseMatrix | Source code |
colBases | Man page Source code |
contour_blob | Source code |
convert3Dto2DrotationMatrix | Source code |
convertSelectedPoints | Source code |
coordDensityBlob | Source code |
coord_lims | Source code |
data2json | Source code |
deprecated_fn | Source code |
deprecated_functions | Man page |
dilutionStepsize | Man page Source code |
dilutionStepsize<- | Man page |
dimensionTestMap | Man page Source code |
dimtest_summary | Source code |
drawDetails.acpoint | Source code |
edit_agNames | Man page Source code |
edit_srNames | Man page Source code |
eulerFromMatrix | Source code |
expand_lims | Source code |
export.plot.test | Source code |
export.plotly.test | Source code |
export.viewer.test | Source code |
export_viewer | Man page Source code |
fixedColBases | Man page |
fixedColBases<- | Man page |
format_titers | Source code |
geom_acpoint | Source code |
getOptimization | Man page Source code |
get_ag_indices | Source code |
get_col_opacity | Source code |
get_pts_sequence_matrix | Source code |
get_sr_indices | Source code |
ggplot.acmap | Man page Source code |
ggplot_theme | Source code |
group_cols | Source code |
hasBootstrapBlobs | Source code |
hasBootstrapData | Source code |
hasHemisphering | Source code |
hasProcrustes | Source code |
hasTriangulationBlobs | Source code |
hist_ggplot | Source code |
htmlAdjustedTiterTable | Man page Source code |
htmlMergeReport | Man page Source code |
htmlTiterTable | Man page Source code |
html_titer_table | Source code |
interp2d | Source code |
is.wholenumber | Source code |
json_to_acmap | Source code |
keepBestOptimization | Man page Source code |
keepOptimizations | Man page Source code |
keepSingleOptimization | Man page Source code |
layerNames | Man page Source code |
layerNames<- | Man page |
list2matrix | Source code |
listOptimizations | Man page Source code |
log_titers | Source code |
logtiterTable | Man page Source code |
logtiterTableLayers | Man page Source code |
longAgData | Source code |
longMapData | Source code |
longSrData | Source code |
longTiterData | Source code |
lowerDrawingOrder | Source code |
make.acmap | Man page Source code |
make_html_legend | Source code |
make_titers | Source code |
map-table-distances | Man page |
mapBootstrapCoords | Man page |
mapBootstrap_agBaseCoords | Source code |
mapBootstrap_agCoords | Man page Source code |
mapBootstrap_ptBaseCoords | Man page Source code |
mapBootstrap_ptCoords | Source code |
mapBootstrap_srBaseCoords | Source code |
mapBootstrap_srCoords | Man page Source code |
mapCohesion | Man page Source code |
mapComment | Man page |
mapComment<- | Man page |
mapConnectivityDistances | Source code |
mapConnectivityGraph | Source code |
mapDescription | Man page Source code |
mapDescription<- | Man page |
mapDimensions | Man page |
mapDisconnected | Source code |
mapDistances | Man page Source code |
mapGUI | Source code |
mapGUI_server | Source code |
mapGUI_ui | Source code |
mapGadget | Man page Source code |
mapLims | Source code |
mapName | Man page Source code |
mapName<- | Man page |
mapPlotLims | Source code |
mapPoints | Source code |
mapRelaxed | Man page Source code |
mapResiduals | Man page Source code |
mapStress | Man page Source code |
mapTransformation | Man page |
mapTransformation<- | Man page |
mapTranslation | Man page |
mapTranslation<- | Man page |
matchStrains | Man page |
match_mapAntigens | Man page Source code |
match_mapSera | Man page Source code |
matrixFromEuler | Source code |
mergeMaps | Man page Source code |
mergeReport | Man page Source code |
mesh_volume | Source code |
minColBasis | Man page |
minColBasis<- | Man page |
moveTrappedPoints | Man page Source code |
numAntigens | Man page Source code |
numLayers | Man page Source code |
numOptimizations | Man page Source code |
numPoints | Man page Source code |
numSera | Man page Source code |
numSeraGroups | Man page Source code |
numeric_min_tabledists | Source code |
numeric_titers | Source code |
numerictiterTable | Source code |
optimizationProperties | Man page |
optimization_getter | Source code |
optimization_setter | Source code |
optimizeAgReactivity | Man page Source code |
optimizeMap | Man page Source code |
orderAntigens | Man page Source code |
orderPoints | Man page |
orderSera | Man page Source code |
package_required | Source code |
parallel_mode | Source code |
plot.acmap | Man page Source code |
plot_agMeanResiduals | Source code |
plot_agStressPerTiter | Source code |
plot_lims | Source code |
plot_map_table_distance | Man page Source code |
plot_srMeanResiduals | Source code |
plot_srStressPerTiter | Source code |
plot_sr_titers | Source code |
plotly_agMeanResiduals | Source code |
plotly_agStressPerTiter | Source code |
plotly_map_table_distance | Man page Source code |
plotly_srMeanResiduals | Source code |
plotly_srStressPerTiter | Source code |
plotly_sr_titers | Source code |
plotlyfn | Source code |
plotspec_getter | Source code |
plotspec_setter | Source code |
pointStress | Man page |
polygon_area | Source code |
postDrawDetails.acpoint | Source code |
preDrawDetails.acpoint | Source code |
print.Rac_html_merge_report | Source code |
print.acmap | Source code |
procrustesData | Man page Source code |
procrustesMap | Man page Source code |
ptAnnotations | Man page |
ptBaseBootstrapBlobs | Source code |
ptBaseCoords | Man page Source code |
ptBaseTriangulationBlobs | Source code |
ptBootstrapBlob | Man page |
ptBootstrapBlobs | Man page Source code |
ptBootstrapCoords | Man page Source code |
ptClades | Man page |
ptCoords | Man page Source code |
ptCoords<- | Man page |
ptDiagnostics | Source code |
ptDrawingOrder | Man page Source code |
ptDrawingOrder<- | Man page |
ptHemisphering | Source code |
ptLeverage | Man page |
ptOpacity | Man page |
ptProcrustes | Source code |
ptStyles | Man page |
ptTriangulationBlob | Man page |
ptTriangulationBlobs | Man page Source code |
randomizeCoords | Man page Source code |
rbind_list_to_matrix | Source code |
reactivity_adjust_titers | Source code |
read.acmap | Man page Source code |
read.titerTable | Man page Source code |
read_brotli | Source code |
realignMap | Man page Source code |
realignOptimizations | Man page Source code |
recalculateStress | Man page Source code |
reduce_matrix_dimensions | Source code |
reflectMap | Man page Source code |
reflect_coords_in_axis | Source code |
relaxMap | Man page Source code |
relaxMapOneStep | Man page Source code |
removeAntigens | Man page Source code |
removeOptimizations | Man page Source code |
removePoints | Man page |
removeSera | Man page Source code |
renderRacViewer | Man page Source code |
reqOptimizations | Source code |
reqRelaxed | Source code |
rotateMap | Man page Source code |
rotate_coords_by_degrees | Source code |
rotate_coords_by_radians | Source code |
rotation_matrix_2D | Source code |
rotation_matrix_3D | Source code |
roxygen_tags | Source code |
runDimensionTestMap | Source code |
runGUI | Man page Source code |
save.acmap | Man page Source code |
save.coords | Man page Source code |
save.titerTable | Man page Source code |
separate_meshes | Source code |
sera_getter | Source code |
sera_setter | Source code |
server_alignOptimizations | Source code |
server_checkHemisphering | Source code |
server_coordsChanged | Source code |
server_loadMapData | Source code |
server_loadPointStyleData | Source code |
server_loadTableData | Source code |
server_moveTrappedPoints | Source code |
server_optimizationChanged | Source code |
server_procrustesMap | Source code |
server_randomizeMap | Source code |
server_reflectMap | Source code |
server_relaxMap | Source code |
server_relaxMapOneStep | Source code |
server_removeOptimizations | Source code |
server_runOptimizations | Source code |
server_saveCoordsData | Source code |
server_saveMapData | Source code |
server_saveTableData | Source code |
server_triangulationBlobs | Source code |
setLegend | Man page Source code |
set_col_opacity | Source code |
set_pts_sequence_matrix | Source code |
setup_acmap | Source code |
simpleCap | Source code |
singleline | Source code |
sortOptimizations | Man page Source code |
splitTiterLayers | Man page Source code |
srAnnotations | Man page Source code |
srAnnotations<- | Man page |
srAspect | Man page |
srAspect<- | Man page |
srAttributes | Man page |
srBaseBlob | Source code |
srBaseBootstrapBlobs | Source code |
srBaseCoords | Man page |
srBaseCoords<- | Man page |
srBaseTriangulationBlobs | Source code |
srBlob | Source code |
srBootstrapBlob | Man page Source code |
srBootstrapBlobs | Man page Source code |
srBootstrapCoords | Man page Source code |
srClades | Man page Source code |
srClades<- | Man page |
srCohesion | Man page Source code |
srCoords | Man page Source code |
srCoords<- | Man page |
srDates | Man page |
srDates<- | Man page |
srDiagnostics | Source code |
srExtra | Man page |
srExtra<- | Man page |
srExtraMatrix | Source code |
srFill | Man page |
srFill<- | Man page |
srGroupMatrix | Source code |
srGroupOutline | Source code |
srGroups | Man page Source code |
srGroups<- | Man page |
srHemisphering | Source code |
srHomologousAgs | Man page Source code |
srHomologousAgs<- | Man page |
srHomologousAgsReindexed | Source code |
srIDs | Man page |
srIDs<- | Man page |
srLeverage | Man page Source code |
srLineage | Man page |
srLineage<- | Man page |
srMeanResiduals | Source code |
srNameMatrix | Source code |
srNames | Man page |
srNames<- | Man page |
srNucleotideSequences | Man page Source code |
srNucleotideSequences<- | Man page |
srNumMatrix | Source code |
srOpacity<- | Man page |
srOutline | Man page |
srOutline<- | Man page |
srOutlineWidth | Man page |
srOutlineWidth<- | Man page |
srPassage | Man page |
srPassage<- | Man page |
srReassortant | Man page |
srReassortant<- | Man page |
srReference | Man page |
srReference<- | Man page |
srRotation | Man page |
srRotation<- | Man page |
srSequences | Man page Source code |
srSequences<- | Man page |
srShape | Man page |
srShape<- | Man page |
srShown | Man page |
srShown<- | Man page |
srSize | Man page |
srSize<- | Man page |
srSpecies | Man page |
srSpecies<- | Man page |
srStress | Man page Source code |
srStressPerTiter | Man page Source code |
srStrings | Man page |
srStrings<- | Man page |
srTriangulationBlob | Man page Source code |
srTriangulationBlobs | Man page Source code |
standardizeStrainName | Source code |
standardizeStrainNames | Man page Source code |
strain_list_error | Source code |
strain_list_warning | Source code |
stressBlobs | Man page |
stressTable | Man page Source code |
subsetAntigens | Source code |
subsetCommonAgs | Man page Source code |
subsetCommonPoints | Man page |
subsetCommonSrGroups | Man page Source code |
subsetMap | Man page Source code |
subsetSera | Source code |
tab_img | Source code |
tableColbases | Man page Source code |
tableDistances | Man page Source code |
table_arg_deprecated | Source code |
titerLeverage | Man page Source code |
titerTable | Man page Source code |
titerTable<- | Man page |
titerTableFlat | Man page Source code |
titerTableFlat<- | Man page |
titerTableLayers | Man page Source code |
titerTableLayers<- | Man page |
titer_types_int | Source code |
titertypesTable | Source code |
titertypesTableLayers | Source code |
transformMapBlob | Source code |
translateMap | Man page Source code |
translate_coords | Source code |
triangulationBlobs | Man page Source code |
unstableMaps | Man page |
update_ferret_seraNames | Man page Source code |
validate_colors | Source code |
view | Man page Source code |
view.acmap | Man page Source code |
view.default | Man page Source code |
vmessage | Source code |
warn_disconnected | Source code |
warn_underconstrained | Source code |
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