{ "_id": "6a103ef9acfb0bcc41c9cb4a", "Package": "Racmacs", "Type": "Package", "Title": "Antigenic Cartography Macros", "Version": "1.2.9", "Date": "2023-11-30", "Authors@R": "c(person(given = \"Sam\",\nfamily = \"Wilks\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sw463@cam.ac.uk\"))", "Description": "A toolkit for making antigenic maps from immunological\nassay data, in order to quantify and visualize antigenic\ndifferences between different pathogen strains as described in\nSmith et al. (2004) and used in\nthe World Health Organization influenza vaccine strain\nselection process. Additional functions allow for the\ndiagnostic evaluation of antigenic maps and an interactive\nviewer is provided to explore antigenic relationships amongst\nseveral strains and incorporate the visualization of associated\ngenetic information.", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://acorg.github.io/Racmacs/,\nhttps://github.com/acorg/Racmacs/", "BugReports": "https://github.com/acorg/Racmacs/issues", "License": "AGPL-3", "Language": "en-GB", "Config/pak/sysreqs": "cmake libglpk-dev make libuv1-dev libxml2-dev\nzlib1g-dev", "Repository": "https://acorg.r-universe.dev", "Date/Publication": "2024-06-27 10:26:25 UTC", "RemoteUrl": "https://github.com/acorg/racmacs", "RemoteRef": "HEAD", "RemoteSha": "f75f9cd2d6b24f101ce71e39e2188490efa9ef1d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-11 09:05:33 UTC", "User": "root" }, "Author": "Sam Wilks [aut, cre]", "Maintainer": "Sam Wilks ", 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], "_help": [ { "page": "acmap", "title": "Generate a new acmap object", "concept": [ "functions for working with map data" ], "topics": [ "acmap" ] }, { "page": "acmapAttributes", "title": "Get acmap attributes", "concept": [ "map attribute functions" ], "topics": [ "acmapAttributes", "numAntigens", "numLayers", "numOptimizations", "numPoints", "numSera", "numSeraGroups" ] }, { "page": "addOptimization", "title": "Add a new optimization to an acmap object", "concept": [ "functions for working with map data" ], "topics": [ "addOptimization" ] }, { "page": "adjustedLogTiterTable", "title": "Get the reactivity adjusted log titer table", "concept": [ "map attribute functions" ], "topics": [ "adjustedLogTiterTable" ] }, { "page": "adjustedTiterTable", "title": "Get the reactivity adjusted titer table", "concept": [ "map attribute functions" ], "topics": [ "adjustedTiterTable" ] }, { "page": "agAttributes", "title": "Getting and setting antigen attributes", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agAttributes", "agContinent", "agContinent<-", "agDates", "agDates<-", "agExtra", "agExtra<-", "agIDs", "agIDs<-", "agLineage", "agLineage<-", "agNames", "agNames<-", "agPassage", "agPassage<-", "agReassortant", "agReassortant<-", "agReference", "agReference<-", "agStrings", "agStrings<-" ] }, { "page": "mapCohesion", "title": "Check map cohesion", "concept": [ "map diagnostic functions" ], "topics": [ "agCohesion", "mapCohesion", "srCohesion" ] }, { "page": "agGroups", "title": "Getting and setting antigen groups", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agGroups", "agGroups<-" ] }, { "page": "agHomologousSr", "title": "Get homologous sera for each antigen", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agHomologousSr" ] }, { "page": "agLabIDs", "title": "Getting and setting antigen lab id information", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agLabIDs", "agLabIDs<-" ] }, { "page": "agReactivityAdjustments", "title": "Get and set antigen reactivity adjustments", "concept": [ "functions for working with map data" ], "topics": [ "agReactivityAdjustments", "agReactivityAdjustments<-" ] }, { "page": "agSequences", "title": "Getting and setting antigen sequence information", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agNucleotideSequences", "agNucleotideSequences<-", "agSequences", "agSequences<-" ] }, { "page": "applyMapTransform", "title": "Apply the current map transformation", "concept": [ "functions relating to map transformation" ], "topics": [ "applyMapTransform" ] }, { "page": "applyPlotspec", "title": "Apply a plotspec from another acmap", "concept": [ "map point style functions" ], "topics": [ "applyPlotspec" ] }, { "page": "as.json", "title": "Convert map to json format", "concept": [ "functions for working with map data" ], "topics": [ "as.json" ] }, { "page": "blob", "title": "Plot a blob object", "concept": [ "additional plotting functions" ], "topics": [ "blob" ] }, { "page": "blobsize", "title": "Calculate size of a blob object", "concept": [ "additional plotting functions" ], "topics": [ "blobsize" ] }, { "page": "bootstrapBlobs", "title": "Calculate bootstrap blob data for an antigenic map", "concept": [ "map diagnostic functions" ], "topics": [ "bootstrapBlobs" ] }, { "page": "bootstrapMap", "title": "Perform a bootstrap on a map", "concept": [ "map diagnostic functions" ], "topics": [ "bootstrapMap" ] }, { "page": "checkHemisphering", "title": "Check for hemisphering or trapped points", "concept": [ "map diagnostic functions" ], "topics": [ "checkHemisphering" ] }, { "page": "colBases", "title": "Getting and setting column bases", "concept": [ "map optimization attribute functions" ], "topics": [ "colBases", "fixedColBases", "fixedColBases<-", "minColBasis", "minColBasis<-" ] }, { "page": "deprecated_functions", "title": "Deprecated functions", "topics": [ "deprecated_functions", "stressBlobs" ] }, { "page": "dilutionStepsize", "title": "Get or set the dilution stepsize associated with a map", "concept": [ "map attribute functions" ], "topics": [ "dilutionStepsize", "dilutionStepsize<-" ] }, { "page": "dimensionTestMap", "title": "Perform dimension testing on a map object", "concept": [ "map diagnostic functions" ], "topics": [ "dimensionTestMap" ] }, { "page": "edit_agNames", "title": "Edit antigen names in an acmap", "concept": [ "functions for working with map data" ], "topics": [ "edit_agNames" ] }, { "page": "edit_srNames", "title": "Edit sera names in an acmap", "concept": [ "functions for working with map data" ], "topics": [ "edit_srNames" ] }, { "page": "export_viewer", "title": "Export the map viewer", "concept": [ "functions to view maps" ], "topics": [ "export_viewer" ] }, { "page": "getOptimization", "title": "Get optimization details from an acmap object", "topics": [ "getOptimization" ] }, { "page": "ggplot.acmap", "title": "Plot an antigenic map using ggplot", "concept": [ "functions to view maps" ], "topics": [ "ggplot.acmap" ] }, { "page": "htmlAdjustedTiterTable", "title": "Return an html formatted titer table with antigen reactivity adjustments applied", "topics": [ "htmlAdjustedTiterTable" ] }, { "page": "htmlMergeReport", "title": "Return an html formatted merge report", "concept": [ "map merging functions" ], "topics": [ "htmlMergeReport" ] }, { "page": "htmlTiterTable", "title": "Return an html formatted titer table", "topics": [ "htmlTiterTable" ] }, { "page": "keepBestOptimization", "title": "Keep only the lowest stress map optimization", "concept": [ "functions for working with map data" ], "topics": [ "keepBestOptimization" ] }, { "page": "keepOptimizations", "title": "Keep specified optimization runs", "concept": [ "functions to work with map optimizations" ], "topics": [ "keepOptimizations" ] }, { "page": "keepSingleOptimization", "title": "Keep only a single optimization run", "concept": [ "functions for working with map data" ], "topics": [ "keepSingleOptimization" ] }, { "page": "layerNames", "title": "Get and set map layer names", "concept": [ "functions for working with map data" ], "topics": [ "layerNames", "layerNames<-" ] }, { "page": "listOptimizations", "title": "Get all optimization details from an acmap object", "topics": [ "listOptimizations" ] }, { "page": "logtiterTable", "title": "Get the log titers from an acmap", "concept": [ "functions relating to map stress calculation", "map diagnostic functions" ], "topics": [ "logtiterTable" ] }, { "page": "logtiterTableLayers", "title": "Return a list of logtiter table layers", "concept": [ "map attribute functions" ], "topics": [ "logtiterTableLayers" ] }, { "page": "make.acmap", "title": "Make an antigenic map from scratch", "concept": [ "map optimization functions" ], "topics": [ "make.acmap" ] }, { "page": "map-table-distances", "title": "Plot map vs table distances", "concept": [ "map diagnostic functions" ], "topics": [ "map-table-distances", "plotly_map_table_distance", "plot_map_table_distance" ] }, { "page": "mapBootstrapCoords", "title": "Get bootstrap coordinates associated with a map", "concept": [ "map diagnostic functions" ], "topics": [ "mapBootstrapCoords", "mapBootstrap_agCoords", "mapBootstrap_ptBaseCoords", "mapBootstrap_srCoords" ] }, { "page": "mapComment", "title": "Get or set an optimization run comment", "concept": [ "map optimization attribute functions" ], "topics": [ "mapComment", "mapComment<-" ] }, { "page": "mapDescription", "title": "Getting and setting the map description", "concept": [ "map attribute functions" ], "topics": [ "mapDescription", "mapDescription<-" ] }, { "page": "mapDimensions", "title": "Get the current map dimensions", "concept": [ "map optimization attribute functions" ], "topics": [ "mapDimensions" ] }, { "page": "mapDistances", "title": "Return calculated map distances for an acmap", "concept": [ "functions relating to map stress calculation", "map diagnostic functions" ], "topics": [ "mapDistances" ] }, { "page": "mapGadget", "title": "Open a shiny gadget to view the map", "concept": [ "functions to view maps" ], "topics": [ "mapGadget" ] }, { "page": "mapName", "title": "Getting and setting the map name", "concept": [ "map attribute functions" ], "topics": [ "mapName", "mapName<-" ] }, { "page": "mapRelaxed", "title": "Check if a map has been fully relaxed", "concept": [ "map diagnostic functions" ], "topics": [ "mapRelaxed" ] }, { "page": "mapResiduals", "title": "Get a table of residuals from an acmap", "concept": [ "functions relating to map stress calculation", "map diagnostic functions" ], "topics": [ "mapResiduals" ] }, { "page": "mapStress", "title": "Calculate the current map stress", "concept": [ "map optimization attribute functions" ], "topics": [ "mapStress" ] }, { "page": "mapTransformation", "title": "Reading map transformation data", "concept": [ "map optimization attribute functions" ], "topics": [ "mapTransformation", "mapTransformation<-", "mapTranslation", "mapTranslation<-" ] }, { "page": "matchStrains", "title": "Find matching antigens or sera between 2 maps", "concept": [ "functions to compare maps" ], "topics": [ "matchStrains", "match_mapAntigens", "match_mapSera" ] }, { "page": "mergeMaps", "title": "Merging maps", "concept": [ "map merging functions" ], "topics": [ "mergeMaps" ] }, { "page": "mergeReport", "title": "Return a merge report", "concept": [ "map merging functions" ], "topics": [ "mergeReport" ] }, { "page": "moveTrappedPoints", "title": "Move trapped points", "concept": [ "map optimization functions" ], "topics": [ "moveTrappedPoints" ] }, { "page": "optimizationProperties", "title": "Get optimization properties", "concept": [ "functions to work with map optimizations" ], "topics": [ "allMapDimensions", "allMapStresses", "optimizationProperties" ] }, { "page": "optimizeAgReactivity", "title": "Optimize antigen reactivity adjustments", "topics": [ "optimizeAgReactivity" ] }, { "page": "optimizeMap", "title": "Optimize an acmap", "concept": [ "map optimization functions" ], "topics": [ "optimizeMap" ] }, { "page": "orderPoints", "title": "Order antigens and sera", "concept": [ "functions for working with map data" ], "topics": [ "orderAntigens", "orderPoints", "orderSera" ] }, { "page": "plot.acmap", "title": "Plot an antigenic map", "concept": [ "functions to view maps" ], "topics": [ "plot.acmap" ] }, { "page": "pointStress", "title": "Get individual point stress", "concept": [ "functions relating to map stress calculation", "map diagnostic functions" ], "topics": [ "agStress", "agStressPerTiter", "pointStress", "srStress", "srStressPerTiter" ] }, { "page": "procrustesData", "title": "Return procrustes data on a map comparison", "concept": [ "functions to compare maps" ], "topics": [ "procrustesData" ] }, { "page": "procrustesMap", "title": "Return procrustes information", "concept": [ "functions to compare maps" ], "topics": [ "procrustesMap" ] }, { "page": "ptAnnotations", "title": "Getting and setting point annotation information", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agAnnotations", "agAnnotations<-", "ptAnnotations", "srAnnotations", "srAnnotations<-" ] }, { "page": "ptBaseCoords", "title": "Getting and setting base coordinates", "concept": [ "map optimization attribute functions" ], "topics": [ "agBaseCoords", "agBaseCoords<-", "ptBaseCoords", "srBaseCoords", "srBaseCoords<-" ] }, { "page": "ptBootstrapBlob", "title": "Get antigen or serum bootstrap blob information", "concept": [ "map diagnostic functions" ], "topics": [ "agBootstrapBlob", "agBootstrapBlobs", "ptBootstrapBlob", "ptBootstrapBlobs", "srBootstrapBlob", "srBootstrapBlobs" ] }, { "page": "ptBootstrapCoords", "title": "Get antigen or serum bootstrap coordinates information", "concept": [ "map diagnostic functions" ], "topics": [ "agBootstrapCoords", "ptBootstrapCoords", "srBootstrapCoords" ] }, { "page": "ptClades", "title": "Getting and setting point clade information", "concept": [ "antigen and sera attribute functions" ], "topics": [ "agClades", "agClades<-", "ptClades", "srClades", "srClades<-" ] }, { "page": "ptCoords", "title": "Getting and setting point coordinates", "concept": [ "map optimization attribute functions" ], "topics": [ "agCoords", "agCoords<-", "ptCoords", "ptCoords<-", "srCoords", "srCoords<-" ] }, { "page": "ptDrawingOrder", "title": "Get and set point drawing order in map", "concept": [ "map point style functions" ], "topics": [ "ptDrawingOrder", "ptDrawingOrder<-" ] }, { "page": "ptLeverage", "title": "Calculate point leverage", "concept": [ "map diagnostic functions" ], "topics": [ "agLeverage", "ptLeverage", "srLeverage", "titerLeverage" ] }, { "page": "ptOpacity", "title": "Set point opacity in a map", "concept": [ "map point style functions" ], "topics": [ "agOpacity<-", "ptOpacity", "srOpacity<-" ] }, { "page": "ptStyles", "title": "Getting and setting 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