Package ‘archetypes’ October12,2022 Type Package Title ArchetypalAnalysis Version 2.2-0.1 Date 2014-04-08 Depends methods,stats,modeltools,nnls(>=1.1) Suggests MASS,vcd,mlbench,ggplot2,TSP Description Themainfunctionarchetypesimplementsa frameworkforarchetypalanalysissupportingarbitrary problemsolvingmechanismsforthedifferentconceptual partsofthealgorithm. License GPL(>=2) Collate 'archetypes-barplot.R''generics.R''archetypes-class.R' 'archetypes-kit-blocks.R''archetypes-kit.R''archetypes-map.R' 'archetypes-movie.R''archetypes-panorama.R''pcplot.R' 'archetypes-pcplot.R''archetypes-robust.R' 'archetypes-screeplot.R''archetypes-step.R' 'archetypes-weighted.R''archetypes-xyplot.R''memento.R' 'simplex-pot.R''skeletonplot.R' Author ManuelJ.A.Eugster[aut,cre], FriedrichLeisch[aut], SohanSeth[ctb] Maintainer ManuelJ.A.Eugster<[email protected]> NeedsCompilation no Repository CRAN Date/Publication 2019-04-2206:55:33UTC R topics documented: archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 archetypesFamily . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 archmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1 2 archetypes as.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 barplot.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 bestModel.stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 coef.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 fitted.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 kappa.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 lines.pcplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 movieplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 nparameters.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 panorama.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 parameters,archetypes-method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 pcplot.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 pcplot.default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 predict.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 residuals.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 robustArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 rss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 rss.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 screeplot.stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 simplexplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 simplex_projection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 skel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 skeletonplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 summary.stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 toy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 weightedArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 weights.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 xyplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 xyplot.archetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 xyplot.robustArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 xyplot.stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 xyplot.weightedArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 [.stepArchetypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Index 30 archetypes Performarchetypalanalysisonadatamatrix. Description Performarchetypalanalysisonadatamatrix. archetypes 3 Usage archetypes(data, k, weights = NULL, maxIterations = 100, minImprovement = sqrt(.Machine$double.eps), maxKappa = 1000, verbose = FALSE, saveHistory = TRUE, family = archetypesFamily("original"), ...) Arguments data Anumericn×mdatamatrix. k Thenumberofarchetypes. weights Dataweightsmatrixorvector(usedaselementsofthediagonalweightsmatrix). maxIterations Themaximumnumberofiterations. minImprovement Theminimalvalueofimprovementbetweentwoiterations. maxKappa Thelimitofkappatoreportanill-nesswarning. verbose Printsomedetailsduringexecution. saveHistory Saveeachexecutionstepinanenvironmentforfurtheranalyses. family Blocksdefiningtheunderlyingproblemsolvingmechanisms;seearchetypesFamily. ... Additionalargumentsforfamilyblocks. Value Anobjectofclassarchetypes,seeas.archetypes. References CutlerandBreiman. ArchetypalAnalysis. Technometrics,36(4),1994. 338-348. SeeAlso Otherarchetypes:archetypesFamily;as.archetypes;robustArchetypes;weightedArchetypes Examples data(toy) a <- archetypes(toy, 3) 4 archmap archetypesFamily Archetypesfamilyconstructor Description This function returns a problem solving block for each of the different conceptual parts of the algorithm. Usage archetypesFamily(which = c("original", "weighted", "robust"), ...) Arguments which Thekindofarchetypesfamily. ... Exchangepredefinedfamilyblockswithself-definedfunctions. Value Alistcontainingafunctionforeachofthedifferentparts. SeeAlso Otherarchetypes: archetypes;as.archetypes;robustArchetypes;weightedArchetypes archmap Archetypalmaps Description Two-dimensionalprojectionoftheobservationsbasedonthealphacoefficientsintoaspacespanned bythe(projected)archetypes. Usage archmap(object, projection = simplex_projection, projection_args = list(), rotate = 0, cex = 1.5, col = 1, pch = 1, xlab = "", ylab = "", axes = FALSE, asp = TRUE, ...) archmap 5 Arguments object Anarchetypesobject projection Projectionfunction;seearchmap_projections projection_args Argumentspassedtotheprojectionfunction;seearchmap_projections rotate Rotationangletorotatetheprojection cex Characterexpansionofarchetypes col Colorofobservations pch Pointcharacterofobservations xlab Alabelforthex-axis ylab Alabelforthey-axis axes Logicalvaluetodrawaxesornot asp They/xaspectratio ... Argumentspassedtotheunderlyingplotfunction Value Invisiblematrixwiththeprojectedarchetypes SeeAlso Otherarchmap:archmap_projections,atypes_projection,simplex_projection,tspsimplex_projection Examples ## Not run: data("skel", package = "archetypes") skel2 <- subset(skel, select = -Gender) set.seed(1981) a <- archetypes(skel2, k = 5) ## Simplex projection: archmap(a, col = skel$Gender) ## Simplex projection with archetypes arranged according to their ## distances: archmap(a, col = skel$Gender, projection = tspsimplex_projection) archmap(a, col = skel$Gender, projection = tspsimplex_projection, projection_args = list(equidist = TRUE)) ## MDS projection: archmap(a, col = skel$Gender, projection = atypes_projection) ## End(Not run) 6 as.archetypes as.archetypes Archetypesobjectconstructor Description Archetypesobjectconstructor Usage as.archetypes(object, k, alphas, rss, iters = NULL, call = NULL, history = NULL, kappas = NULL, betas = NULL, zas = NULL, family = NULL, familyArgs = NULL, residuals = NULL, weights = NULL, reweights = NULL, scaling = NULL) Arguments object Thearchetypes;ap×mmatrix,seeparameters. k Thenumberofarchetypes; alphas Thecoefficients;an×pmatrix,seecoef. rss Theresidualsumofsquares;seerss.archetypes. iters Thenumberofiterationstotheconvergence. call Thecallofthearchetypesfunction. history If saveHistory set then an environment with the archetypes object for each executionstep; kappas Thekappasforeachsystemoflinearequations. betas Thedatacoefficients;ap×nmatrix. zas Thetemporaryarchetypes. family Thearchetypesfamily. familyArgs Additionalargumentsforfamilyblocks. residuals Theresiduals. weights Thedataweights. reweights Thedatareweights. scaling Thescalingparametersofthedata. Value Alistwithanelementforeachparameterandclassattributearchetypes. SeeAlso Otherarchetypes: archetypesFamily;archetypes;robustArchetypes;weightedArchetypes barplot.archetypes 7 barplot.archetypes Barplotofarchetypes. Description Barplotofarchetypes. Usage ## S3 method for class 'archetypes' barplot(height, data, which = c("below", "beside"), which.beside = c("atypes", "variables"), which.below = c("compressed", "default"), percentiles = FALSE, below.compressed.height = 0.1, below.compressed.srt = 0, col.atypes = NULL, ...) Arguments height Anarchetypesobject. data Theoriginaldatamatrix. which belowcreatesabarplotforeacharchetype,besidecreatesonebarplotwithbars sidebyside. which.beside Barplotaccordingtoatypesorvariables. which.below compressedplotsthelabelsonlyonce. percentiles Showrealvaluesorpercentileprofiles. below.compressed.height Heightofadditionaltailsubplot. below.compressed.srt Rotationsofthex-labels. col.atypes Colorofarchetypes;onlyusedinbelow.compressed. ... Passedtotheunderlyingbarplotcall. Value Undefined. 8 body bestModel.stepArchetypes Returnbestmodel Description Returnbestmodel Usage ## S3 method for class 'stepArchetypes' bestModel(object, ...) ## S3 method for class 'repArchetypes' bestModel(object, ...) Arguments object Anarchetypesobject. ... Ignored body Exploringrelationshipsinbodydimensions Description Bodygirthmeasurementsandskeletaldiametermeasurements, aswellasage, weight, heightand gender,aregivenfor507physicallyactiveindividuals-247menand260women. Usage body Format Adata.framecontaining507observationsof25variables. References Heinz, Peterson, Johnson and Kerk. "Exploring relationships in body dimensions". Journal of StatisticsEducation,11(2). http://www.amstat.org/publications/jse/v11n2/datasets.heinz.html SeeAlso skel coef.archetypes 9 coef.archetypes Returncoefficients Description Returncoefficients Usage ## S3 method for class 'archetypes' coef(object, type = c("alphas", "betas"), ...) Arguments object Anarchetypesobject. type Returnalphaorbetacoefficients. ... Ignored. Value Coefficientmatrix. fitted.archetypes Returnfitteddata Description Returnstheapproximateddata. Usage ## S3 method for class 'archetypes' fitted(object, ...) Arguments object Anarchetypesobject. ... Ignored. Value Matrixwithapproximateddata. 10 lines.pcplot kappa.archetypes Returnkappa Description Returnkappa Usage ## S3 method for class 'archetypes' kappa(z, ...) Arguments z Anarchetypesobject. ... Ignored. Value Avectorofkappas. lines.pcplot Addlinestoanexistingparallelcoordinatesplot. Description Addlinestoanexistingparallelcoordinatesplot. Usage ## S3 method for class 'pcplot' lines(x, data, col = 1, lty = 1, ...) Arguments x Amatrixordataframecontainingtheadditionaldata. data Thedataoftheexistingparallelcoordinatesplot. col Linecolors. lty Linetypes. ... Passedtounderlyingmatlines. Value Undefined.