diff --git a/NAMESPACE b/NAMESPACE index f35c043..d236ec3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,205 +1,200 @@ S3method("+",ggList) S3method(print,ggList) export("%++%") #export("%+%") export( "aggregate.bootstrap", "aggregate.bootstrap.list", "aggregate.challenge", "aggregate.ranked.list", "aggregateThenRank", "as.challenge", "as.relation.challenge.incidence", "as.relation.ranked.list", - "bootstrap", "bootstrap.ranked.list", #"bootstrap.default", + "bootstrap", "bootstrap.ranked.list", "boxplot.ranked.list", "boxplot.bootstrap.list", "boxplot.comparedRanks.list", - #"check_strict_preference", - "compareRanks", "compareRanks.ranked", "compareRanks.ranked.list", # "compareRanks.default", - "consensus", "consensus.ranked.list", #"consensus.default", + "compareRanks", "compareRanks.ranked.list", + "consensus", "consensus.ranked.list", "Decision", "decision.challenge", "default_colors", "density.bootstrap.list", "dendrogram", "dendrogram.ranked.list", "extract.workflow", "kendall", "kendall.bootstrap.list", - # "merge.list", "lineplot.challenge", "methodsplot","methodsplot.challenge", "network", "plot.network", - "podium","podium.ranked.list", "podium.challenge",#"podium.default", + "podium","podium.ranked.list", "podium.challenge", "print.aggregated", "print.aggregated.list", "print.comparedRanks", "print.ranked", "print.ranked.list", - #"quickmerge.list", - "rank", "rank.aggregated.list", "rank.aggregatedRanks.list", "rank.challenge", #"rank.default", - "rankFrequencies", "rankFrequencies.bootstrap", "rankFrequencies.bootstrap.list", #"rankFrequencies.default", - #"rankNA2", + "rank", "rank.aggregated.list", "rank.aggregatedRanks.list", "rank.challenge", + "rankFrequencies", "rankFrequencies.bootstrap", "rankFrequencies.bootstrap.list", "rankThenAggregate", "rankingHeatmap", "rankingHeatmap.ranked.list", "relation_dissimilarity.ranked.list", "report", "report.bootstrap.list", "select.if", "select.if.aggregated.list", "select.if.comparedRanks.list", "select.if.list", "select.if.ranked.list", "significanceMap", "spearmansFootrule", "spearmansWeightedFootrule", "splitby", "stability", "stabilityByAlgorithm", "stabilityByTask", "stability.ranked.list", "relation_dissimilarity", "stabilityByAlgorithm.bootstrap.list", "stabilityByTask.bootstrap.list", "subset", - "subset.aggregated.list", "subset.comparedRanks.list", "subset.list", "subset.ranked.list", "subset.bootstrap.list", #"which.top", + "subset.aggregated.list", "subset.comparedRanks.list", "subset.list", "subset.ranked.list", "subset.bootstrap.list", "test", "test.challenge", "test.default", "testThenRank", "violin", "violin.bootstrap.list", "winner", "winner.bootstrap.list", "winner.default", "winner.ranked.list", "winnerFrequencies", "winnerFrequencies.bootstrap", "winnerFrequencies.bootstrap.list", "winnerFrequencies.default" ) importFrom("dplyr", "bind_rows","group_by","summarise","select_if","filter","mutate","right_join","anti_join","ungroup","arrange","desc") importFrom("rlang",":=",".data","!!") importFrom("reshape2","melt", "acast") importFrom("utils", "capture.output", "methods") importFrom("plyr", "llply") importFrom("knitr", "kable") importFrom("tidyr", "complete","expand") importFrom("purrr", "%>%") importFrom("rmarkdown", "render","word_document","pdf_document","html_document") importFrom("viridisLite", "viridis","cividis") importFrom("ggplot2", "aes","aes_string","geom_abline", "geom_bar", "geom_boxplot", "geom_count", "geom_density", "geom_jitter", "geom_line", "geom_point", "geom_raster", "geom_step", "geom_text", "geom_violin","annotate","guide_legend", "geom_vline", "ggplot", "ggtitle","vars","xlab","ylab","scale_size_area","theme_get","rel","geom_hline","ggplot_build","scale_fill_manual", "scale_y_continuous","coord_cartesian", "element_text", "facet_wrap", "position_jitter", "stat", "stat_summary", "theme", "unit","guides","scale_fill_viridis_c", "theme_set", "theme_light", "scale_color_manual", "element_blank") importFrom("grDevices", "col2rgb", "gray", "rgb", "grey") importFrom("graphics", "abline", "axis", "barplot", "box", "layout", "legend", "par", "plot", "points", "segments","boxplot", "stripchart", "title", "grconvertX", "plot.new") importFrom("stats", "as.dist", "as.formula", "median", "p.adjust", "density", "quantile", "aggregate", "cor", "wilcox.test", "terms.formula", "complete.cases") importFrom("methods", "new") importFrom("relations","relation","as.relation", "relation_domain", "relation_incidence", "relation_is_asymmetric","relation_consensus","relation_ensemble", "relation_is_irreflexive", "relation_is_negatively_transitive", "relation_is_transitive", "relation_is_trichotomous", "relation_scores", "relation_violations","relation_dissimilarity") importFrom("graph", "addEdge") S3method(print, comparedRanks) S3method(print, aggregated) S3method(print, ranked) S3method(print, aggregated.list) S3method(print, ranked.list) S3method(aggregate, challenge) S3method(aggregate, ranked.list) S3method(aggregate, bootstrap.list) S3method(aggregate, bootstrap) S3method(test, default) S3method(test, challenge) S3method(Aggregate, default) S3method(Aggregate, list) S3method(Rank, default) S3method(Rank, list) S3method(rank, default) S3method(rank, challenge) S3method(rank, aggregated.list) S3method(rank, aggregatedRanks.list) S3method(bootstrap, default) S3method(bootstrap, ranked.list) S3method(dendrogram, default) S3method(dendrogram, ranked.list) S3method(winner, default) S3method(winner, ranked.list) S3method(winner, bootstrap.list) S3method(rankFrequencies, default) S3method(rankFrequencies, bootstrap) S3method(rankFrequencies, bootstrap.list) S3method(winnerFrequencies, default) S3method(winnerFrequencies, bootstrap) S3method(winnerFrequencies, bootstrap.list) S3method(compareRanks,default) -S3method(compareRanks,ranked) S3method(compareRanks,ranked.list) S3method(merge,list) S3method(melt,ranked.list) S3method(melt,aggregated.list) S3method(boxplot,ranked.list) S3method(boxplot,comparedRanks.list) S3method(boxplot,bootstrap.list) S3method(select.if,default) S3method(select.if,list) S3method(select.if,aggregated.list) S3method(select.if,ranked.list) S3method(select.if,comparedRanks.list) S3method(subset,list) S3method(subset,bootstrap.list) S3method(subset,aggregated.list) S3method(subset,ranked.list) S3method(subset,comparedRanks.list) S3method(podium,default) S3method(podium,challenge) S3method(podium,ranked.list) S3method(network,default) S3method(network,ranked.list) S3method(network,dist) S3method(plot,network) S3method(density,bootstrap.list) S3method(as.relation,challenge.incidence) S3method(as.relation,ranked.list) S3method(subset,bootstrap.list) S3method(subset,ranked.list) S3method(subset,list) S3method(subset,comparedRanks.list) S3method(subset,aggregated.list) S3method(decision,challenge) S3method(decision,default) S3method(lineplot,challenge) S3method(lineplot,default) S3method(methodsplot,challenge) S3method(methodsplot,default) S3method(significanceMap,data.frame) S3method(significanceMap,ranked.list) S3method(significanceMap,default) S3method(violin,bootstrap.list) S3method(violin,default) S3method(rankingHeatmap,ranked.list) S3method(rankingHeatmap,default) S3method(relation_dissimilarity,ranked.list) S3method(relation_dissimilarity,default) S3method(stabilityByTask,bootstrap.list) S3method(stabilityByTask,default) S3method(stability,default) S3method(stability,ranked.list) S3method(stabilityByAlgorithm,bootstrap.list) S3method(stabilityByAlgorithm,default) S3method(consensus,ranked.list) S3method(consensus,default) S3method(report,bootstrap.list) S3method(report,ranked.list) S3method(report,default) diff --git a/R/compareRanks.R b/R/compareRanks.R index 34c1f05..0832bc1 100644 --- a/R/compareRanks.R +++ b/R/compareRanks.R @@ -1,58 +1,42 @@ kendall=function(a,b) cor(a,b,method="kendall") spearmansWeightedFootrule=function(a,b) sum(abs(a-b)/pmin(a,b)) spearmansFootrule=function(a,b) sum(abs(a-b)) # SpearmansFootrule=function(a,b) sum(abs(match(a, b) - a)) # SpearmansWeightedFootrule=function(a,b) sum(abs(match(a, b) - a)/pmin(a,b)) compareRanks <- function(x,...) UseMethod("compareRanks") compareRanks.default <- function(x, ...) stop("not implemented for this class") -compareRanks.ranked <-function(x, - y, - FUN=kendall,...){ - mat=merge(x$mat, - y$mat, - by="row.names", - suffixes = c(".1",".2"), - ...) - tau=FUN(mat$rank.1, - mat$rank.2) - res=list(tau=tau, - mat=mat) - class(res)="comparedRanks" - res - } - compareRanks.ranked.list <-function(x, y, FUN=kendall,...){ matlist=merge.list(x$matlist, y$matlist ,...) res=lapply(1:length(matlist), function(z){ tau=FUN(matlist[[z]][,"rank.1"], matlist[[z]][,"rank.2"]) res=list(tau=tau, mat=matlist[[z]]) class(res)="comparedRanks" res }) names(res)=names(matlist) class(res)="comparedRanks.list" res } print.comparedRanks <- function(x,...) { cat("\n") print(x$mat) cat("\nKendall's tau =",x$tau,"\n-------------------------------------------------------\n") }