diff --git a/NAMESPACE b/NAMESPACE index bc1eca7..f4579ec 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,223 +1,222 @@ #exportPattern("^[[:alpha:]]+") export( "aggregate.bootstrap", "aggregate.bootstrap.list", "aggregate.challenge", "aggregate.ranked", "aggregate.ranked.list", "aggregateList", #? "aggregateThenRank", "as.challenge", "as.relation.challenge.incidence", "as.relation.ranked.list", "bootstrap", "bootstrap.ranked", "bootstrap.ranked.list", #"bootstrap.default", "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", "Decision", "decision.challenge", "blobplot","blobplot.ranked", "default_colors", "density.bootstrap.list", "extract.workflow", "kendall", "kendall.bootstrap.list", # "melt.aggregated.list", "melt.ranked", "melt.ranked.list", # "merge.list", "lineplot.challenge", "methodsplot","methodsplot.challenge", "network", "plot.network", "podium", "podium.ranked","podium.ranked.list", "podium.challenge",#"podium.default", "print.aggregated", "print.aggregated.list", "print.comparedRanks", "print.ranked", "print.ranked.list", #"quickmerge.list", "rank", "rank.aggregated", "rank.aggregated.list", "rank.aggregatedRanks", "rank.aggregatedRanks.list", "rank.challenge", #"rank.default", "rankFrequencies", "rankFrequencies.bootstrap", "rankFrequencies.bootstrap.list", #"rankFrequencies.default", #"rankNA2", "rankThenAggregate", "rankingHeatmap", "rankingHeatmap.ranked.list", "relation_dissimilarity.ranked.list", "report", "report.bootstrap.list", "second", "select.if", "select.if.aggregated.list", "select.if.comparedRanks.list", "select.if.list", "select.if.ranked.list", "significanceMap", "spearmansFootrule", "spearmansWeightedFootrule", "splitby", "stability", "stabilityByAlgorithm", "stabilityByAlgorithmStacked","stabilityByTask", "stability.ranked.list", "stability.bootstrap","relation_dissimilarity", "stabilityByAlgorithm.bootstrap.list", "stabilityByAlgorithmStacked.bootstrap.list", "stabilityByTask.bootstrap.list", "subset.aggregated.list", "subset.comparedRanks.list", "subset.list", "subset.ranked.list", "subset.bootstrap.list", "subset.ranked","subset.bootstrap",#"which.top", "test", "test.challenge", "test.default", "testThenRank", - "violin", "violin.bootstrap.list","violin.bootstrap", + "violin", "violin.bootstrap.list", "winner", "winner.bootstrap", "winner.bootstrap.list", "winner.default", "winner.ranked", "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") 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) S3method(aggregate, ranked.list) S3method(aggregate, bootstrap.list) S3method(aggregate, bootstrap) S3method(test, default) S3method(test, challenge) S3method(Aggregate, default) S3method(Aggregate, data.frame) S3method(Aggregate, list) S3method(Rank, default) S3method(Rank, data.frame) S3method(Rank, list) S3method(rank, default) S3method(rank, challenge) S3method(rank, aggregated) S3method(rank, aggregated.list) S3method(rank, aggregatedRanks) S3method(rank, aggregatedRanks.list) S3method(blobplot, default) S3method(blobplot, ranked) S3method(bootstrap, default) S3method(bootstrap, ranked) S3method(bootstrap, ranked.list) S3method(winner, default) S3method(winner, ranked) S3method(winner, ranked.list) S3method(winner, bootstrap) 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,ranked) 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(subset,ranked) S3method(subset,bootstrap) S3method(podium,default) S3method(podium,challenge) S3method(podium,ranked) 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,bootstrap) 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,bootstrap) S3method(stability,default) S3method(stability,ranked.list) S3method(stabilityByAlgorithm,bootstrap.list) S3method(stabilityByAlgorithm,default) S3method(stabilityByAlgorithmStacked,bootstrap.list) S3method(stabilityByAlgorithmStacked,default) S3method(consensus,ranked.list) S3method(consensus,default) S3method(report,bootstrap.list) S3method(report,ranked.list) S3method(report,default) diff --git a/R/violin.R b/R/violin.R index e8c2968..2d17676 100644 --- a/R/violin.R +++ b/R/violin.R @@ -1,87 +1,78 @@ violin <- function(x,...) UseMethod("violin") violin.default <- function(x, ...) stop("not implemented for this class") -violin.bootstrap=function(x,...){ - a=list(bootsrappedRanks=list(x$bootsrappedRanks), - matlist=list(x$mat)) - names(a$bootsrappedRanks)=names(a$matlist)="" - violin.bootstrap.list(a,...) - -} - - violin.bootstrap.list=function(x,...){ ken=melt(kendall.bootstrap.list(x)) colnames(ken)[2]="Task" cat("\n\nSummary Kendall's tau\n") ss=ken%>%group_by(Task)%>% summarise(mean=mean(value,na.rm=T), median=median(value,na.rm=T), q25=quantile(value,probs = .25,na.rm=T), q75=quantile(value,probs = .75,na.rm=T))%>% arrange(desc(median)) print(as.data.frame(ss)) xAxisText <- element_blank() # Show task names as tick mark labels only for multi-task data set if (length(x$data) > 1) { xAxisText <- element_text(angle = 90, vjust = 0.5, hjust = 1) } ken%>%mutate(Task=factor(.data$Task, levels=ss$Task))%>% ggplot(aes(Task,value))+ geom_violin(alpha=.3, color=NA, fill="blue")+ geom_boxplot(width=0.1, fill="white")+ theme(axis.text.x = xAxisText, legend.position = "none")+ ylab("Kendall's tau")+ scale_y_continuous(limits=c(min(min(ken$value),0), max(max(ken$value),1))) } kendall.bootstrap.list=function(x){ ken=lapply(1:length(x$bootsrappedRanks),function(Task){ id=match(rownames( x$bootsrappedRanks[[Task]]), rownames(x$matlist[[Task]]) ) sapply(x$bootsrappedRanks[[Task]], function(bootSample) suppressWarnings(kendall(bootSample, x$matlist[[Task]]$rank[id]))) } ) names(ken)=names((x$bootsrappedRanks)) if (sum(is.na(x))>0){ cat("Bootstrap samples without variability in rankings (all algorithms ranked 1) excluded.\n Frequency of such samples by task:\n",fill = T) sapply(ken,function(x) sum(is.na(x))) } return(ken) } density.bootstrap.list=function(x,...){ ken=melt(kendall.bootstrap.list(x)) colnames(ken)[2]="Task" cat("\n\nSummary Kendall's tau\n") ss=ken%>%group_by(Task)%>% summarise(mean=mean(value,na.rm=T), median=median(value,na.rm=T), q25=quantile(value,probs = .25,na.rm=T), q75=quantile(value,probs = .75,na.rm=T))%>% arrange(desc(median)) print(as.data.frame(ss)) ggplot(ken)+ geom_density(aes(value,fill=Task),alpha=.3,color=NA) }