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")
}