diff --git a/man/aggregate.challenge.Rd b/man/aggregate.challenge.Rd
new file mode 100644
index 0000000..b452a41
--- /dev/null
+++ b/man/aggregate.challenge.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/aaggregate.R
+\name{aggregate.challenge}
+\alias{aggregate.challenge}
+\title{Title}
+\usage{
+\method{aggregate}{challenge}(
+  x,
+  FUN = mean,
+  na.treat,
+  alpha = 0.05,
+  p.adjust.method = "none",
+  parallel = FALSE,
+  progress = "none",
+  ...
+)
+}
+\arguments{
+\item{...}{}
+}
+\value{
+
+}
+\description{
+Title
+}
diff --git a/man/aggregateThenRank.Rd b/man/aggregateThenRank.Rd
new file mode 100644
index 0000000..8e57e32
--- /dev/null
+++ b/man/aggregateThenRank.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rankingMethods.R
+\name{aggregateThenRank}
+\alias{aggregateThenRank}
+\title{Performs ranking via aggregate-then-rank}
+\usage{
+aggregateThenRank(object, FUN, ties.method = "min", ...)
+}
+\arguments{
+\item{object}{The challenge object.}
+
+\item{FUN}{The aggregation function, e.g. mean, median, min, max, function(x), quantile(x, probs=0.05).}
+
+\item{ties.method}{A string specifying how ties are treated, see \code{\link[base:rank]{base::rank()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+An S3 object of class "ranked.list" to represent a ranked assessment data set.
+}
+\description{
+Performs ranking by first aggregating performance values across all cases (e.g., with the mean, median or another quantile) for each algorithm.
+This aggregate is then used to compute a rank for each algorithm.
+}
+\examples{
+
+\dontrun{
+ aggregateThenRank(challenge, FUN = mean, ties.method = "average", na.treat = 0)
+}
+
+}
+\seealso{
+Other ranking functions: 
+\code{\link{rankThenAggregate}()},
+\code{\link{testThenRank}()}
+}
+\concept{ranking functions}
diff --git a/man/as.challenge.Rd b/man/as.challenge.Rd
new file mode 100644
index 0000000..c08e63f
--- /dev/null
+++ b/man/as.challenge.Rd
@@ -0,0 +1,88 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/challengeR.R
+\name{as.challenge}
+\alias{as.challenge}
+\title{Constructs a challenge object}
+\usage{
+as.challenge(
+  object,
+  case,
+  algorithm,
+  value,
+  by = NULL,
+  taskName = NULL,
+  annotator = NULL,
+  smallBetter = FALSE,
+  na.treat = NULL,
+  check = TRUE
+)
+}
+\arguments{
+\item{object}{A data frame containing the assessment data.}
+
+\item{case}{A string specifying the name of the column that contains the case identifiers.}
+
+\item{algorithm}{A string specifying the name of the column that contains the algorithm identifiers.}
+
+\item{value}{A string specifying the name of the column that contains the performance values.}
+
+\item{by}{A string specifying the name of the column that contains the task identifiers. Required for multi-task data set.}
+
+\item{taskName}{A string specifying the task name for single-task data set that does not contain a task column.
+This argument is optional for a single-task data set and is ignored for a multi-task data set.}
+
+\item{annotator}{Not supported}
+
+\item{smallBetter}{A boolean specifying whether small performance values indicate better algorithm performance.}
+
+\item{na.treat}{Indicates how missing perfomance values are treated if sanity check is enabled. It can be 'na.rm', numeric value or function.
+For a numeric value or function, NAs will be replaced by the specified values. For 'na.rm', rows that contain missing values will be removed.}
+
+\item{check}{A boolean to indicate to perform a sanity check of the specified data set and arguments if set to \code{TRUE}.}
+}
+\value{
+An S3 object to represent the configuration of an assessment data set.
+}
+\description{
+Constructs an S3 object to represent the configuration of an assessment data set originating from a benchmarking competition (so-called "challenge").
+}
+\section{Assessment data set}{
+
+The toolkit provides visualization approaches for both challenges designed around a single task (single-task challenges) and for challenges comprising multiple tasks (multi-task challenges).
+For a single-task challenge, the assessment data set (argument \code{object}) requires the following columns:
+\itemize{
+\item test case identifier (string or numeric)
+\item algorithm identifier (string or numeric)
+\item performance value (numeric)
+}
+
+For a multi-task challenge, the assessment data set (argument \code{object}) requires the following columns:
+\itemize{
+\item task identifier (string or numeric)
+\item test case identifier (string or numeric)
+\item algorithm identifier (string or numeric)
+\item performance value (numeric)
+}
+}
+
+\section{Sanity check}{
+
+It is highly recommended that the sanity check is not disabled when the data set is provided initially.
+It checks that:
+\itemize{
+\item performance values are numeric (if not, raises error)
+\item algorithm performances are observed for all cases (if not, adds them as NA and emits a message)
+\item cases appear only once for the same algorithm (if not, raises error)
+}
+If the argument \code{na.treat} for treatment of NA is specified, NAs will be handled respectively.
+
+It might be reasonable to disable the sanity check for further computations (e.g., for performance reasons
+during bootstrapping (\code{\link{bootstrap.ranked.list}}) where cases are actually allowed to appear more than once for the same algorithm).
+}
+
+\examples{
+# single-task data set
+
+# multi-task data set
+
+}
diff --git a/man/bootstrap.ranked.list.Rd b/man/bootstrap.ranked.list.Rd
new file mode 100644
index 0000000..45106ba
--- /dev/null
+++ b/man/bootstrap.ranked.list.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Bootstrap.R
+\name{bootstrap.ranked.list}
+\alias{bootstrap.ranked.list}
+\title{Performs bootstrapping}
+\usage{
+\method{bootstrap}{ranked.list}(object, nboot, parallel = FALSE, progress = "text", ...)
+}
+\arguments{
+\item{object}{The ranked assessment data set.}
+
+\item{nboot}{The number of bootstrap samples.}
+
+\item{parallel}{A boolean specifying whether parallel processing should be enabled.}
+
+\item{progress}{A string specifying the type of progress indication.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+An S3 object of class "bootstrap.list" to represent a bootstrapped, ranked assessment data set.
+}
+\description{
+Performs bootstrapping on a ranked assessment data set and applies the ranking method to each bootstrap sample. One bootstrap sample of
+a task with \code{n} cases consists of \code{n} cases randomly drawn with replacement from this task.
+A total of \code{nboot} of these bootstrap samples are drawn.
+}
+\examples{
+
+\dontrun{
+ # perform bootstrapping with 1000 bootstrap samples using one CPU
+ set.seed(1)
+ ranking_bootstrapped <- bootstrap(ranking, nboot = 1000)
+}
+
+\dontrun{
+ # perform bootstrapping using multiple CPUs (here: 8 CPUs)
+ library(doParallel)
+ registerDoParallel(cores=8)
+ set.seed(1)
+ ranking_bootstrapped <- bootstrap(ranking, nboot = 1000, parallel = TRUE, progress = "none")
+ stopImplicitCluster()
+}
+
+}
diff --git a/man/boxplot.ranked.list.Rd b/man/boxplot.ranked.list.Rd
new file mode 100644
index 0000000..8fccd50
--- /dev/null
+++ b/man/boxplot.ranked.list.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/boxplot.R
+\name{boxplot.ranked.list}
+\alias{boxplot.ranked.list}
+\title{Creates dot- and boxplots}
+\usage{
+\method{boxplot}{ranked.list}(x, color = "blue", jitter.width = 0.25, ...)
+}
+\arguments{
+\item{x}{The ranked assessment data set.}
+
+\item{color}{A string specifying the color of the dots.}
+
+\item{jitter.width}{A numeric value specifying the jitter width of the dots.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates dot- and boxplots visualizing the assessment data separately for each algorithm.
+Boxplots representing descriptive statistics for all test cases (median, quartiles and outliers)
+are combined with horizontally jittered dots representing individual test cases.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize assessment data: 
+\code{\link{podium.challenge}()},
+\code{\link{podium.ranked.list}()},
+\code{\link{rankingHeatmap.challenge}()},
+\code{\link{rankingHeatmap.ranked.list}()}
+}
+\concept{functions to visualize assessment data}
diff --git a/man/consensus.ranked.list.Rd b/man/consensus.ranked.list.Rd
new file mode 100644
index 0000000..3e8a9e6
--- /dev/null
+++ b/man/consensus.ranked.list.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/consensus.R
+\name{consensus.ranked.list}
+\alias{consensus.ranked.list}
+\title{Computes a consensus ranking}
+\usage{
+\method{consensus}{ranked.list}(object, method, ...)
+}
+\arguments{
+\item{object}{The ranked asssessment data set.}
+
+\item{method}{A string specifying the method to derive the consensus ranking, see \code{\link[relations:consensus]{relations::consensus()}} for the methods.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Computes a consensus ranking (rank aggregation) across tasks.
+}
diff --git a/man/dendrogram.ranked.list.Rd b/man/dendrogram.ranked.list.Rd
new file mode 100644
index 0000000..0a3abc3
--- /dev/null
+++ b/man/dendrogram.ranked.list.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dendrogram.R
+\name{dendrogram.ranked.list}
+\alias{dendrogram.ranked.list}
+\title{Creates a cluster dendrogram}
+\usage{
+\method{dendrogram}{ranked.list}(object, dist = "symdiff", method = "complete", ...)
+}
+\arguments{
+\item{object}{The ranked assessment data set.}
+
+\item{dist}{A string specifying the distance measure to be used, see \code{\link[relations:dissimilarity]{relations::dissimilarity()}}.}
+
+\item{method}{A string specifying agglomeration method to be used, see \code{\link[stats:hclust]{stats::hclust()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates a cluster dendrogram from a ranked assessment data set.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize cross-task insights: 
+\code{\link{stability.ranked.list}()},
+\code{\link{stabilityByAlgorithm.bootstrap.list}()},
+\code{\link{stabilityByTask.bootstrap.list}()}
+}
+\concept{functions to visualize cross-task insights}
diff --git a/man/methodsplot.challenge.Rd b/man/methodsplot.challenge.Rd
new file mode 100644
index 0000000..7f33fd2
--- /dev/null
+++ b/man/methodsplot.challenge.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methodsplot.R
+\name{methodsplot.challenge}
+\alias{methodsplot.challenge}
+\title{Creates line plots}
+\usage{
+\method{methodsplot}{challenge}(
+  x,
+  na.treat = NULL,
+  methods = list(testBased = . \%>\% test() \%>\% rank(ties.method = "min"),
+    meanThenRank = . \%>\% aggregate(FUN = "mean") \%>\% rank(ties.method = "min"),
+    medianThenRank = . \%>\% aggregate(FUN = "median") \%>\% rank(ties.method = "min"),
+    rankThenMean = . \%>\% rank(ties.method = "min") \%>\% aggregate(FUN = "mean") \%>\%
+    rank(ties.method = "min"), rankThenMedian = . \%>\% rank(ties.method = "min") \%>\%
+    aggregate(FUN = "median") \%>\% rank(ties.method = "min")),
+  ordering,
+  ...
+)
+}
+\arguments{
+\item{x}{The challenge object.}
+
+\item{na.treat}{Indicates how missing perfomance values are treated if sanity check is enabled. It can be 'na.rm', numeric value or function.
+For a numeric value or function, NAs will be replaced by the specified values. For 'na.rm', rows that contain missing values will be removed.}
+
+\item{methods}{A list of ranking methods that should be incorporated.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Create line plots that visualize the robustness of ranking across different ranking methods from a challenge object.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize ranking stability: 
+\code{\link{significanceMap.ranked.list}()},
+\code{\link{stabilityByTask.bootstrap.list}()},
+\code{\link{violin.bootstrap.list}()}
+}
+\concept{functions to visualize ranking stability}
diff --git a/man/podium.challenge.Rd b/man/podium.challenge.Rd
new file mode 100644
index 0000000..989f29d
--- /dev/null
+++ b/man/podium.challenge.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/podium.R
+\name{podium.challenge}
+\alias{podium.challenge}
+\title{Creates a podium plot}
+\usage{
+\method{podium}{challenge}(
+  object,
+  ordering,
+  xlab = NULL,
+  ylab = NULL,
+  lines.show = FALSE,
+  lines.alpha = 0.2,
+  lines.lwd = 1,
+  col,
+  lines.col = col,
+  dots.pch = 19,
+  dots.cex = 1,
+  places.lty = 2,
+  places.col = 1,
+  legendfn = function(algs, cols) {     legend("topleft", algs, lwd = 1, col = cols, bg
+    = "white") },
+  layout.heights = c(1, 0.4),
+  ...
+)
+}
+\arguments{
+\item{object}{The challenge object.}
+
+\item{xlab}{A string specifying the x-axis label.}
+
+\item{ylab}{A string specifying the y-axis label.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates a podium plot from a challenge object.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize assessment data: 
+\code{\link{boxplot.ranked.list}()},
+\code{\link{podium.ranked.list}()},
+\code{\link{rankingHeatmap.challenge}()},
+\code{\link{rankingHeatmap.ranked.list}()}
+}
+\concept{functions to visualize assessment data}
diff --git a/man/podium.ranked.list.Rd b/man/podium.ranked.list.Rd
new file mode 100644
index 0000000..6ce2c4f
--- /dev/null
+++ b/man/podium.ranked.list.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/podium.R
+\name{podium.ranked.list}
+\alias{podium.ranked.list}
+\title{Creates podium plots}
+\usage{
+\method{podium}{ranked.list}(
+  object,
+  xlab = "Podium",
+  ylab = "Performance",
+  lines.show = TRUE,
+  lines.alpha = 0.2,
+  lines.lwd = 1,
+  col,
+  lines.col = col,
+  dots.pch = 19,
+  dots.cex = 1,
+  places.lty = 2,
+  places.col = 1,
+  legendfn = function(algs, cols) {     legend("topleft", algs, lwd = 1, col = cols, bg
+    = "white") },
+  layout.heights = c(1, 0.4),
+  ...
+)
+}
+\arguments{
+\item{object}{The ranked asssessment data set.}
+
+\item{xlab}{A string specifying the x-axis label.}
+
+\item{ylab}{A string specifying the y-axis label.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates podium plots from one or more ranked assessment data sets.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize assessment data: 
+\code{\link{boxplot.ranked.list}()},
+\code{\link{podium.challenge}()},
+\code{\link{rankingHeatmap.challenge}()},
+\code{\link{rankingHeatmap.ranked.list}()}
+}
+\concept{functions to visualize assessment data}
diff --git a/man/rankThenAggregate.Rd b/man/rankThenAggregate.Rd
new file mode 100644
index 0000000..116e74b
--- /dev/null
+++ b/man/rankThenAggregate.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rankingMethods.R
+\name{rankThenAggregate}
+\alias{rankThenAggregate}
+\title{Performs ranking via rank-then-aggregate}
+\usage{
+rankThenAggregate(object, FUN, ties.method = "min")
+}
+\arguments{
+\item{object}{The challenge object.}
+
+\item{FUN}{The aggregation function, e.g., mean, median, min, max, function(x), quantile(x, probs=0.05).}
+
+\item{ties.method}{A string specifying how ties are treated, see \code{\link[base:rank]{base::rank()}}.}
+}
+\value{
+An S3 object of class "ranked.list" to represent a ranked assessment data set.
+}
+\description{
+Performs ranking by first computing a rank for each case for each algorithm ("rank first").
+The final rank is based on the aggregated ranks for the cases. This ranking method handles missing values implicitly
+by assigning the worst rank to missing algorithm performances.
+}
+\examples{
+\dontrun{
+ rankThenAggregate(challenge, FUN = mean)
+}
+
+}
+\seealso{
+Other ranking functions: 
+\code{\link{aggregateThenRank}()},
+\code{\link{testThenRank}()}
+}
+\concept{ranking functions}
diff --git a/man/rankingHeatmap.challenge.Rd b/man/rankingHeatmap.challenge.Rd
new file mode 100644
index 0000000..0f6efda
--- /dev/null
+++ b/man/rankingHeatmap.challenge.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rankingHeatmap.R
+\name{rankingHeatmap.challenge}
+\alias{rankingHeatmap.challenge}
+\title{Creates a ranking heatmap}
+\usage{
+\method{rankingHeatmap}{challenge}(x, ordering, ties.method = "min", ...)
+}
+\arguments{
+\item{x}{The challenge object.}
+
+\item{ties.method}{A string specifying how ties are treated, see \code{\link[base:rank]{base::rank()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates a ranking heatmap from a challenge object.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize assessment data: 
+\code{\link{boxplot.ranked.list}()},
+\code{\link{podium.challenge}()},
+\code{\link{podium.ranked.list}()},
+\code{\link{rankingHeatmap.ranked.list}()}
+}
+\concept{functions to visualize assessment data}
diff --git a/man/rankingHeatmap.ranked.list.Rd b/man/rankingHeatmap.ranked.list.Rd
new file mode 100644
index 0000000..a896b69
--- /dev/null
+++ b/man/rankingHeatmap.ranked.list.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rankingHeatmap.R
+\name{rankingHeatmap.ranked.list}
+\alias{rankingHeatmap.ranked.list}
+\title{Creates ranking heatmaps}
+\usage{
+\method{rankingHeatmap}{ranked.list}(x, ties.method = "min", ...)
+}
+\arguments{
+\item{x}{The ranked asssessment data set.}
+
+\item{ties.method}{A string specifying how ties are treated, see \code{\link[base:rank]{base::rank()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates ranking heatmaps from one or more ranked assessment data sets.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize assessment data: 
+\code{\link{boxplot.ranked.list}()},
+\code{\link{podium.challenge}()},
+\code{\link{podium.ranked.list}()},
+\code{\link{rankingHeatmap.challenge}()}
+}
+\concept{functions to visualize assessment data}
diff --git a/man/report.bootstrap.list.Rd b/man/report.bootstrap.list.Rd
new file mode 100644
index 0000000..df0b71a
--- /dev/null
+++ b/man/report.bootstrap.list.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{report.bootstrap.list}
+\alias{report.bootstrap.list}
+\title{Generates a benchmarking report with bootstrapping results}
+\usage{
+\method{report}{bootstrap.list}(
+  object,
+  consensus,
+  file,
+  title = "<Challenge name>",
+  colors = default_colors,
+  format = "PDF",
+  latex_engine = "pdflatex",
+  clean = TRUE,
+  fig.format = NULL,
+  dpi = 150,
+  open = TRUE,
+  ...
+)
+}
+\arguments{
+\item{object}{The ranked (bootstrapped) assessment data set.}
+
+\item{consensus}{The rank aggregation across tasks (consensus ranking). Only needed for a multi-task data set.}
+
+\item{file}{A string specifying the file name of the report. It allows for specifying the output file path as well,
+otherwise the working directory is used. If \code{file} does not have a file extension, an extension will be automatically
+added according to the output format given in \code{format}. If the argument is omitted, the report is created in a
+temporary folder with file name "report".}
+
+\item{title}{A string specifying the title of the report.}
+
+\item{colors}{The color scheme that is applied to the plots.}
+
+\item{format}{A string specifying the format of the report. The options are "PDF", "HTML" or "Word".}
+
+\item{latex_engine}{A string specifying the LaTeX engine for producing PDF output. The Options are "pdflatex", "lualatex", and "xelatex".}
+
+\item{clean}{A boolean indicating whether intermediate files (e.g. individual plots) should be kept. Using \code{TRUE} will clean
+intermediate files that are created during rendering.}
+
+\item{fig.format}{A vector of strings containing the file format of the figures that are not removed if \code{clean} is set to \code{FALSE}.
+The options are "jpeg", "png" and "pdf", e.g. \code{fig.format = c("jpeg", "png", "pdf")}.}
+
+\item{dpi}{A positive integer specifying the resolution of the generated plot (\code{fig.format} "jpeg" or "png") in dots per inch (DPI).}
+
+\item{open}{A boolean specifying whether the report should be opened with the default system viewer after generation.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Generates a benchmarking report in PDF, HTML or Word format with bootstrapping results.
+It contains the rankings, plots of the raw assessment data and plots of the ranking stability.
+For multi-task challenges, it also contains plots of cross-task insights. If you are interested in
+the individual plots as separate files, set argument \code{clean} to \code{FALSE} and specify \code{fig.format}.
+}
diff --git a/man/report.ranked.list.Rd b/man/report.ranked.list.Rd
new file mode 100644
index 0000000..49131e2
--- /dev/null
+++ b/man/report.ranked.list.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/report.R
+\name{report.ranked.list}
+\alias{report.ranked.list}
+\title{Generates a benchmarking report without bootstrapping results}
+\usage{
+\method{report}{ranked.list}(
+  object,
+  consensus,
+  file,
+  title = "<Challenge name>",
+  colors = default_colors,
+  format = "PDF",
+  latex_engine = "pdflatex",
+  clean = TRUE,
+  fig.format = NULL,
+  dpi = 150,
+  open = TRUE,
+  ...
+)
+}
+\arguments{
+\item{object}{The ranked assessment data set.}
+
+\item{consensus}{The rank aggregation across tasks (consensus ranking). Only needed for a multi-task data set.}
+
+\item{file}{A string specifying the file name of the report. It allows for specifying the output file path as well,
+otherwise the working directory is used. If \code{file} does not have a file extension, an extension will be automatically
+added according to the output format given in \code{format}. If the argument is omitted, the report is created in a
+temporary folder with file name "report".}
+
+\item{title}{A string specifying the title of the report.}
+
+\item{colors}{The color scheme that is applied to the plots.}
+
+\item{format}{A string specifying the format of the report. The options are "PDF", "HTML" or "Word".}
+
+\item{latex_engine}{A string specifying the LaTeX engine for producing PDF output. The Options are "pdflatex", "lualatex", and "xelatex".}
+
+\item{clean}{A boolean indicating whether intermediate files (e.g. individual plots) should be kept. Using \code{TRUE} will clean
+intermediate files that are created during rendering.}
+
+\item{fig.format}{A vector of strings containing the file format of the figures that are not removed if \code{clean} is set to \code{FALSE}.
+The options are "jpeg", "png" and "pdf",  e.g. \code{fig.format = c("jpeg", "png", "pdf")}.}
+
+\item{dpi}{A positive integer specifying the resolution of the generated plot (\code{fig.format} "jpeg" or "png") in dots per inch (DPI).}
+
+\item{open}{A boolean specifying whether the report should be opened with the default system viewer after generation.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Generates a benchmarking report in PDF, HTML or Word format without bootstrapping results.
+It contains the rankings, plots of the raw assessment data and plots of the ranking stability.
+For multi-task challenges, it also contains plots of cross-task insights. If you are interested in
+the individual plots as separate files, set argument \code{clean} to \code{FALSE} and specify \code{fig.format}.
+}
diff --git a/man/significanceMap.ranked.list.Rd b/man/significanceMap.ranked.list.Rd
new file mode 100644
index 0000000..b48291b
--- /dev/null
+++ b/man/significanceMap.ranked.list.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/significanceMap.R
+\name{significanceMap.ranked.list}
+\alias{significanceMap.ranked.list}
+\title{Creates significance maps}
+\usage{
+\method{significanceMap}{ranked.list}(
+  object,
+  alpha = 0.05,
+  p.adjust.method = "holm",
+  order = FALSE,
+  size.rank = 0.3 * theme_get()$text$size,
+  ...
+)
+}
+\arguments{
+\item{object}{The ranked assessment data set.}
+
+\item{alpha}{A numeric values specifying the significance level.}
+
+\item{p.adjust.method}{A string specifying the adjustment method for multiple testing, see \code{\link[stats:p.adjust]{stats::p.adjust()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates significance maps from a ranked assessment data set.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize ranking stability: 
+\code{\link{methodsplot.challenge}()},
+\code{\link{stabilityByTask.bootstrap.list}()},
+\code{\link{violin.bootstrap.list}()}
+}
+\concept{functions to visualize ranking stability}
diff --git a/man/stability.ranked.list.Rd b/man/stability.ranked.list.Rd
new file mode 100644
index 0000000..6471bfe
--- /dev/null
+++ b/man/stability.ranked.list.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stability.R
+\name{stability.ranked.list}
+\alias{stability.ranked.list}
+\title{Creates a blob plot across tasks}
+\usage{
+\method{stability}{ranked.list}(
+  x,
+  ordering,
+  probs = c(0.025, 0.975),
+  max_size = 6,
+  freq = FALSE,
+  shape = 4,
+  ...
+)
+}
+\arguments{
+\item{x}{The ranked asssessment data set.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates a blob plots visualizing the ranking variability across tasks.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize cross-task insights: 
+\code{\link{dendrogram.ranked.list}()},
+\code{\link{stabilityByAlgorithm.bootstrap.list}()},
+\code{\link{stabilityByTask.bootstrap.list}()}
+}
+\concept{functions to visualize cross-task insights}
diff --git a/man/stabilityByAlgorithm.bootstrap.list.Rd b/man/stabilityByAlgorithm.bootstrap.list.Rd
new file mode 100644
index 0000000..e0fb356
--- /dev/null
+++ b/man/stabilityByAlgorithm.bootstrap.list.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stability.R
+\name{stabilityByAlgorithm.bootstrap.list}
+\alias{stabilityByAlgorithm.bootstrap.list}
+\title{Creates blob plots or stacked frequency plots stratified by algorithm}
+\usage{
+\method{stabilityByAlgorithm}{bootstrap.list}(
+  x,
+  ordering,
+  stacked = FALSE,
+  probs = c(0.025, 0.975),
+  max_size = 3,
+  shape = 4,
+  freq = FALSE,
+  single = FALSE,
+  ...
+)
+}
+\arguments{
+\item{x}{The bootstrapped, ranked assessment data set.}
+
+\item{stacked}{A boolean specifying whether a stacked frequency plot (\code{stacked = TRUE}) or blob plot (\code{stacked = FALSE}) should be created.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates blob plots (\code{stacked = FALSE}) or stacked frequency plots (\code{stacked = TRUE}) for each algorithm
+from a bootstrapped, ranked assessment data set.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize cross-task insights: 
+\code{\link{dendrogram.ranked.list}()},
+\code{\link{stability.ranked.list}()},
+\code{\link{stabilityByTask.bootstrap.list}()}
+}
+\concept{functions to visualize cross-task insights}
diff --git a/man/stabilityByTask.bootstrap.list.Rd b/man/stabilityByTask.bootstrap.list.Rd
new file mode 100644
index 0000000..d2d4c24
--- /dev/null
+++ b/man/stabilityByTask.bootstrap.list.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stability.R
+\name{stabilityByTask.bootstrap.list}
+\alias{stabilityByTask.bootstrap.list}
+\title{Creates blob plots stratified by task}
+\usage{
+\method{stabilityByTask}{bootstrap.list}(
+  x,
+  ordering,
+  probs = c(0.025, 0.975),
+  max_size = 3,
+  size.ranks = 0.3 * theme_get()$text$size,
+  shape = 4,
+  showLabelForSingleTask = FALSE,
+  ...
+)
+}
+\arguments{
+\item{x}{The bootstrapped, ranked assessment data set.}
+
+\item{showLabelForSingleTask}{A boolean specifying whether the task name should be used as title for a single-task data set.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates blob plots for each task from a bootstrapped, ranked assessment data set.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize ranking stability: 
+\code{\link{methodsplot.challenge}()},
+\code{\link{significanceMap.ranked.list}()},
+\code{\link{violin.bootstrap.list}()}
+
+Other functions to visualize cross-task insights: 
+\code{\link{dendrogram.ranked.list}()},
+\code{\link{stability.ranked.list}()},
+\code{\link{stabilityByAlgorithm.bootstrap.list}()}
+}
+\concept{functions to visualize cross-task insights}
+\concept{functions to visualize ranking stability}
diff --git a/man/subset.bootstrap.list.Rd b/man/subset.bootstrap.list.Rd
new file mode 100644
index 0000000..f12d99f
--- /dev/null
+++ b/man/subset.bootstrap.list.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/subset.R
+\name{subset.bootstrap.list}
+\alias{subset.bootstrap.list}
+\title{Extracts a subset of algorithms or tasks}
+\usage{
+\method{subset}{bootstrap.list}(x, top, tasks, ...)
+}
+\arguments{
+\item{x}{The bootstrapped, ranked asssessment data set.}
+
+\item{top}{A positive integer specifying the amount of top performing algorithms to be retrieved.}
+
+\item{tasks}{A vector of strings containing the task identifiers that should remain in the subset.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+An S3 object of class "bootstrap.list" to represent a bootstrapped, ranked assessment data set.
+}
+\description{
+Extracts the top performing algorithms or a subset of tasks.
+}
+\section{Reports for subsets (top list) of algorithms}{
+
+If ties are present in the ranking, the subset will consist of more than \code{top} algorithms.
+Line plots for ranking robustness can be used to check whether algorithms performing well in other
+ranking methods are excluded. Bootstrapping still takes entire uncertainty into account.
+Podium plots and ranking heatmaps neglect excluded algorithms. Only available for single-task challenges
+(for multi-task challenges not sensible because each task would contain a different set of algorithms).
+}
+
+\section{Reports for subsets of tasks}{
+
+You may want to recompute the consensus ranking after creating the subset. An error will be raised
+if a task identifier is not contained in the assessment data set to avoid subsequent errors.
+}
+
+\examples{
+
+\dontrun{
+ # only show the top 3 algorithms according to the chosen ranking method
+ subset(ranking_bootstrapped, top = 3) \%>\% report(...)
+}
+
+\dontrun{
+ # restrict report to tasks "task1" and "task2" and recompute consensus ranking
+ meanRanks <- subset(ranking, tasks = c("task1", "task2")) \%>\% consensus(method = "euclidean")
+}
+
+}
diff --git a/man/subset.ranked.list.Rd b/man/subset.ranked.list.Rd
new file mode 100644
index 0000000..6203ab1
--- /dev/null
+++ b/man/subset.ranked.list.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/subset.R
+\name{subset.ranked.list}
+\alias{subset.ranked.list}
+\title{Extracts a subset of algorithms or tasks}
+\usage{
+\method{subset}{ranked.list}(x, top, tasks, ...)
+}
+\arguments{
+\item{x}{The ranked asssessment data set.}
+
+\item{top}{A positive integer specifying the amount of top performing algorithms to be retrieved.}
+
+\item{tasks}{A vector of strings containing the task identifiers that should remain in the subset.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+An S3 object of class "ranked.list" to represent a ranked assessment data set.
+}
+\description{
+Extracts the top performing algorithms or a subset of tasks.
+}
+\section{Reports for subsets (top list) of algorithms}{
+
+If ties are present in the ranking, the subset will consist of more than \code{top} algorithms.
+Line plots for ranking robustness can be used to check whether algorithms performing well in other
+ranking methods are excluded. Bootstrapping still takes entire uncertainty into account.
+Podium plots and ranking heatmaps neglect excluded algorithms. Only available for single-task challenges
+(for multi-task challenges not sensible because each task would contain a different set of algorithms).
+}
+
+\section{Reports for subsets of tasks}{
+
+You may want to recompute the consensus ranking after creating the subset. An error will be raised
+if a task identifier is not contained in the assessment data set to avoid subsequent errors.
+}
+
+\examples{
+
+\dontrun{
+ # only show the top 3 algorithms according to the chosen ranking method
+ subset(ranking, top = 3) \%>\% report(...)
+}
+
+\dontrun{
+ # restrict report to tasks "task1" and "task2"
+ subset(ranking, tasks=c("task1", "task2")) \%>\% report(...)
+}
+
+}
diff --git a/man/testThenRank.Rd b/man/testThenRank.Rd
new file mode 100644
index 0000000..fa1f17c
--- /dev/null
+++ b/man/testThenRank.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/rankingMethods.R
+\name{testThenRank}
+\alias{testThenRank}
+\title{Performs ranking via test-then-rank}
+\usage{
+testThenRank(object, ties.method = "min", ...)
+}
+\arguments{
+\item{object}{The challenge object.}
+
+\item{ties.method}{A string specifying how ties are treated, see \code{\link[base:rank]{base::rank()}}.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+An S3 object of class "ranked.list" to represent a ranked assessment data set.
+}
+\description{
+Computes statistical hypothesis tests based on Wilcoxon signed rank test for each possible
+pair of algorithms to assess differences in metric values between the algorithms.
+Then ranking is performed according to the number of significant one-sided test results.
+If algorithms have the same number of significant test results, then they obtain the same rank.
+}
+\examples{
+\dontrun{
+ testThenRank(challenge,
+              alpha=0.05, # significance level
+              p.adjust.method="none", # method for adjustment for multiple testing, see ?p.adjust
+              na.treat = 0)
+}
+
+}
+\seealso{
+Other ranking functions: 
+\code{\link{aggregateThenRank}()},
+\code{\link{rankThenAggregate}()}
+}
+\concept{ranking functions}
diff --git a/man/violin.bootstrap.list.Rd b/man/violin.bootstrap.list.Rd
new file mode 100644
index 0000000..87d90e2
--- /dev/null
+++ b/man/violin.bootstrap.list.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/violin.R
+\name{violin.bootstrap.list}
+\alias{violin.bootstrap.list}
+\title{Creates a violin plot}
+\usage{
+\method{violin}{bootstrap.list}(x, ...)
+}
+\arguments{
+\item{x}{The bootstrapped, ranked assessment data set.}
+
+\item{...}{Further arguments passed to or from other functions.}
+}
+\value{
+
+}
+\description{
+Creates a violin plot from a bootstrapped, ranked assessment data set.
+}
+\examples{
+
+}
+\seealso{
+\code{browseVignettes("challengeR")}
+
+Other functions to visualize ranking stability: 
+\code{\link{methodsplot.challenge}()},
+\code{\link{significanceMap.ranked.list}()},
+\code{\link{stabilityByTask.bootstrap.list}()}
+}
+\concept{functions to visualize ranking stability}