diff --git a/NAMESPACE b/NAMESPACE
index 46fe289..dc430e1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,53 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
-export(addAttributes)
-export(addAttributesLogical)
-export(addAttributesNumeric)
-export(addAttributesRange)
 export(addRankPrefix)
-export(addStrains)
-export(asr)
-export(asrUpstreamLogical)
-export(asrUpstreamNumeric)
-export(asrUpstreamRange)
-export(calcParentScore)
-export(calcParentScores)
-export(chooseColVal)
 export(classif2Table)
 export(cleanNode)
 export(completeBinaryData)
 export(conf2Fct)
-export(fillNAs)
 export(filterData)
 export(filterDataDiscrete)
 export(freq2Scores)
-export(getAgreements)
-export(getConflicts)
 export(getDataReady)
-export(getDistantTips)
-export(getDoubleAnnotations)
-export(getDuplicates)
 export(getMRCATaxPPro)
-export(getMpaTable)
-export(getMpaTree)
-export(getNCBI)
 export(getSetWithIDs)
 export(getSetWithoutIDs)
-export(inh)
 export(inh1)
 export(inh2)
-export(inhDownstreamLogical)
-export(inhDownstreamNumeric)
-export(inhDownstreamRange)
 export(ltp)
-export(mergeOriginalAndEarlyASR)
 export(mpa)
-export(prepareDataForPropagation)
-export(propagate)
-export(removeAccessionAndGenomeID)
-export(removeDuplicates)
-export(resolveAgreements)
-export(resolveConflicts)
 export(scores2Freq)
 export(taxPool)
-export(taxname2taxid)
diff --git a/man/addAttributes.Rd b/man/addAttributes.Rd
deleted file mode 100644
index b739e1c..0000000
--- a/man/addAttributes.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{addAttributes}
-\alias{addAttributes}
-\title{Add attributes to a data.tree object}
-\usage{
-addAttributes(data_tree, df)
-}
-\arguments{
-\item{data_tree}{A data.tree object.}
-
-\item{df}{A data.frame. Output of \code{prepareData2}}
-}
-\value{
-A clone of the original data.tree object.
-}
-\description{
-\code{addAttributes} Adds attributes to a data.tree object
-}
diff --git a/man/addAttributesLogical.Rd b/man/addAttributesLogical.Rd
deleted file mode 100644
index 8d7953f..0000000
--- a/man/addAttributesLogical.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{addAttributesLogical}
-\alias{addAttributesLogical}
-\title{Add attributes to a data.tree (numeric)}
-\usage{
-addAttributesLogical(data_tree, df)
-}
-\arguments{
-\item{data_tree}{A data.tree object.}
-
-\item{df}{A data.frame from bugphyzz. Output of \code{prepareData2}.}
-}
-\value{
-A clone of the original data.tree.
-}
-\description{
-\code{addAttributesLogical} adds attributes to a data.tree object.
-}
diff --git a/man/addAttributesNumeric.Rd b/man/addAttributesNumeric.Rd
deleted file mode 100644
index 32ff726..0000000
--- a/man/addAttributesNumeric.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{addAttributesNumeric}
-\alias{addAttributesNumeric}
-\title{Add attributes to a data.tree object (numeric)}
-\usage{
-addAttributesNumeric(data_tree, df)
-}
-\arguments{
-\item{data_tree}{A data.tree object.}
-
-\item{df}{A data.frame. Output of \code{prepareData2}}
-}
-\value{
-A clone of the data.tree object.
-}
-\description{
-\code{addAttributesNumeric} Add numeric attributes to a data.tree object.
-}
diff --git a/man/addAttributesRange.Rd b/man/addAttributesRange.Rd
deleted file mode 100644
index b8cbb78..0000000
--- a/man/addAttributesRange.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{addAttributesRange}
-\alias{addAttributesRange}
-\title{Add attributes to a data.tree object (range)}
-\usage{
-addAttributesRange(data_tree, df)
-}
-\arguments{
-\item{data_tree}{A data.tree object.}
-
-\item{df}{A data.frame. Output of \code{prepareData2}}
-}
-\value{
-A clone of the input data.tree object with extra attributes.
-}
-\description{
-\code{addAttributesRange} adds range attributes to a data.tree object.
-}
diff --git a/man/addStrains.Rd b/man/addStrains.Rd
deleted file mode 100644
index 657796f..0000000
--- a/man/addStrains.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{addStrains}
-\alias{addStrains}
-\title{Add strains}
-\usage{
-addStrains(node)
-}
-\arguments{
-\item{node}{A node.}
-}
-\value{
-An action on the node.
-}
-\description{
-Add strains
-}
diff --git a/man/asr.Rd b/man/asr.Rd
deleted file mode 100644
index 136c727..0000000
--- a/man/asr.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{asr}
-\alias{asr}
-\title{asr}
-\usage{
-asr(node)
-}
-\arguments{
-\item{node}{A node from a data.tree object.}
-}
-\value{
-None. This functions modifies the data.tree object (R6).
-}
-\description{
-\code{asr} Performs a custom function for ancestral state reconstruction.
-It actually is a weighted majority vote for the parent node. This function
-is meant to used with transversion functions (Do) in a data.tree object.
-}
diff --git a/man/asrUpstreamLogical.Rd b/man/asrUpstreamLogical.Rd
deleted file mode 100644
index ae9d97e..0000000
--- a/man/asrUpstreamLogical.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{asrUpstreamLogical}
-\alias{asrUpstreamLogical}
-\title{ASR / Upstream}
-\usage{
-asrUpstreamLogical(node)
-}
-\arguments{
-\item{node}{A node.}
-}
-\value{
-Node/R6. A data.tree object
-}
-\description{
-\code{asrUpstreamLogical} Propagate attributes and scores.
-}
diff --git a/man/asrUpstreamNumeric.Rd b/man/asrUpstreamNumeric.Rd
deleted file mode 100644
index e8928b5..0000000
--- a/man/asrUpstreamNumeric.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{asrUpstreamNumeric}
-\alias{asrUpstreamNumeric}
-\title{ASR / Upstream (numeric)}
-\usage{
-asrUpstreamNumeric(node)
-}
-\arguments{
-\item{node}{A node.}
-}
-\value{
-node value.
-}
-\description{
-\code{asrUpstreamNumeric} asr for numeric values.
-}
diff --git a/man/asrUpstreamRange.Rd b/man/asrUpstreamRange.Rd
deleted file mode 100644
index 5bf5b26..0000000
--- a/man/asrUpstreamRange.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{asrUpstreamRange}
-\alias{asrUpstreamRange}
-\title{ASR / Upstream (range)}
-\usage{
-asrUpstreamRange(node)
-}
-\arguments{
-\item{node}{A node.}
-}
-\value{
-A modified node.
-}
-\description{
-\code{asrUpstreamRange} asr for range attributes
-}
diff --git a/man/calcParentScore.Rd b/man/calcParentScore.Rd
deleted file mode 100644
index 172bea6..0000000
--- a/man/calcParentScore.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{calcParentScore}
-\alias{calcParentScore}
-\title{Calculate parent score}
-\usage{
-calcParentScore(tbl)
-}
-\arguments{
-\item{tbl}{A data.frame. This data.frame should be stored in a data.tree
-node.}
-}
-\value{
-A data.frame
-}
-\description{
-\code{calcParentScore} calculates parent score based on taxa children.
-First, the score for each attribute is normalized by taxid. Then,
-the score is added for all taxa and re-normalized.
-}
diff --git a/man/calcParentScores.Rd b/man/calcParentScores.Rd
deleted file mode 100644
index 6c53436..0000000
--- a/man/calcParentScores.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{calcParentScores}
-\alias{calcParentScores}
-\title{Calculate parent scores}
-\usage{
-calcParentScores(df)
-}
-\arguments{
-\item{df}{A data.frame.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{calcParentScores} calculate parent scores with ASR.
-}
diff --git a/man/chooseColVal.Rd b/man/chooseColVal.Rd
deleted file mode 100644
index 1660b78..0000000
--- a/man/chooseColVal.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{chooseColVal}
-\alias{chooseColVal}
-\title{Choose column for attribute values}
-\usage{
-chooseColVal(df)
-}
-\arguments{
-\item{df}{A data frame imported with bugphyzz.}
-}
-\value{
-A character string.
-}
-\description{
-\code{chooseColVal} chooses the column where attribute values are
-actually stored.
-}
diff --git a/man/fillNAs.Rd b/man/fillNAs.Rd
deleted file mode 100644
index da480ee..0000000
--- a/man/fillNAs.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{fillNAs}
-\alias{fillNAs}
-\title{Fill NAs}
-\usage{
-fillNAs(x)
-}
-\arguments{
-\item{x}{An atomic vector.}
-}
-\value{
-An atomic vector
-}
-\description{
-\code{fillNAs} changes NAs wit NA\[number\].
-}
diff --git a/man/getAgreements.Rd b/man/getAgreements.Rd
deleted file mode 100644
index af7b7b1..0000000
--- a/man/getAgreements.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{getAgreements}
-\alias{getAgreements}
-\title{Get agreements}
-\usage{
-getAgreements(df)
-}
-\arguments{
-\item{df}{A data frame.}
-}
-\value{
-A data frame.
-}
-\description{
-\code{getAgreements} gets taxa annotated two or more times with the same
-annotation, but from different sources.
-}
-\details{
-An agreement is defined as taxon with the same annotation from different
-sources.
-}
-\seealso{
-\code{\link{resolveAgreements}}
-}
diff --git a/man/getConflicts.Rd b/man/getConflicts.Rd
deleted file mode 100644
index 264a972..0000000
--- a/man/getConflicts.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{getConflicts}
-\alias{getConflicts}
-\title{Get conflicts}
-\usage{
-getConflicts(df)
-}
-\arguments{
-\item{df}{A data frame. Output of the `getDuplicates` function.}
-}
-\value{
-a data frame or NULL.
-}
-\description{
-\code{getConflicts} gets taxa with two or more annotations from different
-sources.
-}
diff --git a/man/getDistantTips.Rd b/man/getDistantTips.Rd
deleted file mode 100644
index bb69707..0000000
--- a/man/getDistantTips.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/trees.R
-\name{getDistantTips}
-\alias{getDistantTips}
-\title{Get distant tips}
-\usage{
-getDistantTips()
-}
-\value{
-A data.frame.
-}
-\description{
-\code{getDistantTips} gets furthest apart tip for every tip in the ltp tree.
-Furthermore, this tip's taxid is present in the ncbi_tree. Additional
-columns describe data in the tip2 column.
-}
diff --git a/man/getDoubleAnnotations.Rd b/man/getDoubleAnnotations.Rd
deleted file mode 100644
index 7fd8a9a..0000000
--- a/man/getDoubleAnnotations.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{getDoubleAnnotations}
-\alias{getDoubleAnnotations}
-\title{Get taxa with double annotations}
-\usage{
-getDoubleAnnotations(df)
-}
-\arguments{
-\item{df}{A data frame.}
-}
-\value{
-A data frame.
-}
-\description{
-\code{getDoubleAnnotations} gets taxa annotated two or more times from the
-same source.
-}
-\seealso{
-\code{\link{getDuplicates}}
-}
diff --git a/man/getDuplicates.Rd b/man/getDuplicates.Rd
deleted file mode 100644
index bfae719..0000000
--- a/man/getDuplicates.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{getDuplicates}
-\alias{getDuplicates}
-\title{Get duplicates}
-\usage{
-getDuplicates(df, verbose = FALSE)
-}
-\arguments{
-\item{df}{A data frame imported with bugphyzz.}
-
-\item{cols}{Columns to look for duplicates.}
-}
-\value{
-A data frame with duplicate rows. If no duplicates are found, this
-function returns a NULL value with a message.
-}
-\description{
-\code{getDuplicates} gets duplicated taxa in a bugphuzz dataset.
-This information could be useful for identifying conflicts of annotations
-between different sources. Duplication is based on both NCBI_ID and
-Taxon_name.
-}
diff --git a/man/getMpaTable.Rd b/man/getMpaTable.Rd
deleted file mode 100644
index 1cdc101..0000000
--- a/man/getMpaTable.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/misc.R
-\name{getMpaTable}
-\alias{getMpaTable}
-\title{Get metaphlan table}
-\usage{
-getMpaTable()
-}
-\value{
-A data.frame
-}
-\description{
-\code{getMpaTable} gets metaphlan table v4.0.0
-}
diff --git a/man/getMpaTree.Rd b/man/getMpaTree.Rd
deleted file mode 100644
index a22e8d1..0000000
--- a/man/getMpaTree.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/misc.R
-\name{getMpaTree}
-\alias{getMpaTree}
-\title{Get metaplhan tree}
-\usage{
-getMpaTree()
-}
-\value{
-A phylo object
-}
-\description{
-\code{getMpaTree} gets metplhan tree. Tips are taxids. v4.0.0.
-}
diff --git a/man/getNCBI.Rd b/man/getNCBI.Rd
deleted file mode 100644
index c3189ed..0000000
--- a/man/getNCBI.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{getNCBI}
-\alias{getNCBI}
-\title{Get NCBI data (tree or table)}
-\usage{
-getNCBI(keyword = "b", format = "table")
-}
-\arguments{
-\item{keyword}{A character string. See}
-
-\item{format}{A character string. Options: 'table' or 'tree'.}
-}
-\value{
-A data.frame or a tree in data.tree format (Node, R6) .
-}
-\description{
-\code{getNCBI} gets data from the NCBI in tree or table format. Tree format
-is in the node format of the data.tree package. For now, it only inlcudes
-taxa from the bacteria superkingdom/domain/kingdom.
-}
diff --git a/man/inh.Rd b/man/inh.Rd
deleted file mode 100644
index 7ffbecc..0000000
--- a/man/inh.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{inh}
-\alias{inh}
-\title{inh}
-\usage{
-inh(node)
-}
-\arguments{
-\item{node}{A node from a data.tree object.}
-}
-\value{
-None. This functions modifies the data.tree object (R6).
-}
-\description{
-\code{inh} inheritance from parent node to children nodes. This functions is
-meant to be used with DO while traversing a data.tree object.
-}
diff --git a/man/inhDownstreamLogical.Rd b/man/inhDownstreamLogical.Rd
deleted file mode 100644
index 7e5a084..0000000
--- a/man/inhDownstreamLogical.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{inhDownstreamLogical}
-\alias{inhDownstreamLogical}
-\title{Inheritance / Downstream (logical)}
-\usage{
-inhDownstreamLogical(node)
-}
-\arguments{
-\item{node}{A node}
-}
-\value{
-Node, R6, data.tree.
-}
-\description{
-\code{inhDownstreamLogical} each node inherits an attribute from it's
-ancestor if values are NA or NULL
-}
diff --git a/man/inhDownstreamNumeric.Rd b/man/inhDownstreamNumeric.Rd
deleted file mode 100644
index b56bc3f..0000000
--- a/man/inhDownstreamNumeric.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{inhDownstreamNumeric}
-\alias{inhDownstreamNumeric}
-\title{Inheritance / Downstream (numeric)}
-\usage{
-inhDownstreamNumeric(node)
-}
-\arguments{
-\item{node}{A node}
-}
-\value{
-Node, R6, data.tree.
-}
-\description{
-\code{inhDownstreamNumeric} each node inherits an attribute from it's ancestor
-if values are NA or NULL
-}
diff --git a/man/inhDownstreamRange.Rd b/man/inhDownstreamRange.Rd
deleted file mode 100644
index e4b45ed..0000000
--- a/man/inhDownstreamRange.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{inhDownstreamRange}
-\alias{inhDownstreamRange}
-\title{Inheritance / Downstream (range)}
-\usage{
-inhDownstreamRange(node)
-}
-\arguments{
-\item{node}{A node}
-}
-\value{
-Node, R6, data.tree.
-}
-\description{
-\code{inhDownstreamRange} each node inherits an attribute from it's ancestor
-if values are NA or NULL
-}
diff --git a/man/mergeOriginalAndEarlyASR.Rd b/man/mergeOriginalAndEarlyASR.Rd
deleted file mode 100644
index a849306..0000000
--- a/man/mergeOriginalAndEarlyASR.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{mergeOriginalAndEarlyASR}
-\alias{mergeOriginalAndEarlyASR}
-\title{Merge original and early ASR}
-\usage{
-mergeOriginalAndEarlyASR(l)
-}
-\arguments{
-\item{l}{A list. Output of \code{prepareDataForPropagation}.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{mergeOriginalAndEarlyASR} merges original bugphyzz annotations
-and early ASR entries (those taxids that couldn't be mapped to the
-data.tree structures, but their parents could).
-}
diff --git a/man/prepareDataForPropagation.Rd b/man/prepareDataForPropagation.Rd
deleted file mode 100644
index 77adcb2..0000000
--- a/man/prepareDataForPropagation.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{prepareDataForPropagation}
-\alias{prepareDataForPropagation}
-\title{Prepare data for propagation}
-\usage{
-prepareDataForPropagation(df)
-}
-\arguments{
-\item{df}{A data.frame.}
-}
-\value{
-A named list.
-}
-\description{
-\code{prepareDataForPropagation} prepares data for propagation.
-}
diff --git a/man/propagate.Rd b/man/propagate.Rd
deleted file mode 100644
index dcde647..0000000
--- a/man/propagate.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{propagate}
-\alias{propagate}
-\title{propagate}
-\usage{
-propagate(data_tree, df)
-}
-\arguments{
-\item{data_tree}{A data.tree object.}
-
-\item{df}{A data.frame.}
-}
-\value{
-A data.tree
-}
-\description{
-\code{propagate} propagates asr/inheritance.
-}
diff --git a/man/removeAccessionAndGenomeID.Rd b/man/removeAccessionAndGenomeID.Rd
deleted file mode 100644
index b11028f..0000000
--- a/man/removeAccessionAndGenomeID.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{removeAccessionAndGenomeID}
-\alias{removeAccessionAndGenomeID}
-\title{Remove Accession_ID and Genome_ID columns}
-\usage{
-removeAccessionAndGenomeID(df)
-}
-\arguments{
-\item{df}{A data.frame imported from bugphyzz.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{removeAcccessionAndGenomeID} removes Accession_ID and Genome_ID from
-a bugphyzz dataset. The reason is that right now these columns can be
-incomplete or inconsistent in some datasets, or just missing in some others.
-I think a solution would be to implement a relational database in which we
-have a data object (data.frame?) with all of the taxids.
-}
diff --git a/man/removeDuplicates.Rd b/man/removeDuplicates.Rd
deleted file mode 100644
index 13eb9ee..0000000
--- a/man/removeDuplicates.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/duplicates.R
-\name{removeDuplicates}
-\alias{removeDuplicates}
-\title{Remove taxa duplicates
-\code{removeDuplicates} removes taxa that are duplicated (output of
-the `getDuplicates` function).}
-\usage{
-removeDuplicates(df)
-}
-\arguments{
-\item{df}{A data frame imported with bugphyzz.}
-}
-\value{
-A data frame without duplicated taxa.
-}
-\description{
-Remove taxa duplicates
-\code{removeDuplicates} removes taxa that are duplicated (output of
-the `getDuplicates` function).
-}
-\seealso{
-\code{\link{getDuplicates}}
-}
diff --git a/man/resolveAgreements.Rd b/man/resolveAgreements.Rd
deleted file mode 100644
index f4c2519..0000000
--- a/man/resolveAgreements.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{resolveAgreements}
-\alias{resolveAgreements}
-\title{Resolve agreements}
-\usage{
-resolveAgreements(df)
-}
-\arguments{
-\item{df}{A data.frame.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{resolveAgreements} resolve all agreements in a bugphyzz dataset.
-Agreements happen when the same annotations comes from two or more
-sources.
-}
diff --git a/man/resolveConflicts.Rd b/man/resolveConflicts.Rd
deleted file mode 100644
index 09eb340..0000000
--- a/man/resolveConflicts.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prepare_data.R
-\name{resolveConflicts}
-\alias{resolveConflicts}
-\title{Resolve conflicts}
-\usage{
-resolveConflicts(df)
-}
-\arguments{
-\item{df}{A data.frame.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{resolveConflicts} resolves are conflicting annotations in a bugphyzz
-dataset. Conflicts happen when a single taxon recieves two or more
-annotations from different sources.
-}
diff --git a/man/taxname2taxid.Rd b/man/taxname2taxid.Rd
deleted file mode 100644
index 225011f..0000000
--- a/man/taxname2taxid.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data_tree.R
-\name{taxname2taxid}
-\alias{taxname2taxid}
-\title{Conver taxname to taxid}
-\usage{
-taxname2taxid(tax_tbl)
-}
-\arguments{
-\item{tax_tbl}{An table with taxnames.}
-}
-\value{
-A data.frame.
-}
-\description{
-\code{taxname2taxid} Converts a taxon name from the ncbi to its corresponding
-taxid
-}