update documentation

waldronlab · Nov 22, 2023 · 8aeeb40 · 8aeeb40
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diff --git 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
diff --git a/man/addAttributesLogical.Rd b/man/addAttributesLogical.Rd
diff --git a/man/addAttributesNumeric.Rd b/man/addAttributesNumeric.Rd
diff --git a/man/addAttributesRange.Rd b/man/addAttributesRange.Rd
diff --git a/man/addStrains.Rd b/man/addStrains.Rd
diff --git a/man/asr.Rd b/man/asr.Rd
diff --git a/man/asrUpstreamLogical.Rd b/man/asrUpstreamLogical.Rd
diff --git a/man/asrUpstreamNumeric.Rd b/man/asrUpstreamNumeric.Rd
diff --git a/man/asrUpstreamRange.Rd b/man/asrUpstreamRange.Rd
diff --git a/man/calcParentScore.Rd b/man/calcParentScore.Rd
diff --git a/man/calcParentScores.Rd b/man/calcParentScores.Rd
diff --git a/man/chooseColVal.Rd b/man/chooseColVal.Rd
diff --git a/man/fillNAs.Rd b/man/fillNAs.Rd
diff --git a/man/getAgreements.Rd b/man/getAgreements.Rd
diff --git a/man/getConflicts.Rd b/man/getConflicts.Rd
diff --git a/man/getDistantTips.Rd b/man/getDistantTips.Rd
diff --git a/man/getDoubleAnnotations.Rd b/man/getDoubleAnnotations.Rd