Man pages for celiason/phenotools
Tools for the analysis and assembly of phenomic data in R

cleantextFunction to remove spaces, punctuation from phenome terms
collapseCollapse taxa in a 'nex' object
concatMerge a list of nexus files
dim.nexDimensions of a 'nex' object
duplicated.nexFind duplicate or overlapping characters in nexus files
dupsumFunction to output a summary table of precision and recall
filterFilter duplicated characters in a nexus file
findgroupsSub-function to get groups of duplicated characters based on...
generate_ontologyGenerate a trait ontology from a nexus file
getcommentsFunction to find comments in text file
head.nexLook at top of a 'nex' object
is.nexCheck if x is a 'nex' object
na.omit.nexRemove NAs from nexus files
plot.nexplot data matrix and phylogeny
printneatPrint character names and states
print.nexPrint data in a 'nex' object
printoutFunction to print an html summary of clusters of similar...
read.nexRead in NEXUS data
read_ontologyFunction to create a trait ontology from a tabular text file
remove.invarRemove invariant characters
searchtreeFunction to grep search labels in tree and plot all connected...
sort.nexSort a nexus file
subset.nexSubset a nexus file
summary.nexSummarize data in a 'nex' object
tail.nexLook at bottom of a 'nex' object
traitlinkFunction to link character descriptions to a trait ontology
twigMorphological character dataset for theropod dinosaurs
update.nexSmall function to update a duplicated nex object
write.nexWrite a nexus data object to a file
celiason/phenotools documentation built on Sept. 12, 2019, 6:49 p.m.