Man pages for celiason/phenotools
Tools for the analysis and assembly of phenomic data in R
| cleantext | Function to remove spaces, punctuation from phenome terms |
| collapse | Collapse taxa in a 'nex' object |
| concat | Merge a list of nexus files |
| dim.nex | Dimensions of a 'nex' object |
| duplicated.nex | Find duplicate or overlapping characters in nexus files |
| dupsum | Function to output a summary table of precision and recall |
| filter | Filter duplicated characters in a nexus file |
| findgroups | Sub-function to get groups of duplicated characters based on... |
| generate_ontology | Generate a trait ontology from a nexus file |
| getcomments | Function to find comments in text file |
| head.nex | Look at top of a 'nex' object |
| is.nex | Check if x is a 'nex' object |
| na.omit.nex | Remove NAs from nexus files |
| plot.nex | plot data matrix and phylogeny |
| printneat | Print character names and states |
| print.nex | Print data in a 'nex' object |
| printout | Function to print an html summary of clusters of similar... |
| read.nex | Read in NEXUS data |
| read_ontology | Function to create a trait ontology from a tabular text file |
| remove.invar | Remove invariant characters |
| searchtree | Function to grep search labels in tree and plot all connected... |
| sort.nex | Sort a nexus file |
| subset.nex | Subset a nexus file |
| summary.nex | Summarize data in a 'nex' object |
| tail.nex | Look at bottom of a 'nex' object |
| traitlink | Function to link character descriptions to a trait ontology |
| twig | Morphological character dataset for theropod dinosaurs |
| update.nex | Small function to update a duplicated nex object |
| write.nex | Write a nexus data object to a file |
