Table 1. Brief descriptions of the functions implemented in treedata.table.
We list functions under eight different categories and provide a brief outline of their main uses.
| Category | Function | Description |
|---|---|---|
| treedata.table object creation | as.treedata.table | Initial step of the workflow in treedata.table. Matches a character matrix (of class data.frame) to a single (of class phylo) or multiple trees (class multiPhylo) |
| Drop taxa from treedata.table objects | droptreedata.table | Drops taxa from a treedata.table object |
| Data manipulation | [ | Performs data.table operations on an object of class treedata.table |
| Data extraction | [[ | Extracts a named vector from an object of class treedata.table |
| extractVector | Returns a named vector from a treedata.table object | |
| pulltreedata.table | Returns a character matrix or tree(s) from a treedata.table object | |
| Run functions from other packages | tdt | Runs a function on a treedata.table object |
| Detect character type | detectCharacterType | Detects whether a character is continuous or discrete |
| detectAllCharacters | Applies detectCharacterType over an entire character matrix | |
| filterMatrix | Filters a matrix, returning either all continuous or all discrete characters | |
| Examine treedata.table objects | summary | Summarizes treedata.table objects by presenting the number of discrete and continious characters, missing values, and general changes to the original treedata.table object |
| Print method treedata.table objects | ||
| head, tail | Returns the first or last part of an treedata.table object | |
| Inspect column/row names | hasNames | Row and column name check |
| forceNames | Force names for rows, columns or both |