Parses Nexus file, reading character states and names
ReadCharacters(filepath, character_num = NULL, session = NULL)ReadTntCharacters(filepath, character_num = NULL, session = NULL)
ReadAsPhyDat(filepath)
ReadTntAsPhyDat(filepath)
PhyDat(dataset)
character string specifying location of file
Index of character(s) to return. `NULL`, the default, returns all characters.
(optionally) a Shiny session with a numericInput named character_num whose maximum should be updated.
list of taxa and characters, in the format produced by [read.nexus.data]: a list of sequences each made of a single vector of mode character, and named with the taxon name.
A matrix whose row names correspond to tip labels, and column names correspond to character labels, with the attribute `state.labels` listing the state labels for each character; or a character string explaining why the character cannot be returned.
ReadTntCharacters: Read characters from TNT file
ReadAsPhyDat: Read nexus characters as phyDat object
ReadTntAsPhyDat: Read TNT characters as phyDat object
PhyDat: A convenient wrapper for phangorn's phyDat,
which converts a *list* of morphological characters into a phyDat object.
If your morphological characters are in the form of a *matrix*, perhaps because
they have been read using `read.table`, try [MatrixToPhyDat] instead.
Tested with nexus files downloaded from MorphoBank with the "no notes" option, but should also work more generally.
Do [report](https://github.org/ms609/TreeSearch/issues "New GitHub Issue") incorrectly parsed files.
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590-621.