From an Excel spreadsheet

If your data is in an Excel spreadsheet, one way to load it into R isusing the ‘readxl’ package.First you’ll have to install it:

install.packages("readxl")# You only need to do this once

Then you should prepare your Excel spreadsheet such that each rowcorresponds to a taxon, and each column to a character.

Then you can read the data from the Excel file by telling R whichsheet, rows and columns contain your data:

library("readxl")raw_data<-as.matrix(read_excel(  filename,sheet =1,# Loads sheet number 1 from the excel filerange ="B1:AA21",# Extracts columns B to AA, rows 1 to 21# Note that the first row is interpreted as column (character) namescol_types ="text"# Read all columns as character strings))# Read row (taxon) names from column A# Again, the first cell will be interpreted as a column nametaxon_names<-unlist(read_excel(filename,sheet =1,range ="A1:A21"))rownames(raw_data)<- taxon_names

From a text or CSV (comma separated values) file

Characters can be read from a text file in a similar manner to Excel.You may need to adjust the R commands to match the particular format ofyour input file.

raw_data<-read.table(  filename,# Path to your input filesep =",",# What character separates columns?header =TRUE,# Does the data contain a header row?row.names =1,# Which column contains the row names?na.strings ="",stringsAsFactors =FALSE)

From a Nexus file

TreeTools contains an inbuilt Nexus parser:

raw_data<-ReadCharacters(filename)# Or, to go straight to PhyDat format:as_phydat<-ReadAsPhyDat(filename)

This will extract character names and codings from a dataset. It’sbeen written to work with datasets downloaded fromMorphoBank, but my aim is for thisfunction to handle most valid (and many invalid) NEXUS files. If youfind a file that this function can’t handle, pleaseletme know and I’ll try to fix it.

In the meantime, alternative Nexus parsers are available: try

raw_data<- ape::read.nexus.data(filename)

Non-standard elements of a Nexus file might be beyond thecapabilities of ape’s parser. In particular, you will need to replacespaces in taxon names with an underscore, and to arrange all data into asingle block startingBEGIN DATA. You’ll need to strip outcomments, character definitions and separate taxon blocks.

The functionreadNexus in packagephylobaseuses the NCL library and promises to be more powerful, but I’ve not beenable to get it to work.

From a TNT file

A TNT format dataset downloaded fromMorphoBank can be parsed withReadTntCharacters, which might also handle otherTNT-compatible files. If there’s a file that’s not being read correctly,pleaseletme know and I’ll try to fix it.

raw_data<-ReadTntCharacters(filename)# Or, to go straight to PhyDat format:my_data<-ReadTntAsPhyDat(filename)

my_data<-PhyDat(raw_data)

my_data<-MatrixToPhyDat(raw_data)

install.packages("phangorn")library("phangorn")my_data<-phyDat(raw_data,type ="USER",levels =c(0:9,"-"))

contrast.matrix<-matrix(data =c(# 0 1 -  # Each column corresponds to a character-state1,0,0,# Each row corresponds to a token, here 0, denoting the# character-state set {0}0,1,0,# 1 | {1}0,0,1,# - | {-}1,1,0,# A | {01}1,1,0,# + | {01}1,1,1# ? | {01-}),ncol =3,# ncol corresponds to the number of columns in the matrixbyrow =TRUE)dimnames(contrast.matrix)<-list(c(0,1,"-","A","+","?"),# A list of the tokens corresponding to each row# in the contrast matrixc(0,1,"-")# A list of the character-states corresponding to the columns# in the contrast matrix)contrast.matrix

my.phyDat<-phyDat(my.data,type ="USER",contrast = contrast.matrix)

ape::write.nexus.data(my.phyDat,"my_data.nex",format ="standard")