solution0 <- AssessMonophyly(phy3, outliercheck=FALSE)
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names'
I think it's line 348 of AssessMonophyly.R: rownames(outframe) <- outframe[, 1] # assign first column as row names
For the same tree (attached):
solution0 <- AssessMonophyly(phy3, outliercheck=TRUE)
Error in if (outframe[tip.states.matrix[i, 2], "Monophyly"] == "Monotypic") { :
missing value where TRUE/FALSE needed
Which I think is line 367 of AssessMonophyly.R: } else if (outframe[tip.states.matrix[i, 2], "Monophyly"] == "Monotypic") { # ...if species is monotypic...
I think it's line 348 of AssessMonophyly.R:
rownames(outframe) <- outframe[, 1] # assign first column as row names
For the same tree (attached):
Which I think is line 367 of AssessMonophyly.R:
} else if (outframe[tip.states.matrix[i, 2], "Monophyly"] == "Monotypic") { # ...if species is monotypic...
sponges.txt