Get character data.frame from nexml
Usage
get_characters(
nex,
rownames_as_col = FALSE,
otu_id = FALSE,
otus_id = FALSE,
include_state_types = FALSE
)Arguments
- nex
a nexml object
- rownames_as_col
option to return character matrix rownames (with taxon ids) as it's own column in the data.frame. Default is FALSE for compatibility with geiger and similar packages.
- otu_id
logical, default FALSE. return a column with the otu id (for joining with otu metadata, etc)
- otus_id
logical, default FALSE. return a column with the otus block id (for joining with otu metadata, etc)
- include_state_types
logical, default FALSE. whether to also return a matrix of state types (with values standard, polymorphic, and uncertain)
Value
the character matrix as a data.frame, or if include_state_types is
TRUE a list of two elements, characters as the character matrix, and
state_types as a matrix of state types. Both matrices will be in the same
ordering of rows and columns.
Details
RNeXML will attempt to return the matrix using the NeXML taxon (otu) labels to name the rows and the NeXML char labels to name the traits (columns). If these are unavailable or not unique, the NeXML id values for the otus or traits will be used instead.
Examples
if (FALSE) { # \dontrun{
# A simple example with a discrete and a continous trait
f <- system.file("examples", "comp_analysis.xml", package="RNeXML")
nex <- read.nexml(f)
get_characters(nex)
# A more complex example -- currently ignores sequence-type characters
f <- system.file("examples", "characters.xml", package="RNeXML")
nex <- read.nexml(f)
get_characters(nex)
# if polymorphic or uncertain states need special treatment, request state
# types to be returned as well:
f <- system.file("examples", "ontotrace-result.xml", package="RNeXML")
nex <- read.nexml(f)
res <- get_characters(nex, include_state_types = TRUE)
row.has.p <- apply(res$state_types, 1,
function(x) any(x == "polymorphic", na.rm = TRUE))
col.has.p <- apply(res$state_types, 2,
function(x) any(x == "polymorphic", na.rm = TRUE))
res$characters[row.has.p, col.has.p, drop=FALSE] # polymorphic rows and cols
res$characters[!row.has.p, drop=FALSE] # drop taxa with polymorphic states
# replace polymorphic state symbols in matrix with '?'
m1 <- mapply(function(s, s.t) ifelse(s.t == "standard", s, "?"),
res$characters, res$state_types)
row.names(m1) <- row.names(res$characters)
m1
} # }