RNeXML (version 2.4.11)

get_characters: Get character data.frame from nexml

Description

Get character data.frame from nexml

Usage

get_characters(
  nex,
  rownames_as_col = FALSE,
  otu_id = FALSE,
  otus_id = FALSE,
  include_state_types = FALSE
)

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.

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)

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) {
# 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
}