readTree | R Documentation |
Return a TreeMan
or TreeMen
object from a Newick treefile
readTree(
file = NULL,
text = NULL,
spcl_slt_nm = "Unknown",
wndmtrx = FALSE,
parallel = FALSE,
progress = "none"
)
file |
file path |
text |
Newick character string |
spcl_slt_nm |
name of special slot for internal node labels, default 'Unknown'. |
wndmtrx |
T/F add node matrix? Default FALSE. |
parallel |
logical, make parallel? |
progress |
name of the progress bar to use, see |
Read a single or multiple trees from a file, or a text string. Parallelizable
when reading multiple trees.
The function will add any internal node labels in the Newick tree as a user-defined data slots.
The name of this slot is defined with the spcl_slt_nm
.
These data can be accessed/manipulated with the `getNdsSlt()`
function.
Trees are always read as rooted. (Unrooted trees have polytomous root nodes.)
https://en.wikipedia.org/wiki/Newick_format,
addNdmtrx
, writeTree
,
randTree
, readTrmn
, writeTrmn
,
saveTreeMan
, loadTreeMan
# tree string with internal node labels as bootstrap results
tree <- readTree(
text = "((A:1.0,B:1.0)0.9:1.0,(C:1.0,D:1.0)0.8:1.0)0.7:1.0;",
spcl_slt_nm = "bootstrap"
)
# retrieve bootstrap values by node
tree["bootstrap"]
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