who
allows you to name a node, or list of nodes, and a phylogeny, and it provides information to help you identify the node(s). This might be useful when looking at short regression output, or the plot from phyreg
.
who(phy, nodes, find = "mm")
phyreg
output as $fullphy
for the full phylogeny or $usedphy
for the reduced phylogeny (reflecting species omitted either because of the subset
argument of phyreg
or because of missing values). The full phylogeny will usually be the right one to use, because all the usual output uses those originalIDs, rather than the reduced ones.
c(101,123)
or 101:137
. If not specified, it will be taken to be the list of all higher nodes.
"sp"
then all the species below the node are printed, if "mm"
then the minimum and maximum of those species numbers are printed, and if "dg"
(or anything else) then the IDs of the daughter nodes are printed.
find="sp"
or find="dg"
, the results are printed out, and nothing is returned.If find="mm"
, a data-frame is returned with three columns: ID
for the number of the higher node, minsp
for the first species, and maxsp
for the last species.find="mm"
(for min and max) will conveniently tell you the first and last species in that set. If your higher nodes have interdigitating sets of species, then you may need to choose "sp"
to see the complete set. For drawing out your own phylogeny, find="dg"
for the daughter nodes could be helpful.
Examples of use are provided in phyreg
phyreg
uses these phylogenies and produces the output that who
can help to interpret.