prune_specimens_to_species: Take a tree and species names/geography table and produce a...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Details Value Note Author(s) See Also Examples

This function takes a tree and species names/geography table and produces a pruned tree and (optionally) a tipranges object.

1
2
3

  prune_specimens_to_species(original_tr, xls,
    group_name = "default", titletxt = "",
    areas_abbr = NULL, plot_intermediate = TRUE)

`original_tr`	The input tree (an `ape` `phylo` object).
`xls`	The input table (a `data.frame`)
`group_name`	The name of the clade in the tree. For use in plots and output files. Default="default".
`titletxt`	Additional text for the plots. Default "".
`areas_abbr`	An optional table, containing the abbreviations (e.g. letters) corresponding to each region in xls$region. Default is NULL, in which case the program imposes A, B, C, D, etc. `areas_abbr` must have column headings `abbr` and `letter`.
`plot_intermediate`	If TRUE, the starting, ending, and intermediate stages of tree pruning are plotted.

Often, users will have an phylogeny where the tips/OTUs (operational taxonomic units) are specimens rather than species. The analyses done by models like DEC, DEC+J, etc., in programs like LAGRANGE and BioGeoBEARS, assume as a core part of the model that species might occupy more than one areas. A phylogeny of specimens, then, would not be an appropriate input to these programs, as each single specimen can only be found in one region. The exception would occur when the researcher is confident that each species lives in only one region; in that case, the specimen geography is representative of the species geography.

This function requires a table containing

(1) Column "OTUs": all tipnames in the input tree (often, original specimen/original OTU names) );

(2) Column "species": the corresponding species names;

(3) optionally, the geographic range inhabited by each specimen (column "region"). If an OTU has more than one geographic range in the original table, these should be split by "|".

When the pruning occurs, all tips belonging to the same species are cut, except the first.

NOTE: Tips that should be cut because they are outgroups, or because they are geographically outside of your domain of analysis, should be represented in xls$region by "out_group" or "Out". These will be cut from the final tree/geography table.

The outputs are a list with a pruned tree and, optionally, a tipranges object.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

drop.tip, define_tipranges_object,

testval=1
tipranges_object = define_tipranges_object()
tipranges_object

areanames = getareas_from_tipranges_object(tipranges_object)
areanames

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges

An object of class "tipranges"
numeric(0)
Slot "df":
     A B C
tip1 1 0 0
tip2 0 1 0
tip3 0 0 1

[1] "A" "B" "C"