read_detections: Read a file with detection counts per area
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

View source: R/BioGeoBEARS_detection_v1.R

This function reads in a tab-delimited text file containing counts of detections of each OTU in each region. These could be from database records or some other source.

1 2	read_detections(detects_fn, OTUnames = NULL, areanames = NULL, tmpskip = 0, phy = NULL)

`detects_fn`	The filename of the detections file.
`OTUnames`	Default `NULL`, in which case the first column of the text file is used as row names/OTU names.
`areanames`	Default `NULL`, in which case the text file column headings are used.
`tmpskip`	How many lines should be skipped before reading the text file? Default `0`.
`phy`	An ape phylo object. If included, the rows will be sorted to match the order of tree tip labels.

dtf

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

Bottjer_Jablonski_1988

rcpp_calc_anclikes_sp_COOweights_faster

testval=1

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