Description Usage Arguments Details Value Author(s) References See Also Examples
This function calculates the number of discrete states that are needed to represent the possible combinations of presence and absence in a set of discrete areas. The number of states is a function of the number of areas, and the maximum allowed range size (in number of areas) of a species.
1 2 | numstates_from_numareas(numareas = 3,
maxareas = numareas, include_null_range = FALSE)
|
numareas |
The number of areas in the analysis. |
maxareas |
The maximum number of areas that any single species/lineage can occupy. |
include_null_range |
If FALSE (default), the null range is not included in the count. If TRUE, the null range is included, adding +1 to the count of the states. |
For example, with 3 areas (A, B, C), there are 8 possible states, if a null range is allowed (null, A, B, C, AB, BC, AC, ABC). If the maximum range size is 2 areas, then there are only 7 possible states.
The formula for the number of geographic states, based on the number of areas (N), is the sum of N choose k, from k=1 to m (maximum range size)
s = sum(k=1...m)(N choose k)
This equation assumes that the null range (a species
lives in no areas, i.e. is extinct) is not allowed. In
the LAGRANGE program of Ree et al. (2008)), the
null range is included in the transition matrix, and thus
this is one more state. This situation is represented in
numstates_from_numareas
by setting
include_null_range=TRUE
.
Users might manually remove states from the states list, if prior information indicates that some configurations of presence/absence in areas are impossible as geographic ranges for species. If so, they should manually subtract from the number of states.
nstates
Number of states
Nicholas Matzke matzke@berkeley.edu
Ree RH and Smith SA (2008). "Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis." _Systematic Biology_, *57*(1), pp. 4-14. <URL: http://dx.doi.org/10.1080/10635150701883881>, <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18253896>.
Matzke N (2012). "Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses." _Frontiers of Biogeography_, *4*(suppl. 1), pp. 210. ISSN 1948-6596, Poster abstract published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual Meeting, Miami, Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster 129B. January 11, 2013, <URL: http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster>.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | numstates_from_numareas(numareas=3, maxareas=3,
include_null_range=FALSE)
numstates_from_numareas(numareas=3, maxareas=3,
include_null_range=TRUE)
numstates_from_numareas(numareas=3, maxareas=2,
include_null_range=TRUE)
numstates_from_numareas(numareas=3, maxareas=1,
include_null_range=TRUE)
numstates_from_numareas(numareas=7, maxareas=7,
include_null_range=TRUE)
numstates_from_numareas(numareas=7, maxareas=2,
include_null_range=TRUE)
numstates_from_numareas(numareas=8, maxareas=8,
include_null_range=TRUE)
numstates_from_numareas(numareas=8, maxareas=2,
include_null_range=TRUE)
numstates_from_numareas(numareas=20, maxareas=20,
include_null_range=TRUE)
numstates_from_numareas(numareas=20, maxareas=2,
include_null_range=TRUE)
numstates_from_numareas(numareas=20, maxareas=3,
include_null_range=TRUE)
|
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