areas_list_to_states_list_old: Convert a list of areas to a list of geographic ranges...

In wrathematics/cladoRcpp: C++ implementations of phylogenetic calculations

Description

This is the original R version of the function which converts a list of possible areas to a list of all possible states (geographic ranges). This gets slow for large numbers of areas.

Usage

  areas_list_to_states_list_old(areas = c("A", "B", "C"),
    maxareas = length(areas), include_null_range = TRUE,
    split_ABC = TRUE)

Arguments

areas	a list of areas (character or number; the function converts these to numbers, starting with 0)
maxareas	maximum number of areas in this analyses
include_null_range	TRUE or FALSE, should the NULL range be included in the possible states? (e.g., LAGRANGE default is yes)
split_ABC	TRUE or FALSE If TRUE the output will consist of a list of lists (c("A","B","C"), c("A","B"), c("A","D"), etc.); if FALSE, the list of areas will be collapsed ("ABC", "AB", "AD", etc.).

Details

The function is mostly replaced by rcpp_areas_list_to_states_list in optimized code, but is still used in some places for display purposes.

Value

states_list A list of the states.

Note

Go BEARS!

Author(s)

Nicholas J. Matzke [e-mail]

References

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

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>.

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>.

See Also

numstates_from_numareas, rcpp_areas_list_to_states_list

Examples

areas = c("A","B","C")
areas_list_to_states_list_old(areas=areas, maxareas=length(areas),
include_null_range=TRUE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=length(areas),
include_null_range=TRUE, split_ABC=FALSE)
areas_list_to_states_list_old(areas=areas, maxareas=length(areas),
include_null_range=FALSE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=length(areas),
include_null_range=FALSE, split_ABC=FALSE)
areas_list_to_states_list_old(areas=areas, maxareas=2,
include_null_range=TRUE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=2,
include_null_range=TRUE, split_ABC=FALSE)
areas_list_to_states_list_old(areas=areas, maxareas=2,
include_null_range=FALSE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=2,
include_null_range=FALSE, split_ABC=FALSE)
areas_list_to_states_list_old(areas=areas, maxareas=1,
include_null_range=TRUE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=1,
include_null_range=TRUE, split_ABC=FALSE)
areas_list_to_states_list_old(areas=areas, maxareas=1,
include_null_range=FALSE, split_ABC=TRUE)
areas_list_to_states_list_old(areas=areas, maxareas=1,
include_null_range=FALSE, split_ABC=FALSE)

wrathematics/cladoRcpp documentation built on May 4, 2019, 9:48 a.m.