rcpp_areas_list_to_states_list: Make a list of 0-based indices of possible combinations of...
In wrathematics/cladoRcpp: C++ implementations of phylogenetic calculations

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

Given a list of areas (actually a list of anything; all that is important is the length of the list) rcpp_areas_list_to_states_list calculates all possible combinations of these areas, listing them by the 0-based indices that specify the position of each area in the list.

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

`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)

Using 0-based indexing is convenient in the C++ code called by the other functions, rather than having to keep track of the various people might label their areas (names, abbreviations, letters, numbers).

As in LAGRANGE (Ree & Smith 2008), the maximum range size (i.e. the maximum number of areas in a range) can be specified by the user. Having a smaller maximum range size drastically reduces the number of states, and thus the size of the transition matrix and the cladogenesis matrix.

R_states_list A list of the states, where each state is a list of areas in the form of 0-based indices

Nicholas Matzke matzke@berkeley.edu

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>.

numstates_from_numareas, areas_list_to_states_list_old

# Specify the areas
areas_list = c("A", "B", "C")
areas_list

# Let's try Rcpp_combn_zerostart, in case that is the source of a
# problem found via AddressSanitizer
Rcpp_combn_zerostart(n_to_choose_from=4, k_to_choose=2, maxlim=1e+07)
Rcpp_combn_zerostart(n_to_choose_from=4, k_to_choose=3, maxlim=1e+07)


## Not run: 

# Calculate the list of 0-based indices for each possible geographic range, i.e.
# each combination of areas
states_list = rcpp_areas_list_to_states_list(areas=areas_list, maxareas=3,
include_null_range=FALSE)
states_list
states_list = rcpp_areas_list_to_states_list(areas=areas_list, maxareas=3,
include_null_range=TRUE)
states_list
states_list = rcpp_areas_list_to_states_list(areas=areas_list, maxareas=2,
include_null_range=TRUE)
states_list
states_list = rcpp_areas_list_to_states_list(areas=areas_list, maxareas=1,
include_null_range=TRUE)
states_list


## End(Not run)