cladoRcpp (version 0.15.1)

rcpp_states_list_to_DEmat: C++ conversion of a states list to a dispersal-extinction matrix (DEmat)

Description

This function takes a list of states/ranges, a matrix describing relative dispersal probability (dmat) for each pair of areas, and a list describing the local extirpation probability for each area (elist), and calculates a transition matrix Qmat accordingly.

Usage

rcpp_states_list_to_DEmat(areas_list, states_list, dmat, elist,
  amat = NULL, include_null_range = TRUE, normalize_TF = TRUE,
  makeCOO_TF = FALSE, min_precision = 1e-26)

Arguments

areas_list

a list of lists of areas (numbers, starting with 0)

states_list

a list of lists of areas (numbers, starting with 0)

dmat

dispersal matrix from area to area

elist

a list of extinction probabilities

amat

A matrix specifying the probability of instantaneous transition from one area to another (as in standard character rate matrices).

include_null_range

include the null () range (NA) in the matrix (LAGRANGE default=TRUE)

normalize_TF

should the columns be -1 * rowsums?

makeCOO_TF

should the returned matrix be COO or standard dense (the latter is default).

min_precision

what is the effective minimum size for 0

Value

dmat (a standard Q matrix)

Details

The size of the matrix will expand dramatically with the number of areas. See numstates_from_numareas for the calculation.

Above 7 or so areas, making Qmat a COO-formatted matrix (COO=Coordinate list, see wikipedia, http://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_.28COO.29 ) which can then be used in rexpokit's sparse-matrix algorithms, should be more efficient. (Sparse matrices are matrices made of mostly 0s.)

References

http://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_.28COO.29 #bibliography /Dropbox/_njm/__packages/cladoRcpp_setup/cladoRcpp_refs.bib @cite Matzke_2013 @cite Matzke_2014 @cite ReeSmith2008

See Also

numstates_from_numareas, convolve

Examples

# NOT RUN {
# Specify the areas
areas_list_txt = c("A", "B", "C")
areas_list_txt

# rcpp_states_list_to_DEmat function requires a 0-based list of areas
areas_list = seq(0, length(areas_list_txt)-1, 1)
areas_list

# }
# 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

# Hard-code the along-branch dispersal and extinction rates
d = 0.2
e = 0.1

# Calculate the dispersal weights matrix and the extinction weights matrix
# Equal dispersal in all directions (unconstrained)
areas = areas_list
distances_mat = matrix(1, nrow=length(areas), ncol=length(areas))
dmat = matrix(d, nrow=length(areas), ncol=length(areas))
dmat

# Equal extinction probability for all areas
elist = rep(e, length(areas))
elist

# Set up the instantaneous rate matrix (Q matrix, Qmat)
# DON'T force a sparse-style (COO-formatted) matrix here
force_sparse = FALSE
Qmat = rcpp_states_list_to_DEmat(areas_list, states_list, dmat, elist, 
include_null_range=TRUE, normalize_TF=TRUE, makeCOO_TF=force_sparse)
Qmat

# DO force a sparse-style (COO-formatted) matrix here
force_sparse = TRUE
Qmat = rcpp_states_list_to_DEmat(areas_list, states_list, dmat, elist, 
include_null_range=TRUE, normalize_TF=TRUE, makeCOO_TF=force_sparse)
Qmat


# Repeat with an amat
amat = dmat
amat[is.numeric(amat)] = 0.33

# Set up the instantaneous rate matrix (Q matrix, Qmat)
# DON'T force a sparse-style (COO-formatted) matrix here
force_sparse = FALSE
Qmat = rcpp_states_list_to_DEmat(areas_list, states_list, dmat, elist, amat, 
include_null_range=TRUE, normalize_TF=TRUE, makeCOO_TF=force_sparse)
Qmat

# DO force a sparse-style (COO-formatted) matrix here
force_sparse = TRUE
Qmat = rcpp_states_list_to_DEmat(areas_list, states_list, dmat, elist, amat, 
include_null_range=TRUE, normalize_TF=TRUE, makeCOO_TF=force_sparse)
Qmat
# }
# NOT RUN {

# }