
LAGRANGE
(Ree et al. (2008),
Smith et al. (2010)).
make_relprob_matrix_de(states_list = default_states_list(), split_ABC = FALSE, split = "", remove_simultaneous_events = TRUE, add_multiple_Ds = TRUE, dispersal_multiplier_matrix = make_dispersal_multiplier_matrix(states_list))
TRUE
or FALSE
If
TRUE
then each state/range in the input geographic
ranges (states_list
) will be split on the argument
contained in split
.TRUE
(default, as in LAGRANGE
and almost all
phylogenetic Markov models), then it is assumed that all
changes in geographic range along branches must happen
one event at a time. If FALSE
, simultaneous
events are not excluded; this is not recommended.
However, notably, a commonly-used biogeographic model
(treating biogeography as a multistate discrete character
in an ML framework, where every species/lineage inhabits
one and only one area at any point in time) effectively
is invoking a simultaneous event: e.g., A->B is a
simultaneous range gain and range loss, from the
perspective of the dispersal-extinction framework.TRUE
(default, as in
LAGRANGE
), the probabilities of dispersal from
each possible source area are added together.make_dispersal_multiplier_matrix
(states_list=states_list).dedf
The output data.frame
,
termed dedf
(dedf=dispersal-extinction
data.frame), contains the actual text of the formulas by
which the transition probability matrix would be
calculated.
data.frame
, termed
dedf
(dedf=dispersal-extinction data.frame),
contains the actual text of the formulas by which the
transition probability matrix would be calculated. E.g.,
the example calculates the matrix corresponding to
Equation 1 on p. 6 of Ree & Smith (2008). Note that the geographic range-change process described
here is a continuous-time process, where the probability
of change is a function of branch length, and all
transitions occur because of dispersal and extinction.
LAGRANGE also implements a cladogenesis model (thus DEC
-- dispersal-extinction-cladogenesis) which describes an
"instantaneous" process of geographic range change at
speciation/lineage-splitting events. BioGeoBEARS
allows users to turn on, turn off, or otherwise customize
both the continuous-time model and the cladogenesis
model.
ReeSmith2008
SmithRee2010_CPPversion
Matzke_2012_IBS
FosterIdiots
make_dispersal_multiplier_matrix
testval=1
states_list = list("_", c("A"), c("B"), c("C"), c
("A","B"), c("B","C"), c("A","C"), c("A","B","C"))
states_list = areas_list_to_states_list_new(
areas=c("A","B","C"), include_null_range=TRUE, split_ABC=TRUE)
states_list
dedf = make_relprob_matrix_de(states_list=states_list,
split_ABC=FALSE, split="", remove_simultaneous_events=TRUE,
add_multiple_Ds=TRUE,
dispersal_multiplier_matrix=make_dispersal_multiplier_matrix(states_list=states_list))
dedf
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