BioGeoBEARS (version 0.2.1)

vfunc: Extract the appropriate probability for a vicariant speciation event, given text code for rangesize of smaller descendant, and ancestor

Description

Extract the appropriate probability for a vicariant speciation event, given text code for rangesize of smaller descendant, and ancestor

Usage

vfunc(charcell, relprob_vicar_matrix)

Arguments

charcell

The text in the cell, indicating the type of speciation/cladogenesis range inheritance event.

relprob_vicar_matrix

A numeric matrix describing the relative probability of each smaller daughter range, conditional on the ancestral rangesize.

Value

prob_of_this_v, a numeric value giving the relative probability of that descendent-ancestor rangesize pair.

References

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster http://en.wikipedia.org/wiki/Maximum_entropy_probability_distribution

Matzke_2012_IBS

Harte2011

ReeSmith2008

Ronquist1996_DIVA

Ronquist_1997_DIVA

Ronquist_Sanmartin_2011

Landis_Matzke_etal_2013_BayArea

See Also

sfunc, vfunc, relative_probabilities_of_subsets, symbolic_to_relprob_matrix_sp, get_probvals, maxent, calcZ_part, calcP_n

Examples

testval=1
# Examples

# Probabilities of different descendant rangesizes, for the smaller descendant,
# under sympatric/subset speciation
# (plus sympatric/range-copying, which is folded in):
relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.0001, NA_val=NA)
relprob_subsets_matrix
sfunc(charcell="s1_1", relprob_subsets_matrix)
sfunc(charcell="s1_2", relprob_subsets_matrix)
sfunc(charcell="s1_3", relprob_subsets_matrix)
sfunc(charcell="s2_3", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.5, NA_val=NA)
relprob_subsets_matrix
sfunc(charcell="s1_1", relprob_subsets_matrix)
sfunc(charcell="s1_2", relprob_subsets_matrix)
sfunc(charcell="s1_3", relprob_subsets_matrix)
sfunc(charcell="s2_3", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.9999, NA_val=NA)
relprob_subsets_matrix
sfunc(charcell="s1_1", relprob_subsets_matrix)
sfunc(charcell="s1_2", relprob_subsets_matrix)
sfunc(charcell="s1_3", relprob_subsets_matrix)
sfunc(charcell="s2_3", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.0001, NA_val=NA)
relprob_subsets_matrix
yfunc(charcell="y1", relprob_subsets_matrix)
yfunc(charcell="y2", relprob_subsets_matrix)
yfunc(charcell="y3", relprob_subsets_matrix)
yfunc(charcell="y4", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.5, NA_val=NA)
relprob_subsets_matrix
yfunc(charcell="y1", relprob_subsets_matrix)
yfunc(charcell="y2", relprob_subsets_matrix)
yfunc(charcell="y3", relprob_subsets_matrix)
yfunc(charcell="y4", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_subsets(max_numareas=6,
maxent_constraint_01=0.9999, NA_val=NA)
relprob_subsets_matrix
yfunc(charcell="y1", relprob_subsets_matrix)
yfunc(charcell="y2", relprob_subsets_matrix)
yfunc(charcell="y3", relprob_subsets_matrix)
yfunc(charcell="y4", relprob_subsets_matrix)


# Probabilities of different descendant rangesizes, for the smaller descendant,
# under vicariant speciation
relprob_subsets_matrix = relative_probabilities_of_vicariants(max_numareas=6,
maxent_constraint_01v=0.0001, NA_val=NA)
relprob_subsets_matrix
vfunc(charcell="v1_1", relprob_subsets_matrix)
vfunc(charcell="v1_2", relprob_subsets_matrix)
vfunc(charcell="v1_3", relprob_subsets_matrix)
vfunc(charcell="v1_4", relprob_subsets_matrix)
vfunc(charcell="v2_4", relprob_subsets_matrix)
vfunc(charcell="v2_2", relprob_subsets_matrix)
vfunc(charcell="v1_6", relprob_subsets_matrix)
vfunc(charcell="v2_6", relprob_subsets_matrix)
vfunc(charcell="v3_6", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_vicariants(max_numareas=6,
maxent_constraint_01v=0.5, NA_val=NA)
relprob_subsets_matrix
vfunc(charcell="v1_1", relprob_subsets_matrix)
vfunc(charcell="v1_2", relprob_subsets_matrix)
vfunc(charcell="v1_3", relprob_subsets_matrix)
vfunc(charcell="v1_4", relprob_subsets_matrix)
vfunc(charcell="v2_4", relprob_subsets_matrix)
vfunc(charcell="v2_2", relprob_subsets_matrix)
vfunc(charcell="v1_6", relprob_subsets_matrix)
vfunc(charcell="v2_6", relprob_subsets_matrix)
vfunc(charcell="v3_6", relprob_subsets_matrix)

relprob_subsets_matrix = relative_probabilities_of_vicariants(max_numareas=6,
maxent_constraint_01v=0.9999, NA_val=NA)
relprob_subsets_matrix
vfunc(charcell="v1_1", relprob_subsets_matrix)
vfunc(charcell="v1_2", relprob_subsets_matrix)
vfunc(charcell="v1_3", relprob_subsets_matrix)
vfunc(charcell="v1_4", relprob_subsets_matrix)
vfunc(charcell="v2_4", relprob_subsets_matrix)
vfunc(charcell="v2_2", relprob_subsets_matrix)
vfunc(charcell="v1_6", relprob_subsets_matrix)
vfunc(charcell="v2_6", relprob_subsets_matrix)
vfunc(charcell="v3_6", relprob_subsets_matrix)