vfunc: Extract the appropriate probability for a vicariant...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
Description
Usage
Arguments
Value
Note
Author(s)
References
See Also
Examples
View source: R/BioGeoBEARS_basics_v1.R
Description
Extract the appropriate probability for a vicariant
speciation event, given text code for rangesize of
smaller descendant, and ancestor
Usage
1
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.
Note
Go BEARS!
Author(s)
Nicholas J. Matzke matzke@berkeley.edu
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
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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)
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Description Usage Arguments Value Note Author(s) References See Also Examples
View source: R/BioGeoBEARS_basics_v1.R
Description
Extract the appropriate probability for a vicariant speciation event, given text code for rangesize of smaller descendant, and ancestor
Usage
1 | 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.
Note
Go BEARS!
Author(s)
Nicholas J. Matzke matzke@berkeley.edu
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 | 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)
|
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