View source: R/utilities-misc.R
make.gbm | R Documentation |
controlling reversible-jump Markov chain Monte Carlo sampling
make.gbm(phy, dat, SE=NA, type = c("bm", "rbm", "jump-bm", "jump-rbm"), ...)
phy |
a phylogenetic tree of class 'phylo' |
dat |
a named vector of continuous trait values, associated with each species in |
SE |
a named vector of standard errors for each trait value; applied to all trait values if given a single value |
type |
the class of model to use (see |
... |
arguments passed internally to control other settings (see Details) |
The argument ...
controls the substitution of default settings for Markov-chain Monte Carlo sampling. Below are the settings that are controllable by the user.
These parameters and their default settings can also be found with an empty call to the function (e.g., make.gbm()
).
measurement error (SE): one of the arguments necessary for running rjmcmc.bm
is SE
, which is a statement about the error associated with the values
given in dat
. Measurement error (whose argument is SE
) can be a named vector of numeric values (including NA
) or a single value (including NA
). If given as
a vector, SE
must have names that correspond to the those found for dat
. If given a single value for
SE
, the sampler will apply that value of measurement error to all tips in the tree. If NA
appears for the measurement error for any species,
SE
becomes an additional parameter of the model: this density is consequently sampled by rjmcmc.bm
. The default for rjmcmc.bm
is to estimate a single SE
(which is applied to all species).
control settings: default settings for each control parameter are given below. Note that for the discrete random variables (for which dlnSHIFT
and dlnJUMP
) apply,
certain criteria must be met if the user prefers to supply a different prior density. The function dcount
is useful for building a custom prior density function
for discrete variables.
The items that can be tailored in the resulting control object are as follows:
method |
default |
constrainSHIFT |
default |
constrainJUMP |
default |
dlnSHIFT |
default |
dlnJUMP |
default |
dlnRATE |
default |
dlnSE |
default |
dlnPULS |
default |
dlnROOT |
default |
rate.lim |
default |
se.lim |
default |
root.lim |
default |
jump.lim |
default |
excludeSHIFT |
default |
excludeJUMP |
default |
bm.jump |
default |
mergesplit.shift |
default |
tune.scale |
default |
slide.mult |
default |
prob.dimension |
default |
prob.effect |
default |
prob.SE |
default |
prob.root |
default |
prop.width |
default |
simple.start |
default |
filebase |
default |
JM Eastman
rjmcmc.bm
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