constrain
in Rich Fitzjohn's package diversitree.constrainParPaleo(f, ..., formulae = NULL, names = parnames(f),
extra = NULL)...x. Use this only if
parnames does not return a vector for your function.
Generally this should not be useargnames. This can be used to set up dummy variables
(example coming later).optim, find.mle in diversitree or mcmc.
It will behave like any other function. However, it has a modified
class attribute so that some methods will dispatch differently:
parnames, for example, will return the names of the
parameters of the constrained function and parInit will
return the initial values for those same constrained set of parameters.
All arguments in addition to x will be passed through to the
original function f.
Additional useful information from the diversitree manual (11/01/13):
For help in designing constrained models, the returned function has
an additional argument pars.only, when this is TRUE the
function will return a named vector of arguments rather than evaluate
the function (see Examples).constrain
from the package diversitree. Users should refer to this parent function for
more detailed discussion of model constraint usage and detailed examples.
The parent function was forked to add functionality necessary for dealing with the
high parameter count models typical to some paleontological analyses, particularly
the inverse survivorship method. This necessitated that the new function be entirely
separate from its parent. Names of functions involved (both exported and not)
have been altered to avoid overlap in the package namespaces. Going forward,
the paleotree package maintainer (Bapst) will try to be vigilant with
respect to changes in constrain in the original package, diversitree.
Useful information from the diversitree manual (11/01/13):
"If f is a function that takes a vector x as its first
argument, this function returns a new function that takes a
shorter vector x with some elements constrained in some way;
parameters can be fixed to particular values, constrained to be the
same as other parameters, or arbitrary expressions of free
parameters."
In general, formulae should be of the structure:
LHS ~ RHS
...where the LHS is the 'Parameter We Want to Constrain' and the
RHS is whatever we are constraining the LHS to, usually another
parameter. LHS and RHS are the 'left-hand side' and
'right-hand side' respectively (which I personally find obscure).
Like the original constrain function this function is based on,
this function cannot remove constraints previously placed on a model
object and there may be cases in which the constrained function may not
make sense, leading to an error. The original function will sometimes
issue nonsensical functions with an incorrect number/names of parameters
if the parameters to be constrained are given in the wrong order in
formulae.
modelMethods to set the parameter
bounds as equal. Finally, once parameters with the same bounds are constrained, the
output has updated bounds that reflect the new set of parameters
for the new constrained function.}constrain from the library diversitree.#simulation example with make_durationFreqCont, with three random groups
set.seed(444)
taxa <- simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,maxExtant=0)
rangesCont <- sampleRanges(taxa,r=0.5)
grp1 <- matrix(sample(1:3,nrow(taxa),replace=TRUE),,1) #groupings matrix
likFun <- make_durationFreqCont(rangesCont,groups=grp1)
# can constrain both extinction rates to be equal
constrainFun <- constrainParPaleo(likFun,q.2~q.1)
#see the change in parameter names and bounds
parnames(likFun)
parnames(constrainFun)
parbounds(likFun)
parbounds(constrainFun)
# some more ways to constrain stuff!
#constrain all extinction rates to be equal
constrainFun <- constrainParPaleo(likFun,q.all~q.1)
parnames(constrainFun)
#constrain all rates for everything to be a single parameter
constrainFun <- constrainParPaleo(likFun,r.all~q.all)
parnames(constrainFun)
#constrain all extinction rates to be equal & all sampling to be equal
constrainFun <- constrainParPaleo(likFun,q.all~q.1,r.all~r.1)
parnames(constrainFun)
#similarly, can use match.all to make all matching parameters equal each other
constrainFun <- constrainParPaleo(likFun,match.all~match.all)
parnames(constrainFun)
#Constrain rates in same group to be equal
constrainFun <- constrainParPaleo(likFun,r.match~q.match)
parnames(constrainFun)Run the code above in your browser using DataLab