This is a convenience function that uses a dataframe of parameter
specifications created by create.model.list and it constructs
and runs each model and names the models by concatenating each of the
parameter specification names separated by a period. The results are
returned as a marklist with a model.table constructed by
collect.models.
mark.wrapper(
model.list,
silent = FALSE,
run = TRUE,
use.initial = FALSE,
initial = NULL,
...
)if(run) marklist - list of mark models that were run and a model.table of results; if(!run) a list of models that were constructed but not run.
a dataframe of parameter specification names in the calling frame
if TRUE, errors that are encountered are suppressed
if FALSE, only calls make.mark.model to test for
model errors but does not run the models
if TRUE, initial values are constructed for new models using completed models that have already been run in the set
vector, mark model or marklist for defining initial values
arguments to be passed to mark. These must be
specified as argument=value pairs.
Jeff Laake
The model names in model.list must be in the frame of the function
that calls run.models. If model.list=NULL or the MARK models
are collected from the frame of the calling function (the parent). If
type is specified only the models of that type (e.g., "CJS") are run.
In each case the models are run and saved in the parent frame. To fully
understand, how this function works and its limitations, see
create.model.list.
If use.initial=TRUE, prior to running a model it looks for the first
model that has already been run (if any) for each parameter formula and
constructs an initial vector from that previous run. For example, if
you provided 5 models for p and 3 for Phi in a CJS model, as soon as the
first model for p is run, in the subsequent 2 models with different Phi
models, the initial values for p are assigned based on the run with the
first Phi model. At the outset this seemed like a good idea to speed up
execution times, but from the one set of examples I ran where several
parameters were at boundaries, the results were discouraging because the
models converged to a sub-optimal likelihood value than the runs using the
default initial values. I've left sthis option in but set its default value
to FALSE.
A possibly more useful argument is the argument initial. Previously,
you could use initial=model as part of the ... arguments and it would
use the estimates from that model to assign initial values for any model in
the set. Now I've defined initial as a specific argument and it can
be used as above or you can also use it to specify a marklist of
previously run models. When you do that, the code will lookup each new model
to be run in the set of models specified by initial and if it finds
one with the matching name then it will use the estimates for any matching
parameters as initial values in the same way as initial=model does.
The model name is based on concatenating the names of each of the parameter
specification objects. To make this useful, you'll want to adapt to an
approach that I've started to use of naming the objects something like
p.1,p.2 etc rather than naming them something like p.dot, p.time as done in
many of the examples. I've found that using numeric approach is much less
typing and cumbersome rather than trying to reflect the formula in the name.
By default, the formula is shown in the model selection results table, so it
was a bit redundant. Now where I see this being the most benefit.
Individual covariate models tend to run rather slowly. So one approach is to
run the sequence of models (eg results stored in initial_marklist),
including the set of formulas with all of the variables other than
individual covariates. Then run another set with the same numbering scheme,
but adding the individual covariates to the formula and using
initial=initial_marklist That will work if each parameter
specification has the same name (eg., p.1=list(formula=~time) and then
p.1=list(formula=~time+an_indiv_covariate)). All of the initial values will
be assigned for the previous run except for any added parameters (eg.
an_indiv_covariate) which will start with a 0 initial value.
collect.models, mark,
create.model.list