Defines list of parameters used in the specified type of model
(model) and adds default values for each parameter to the list of
user specified values (eg formula, link etc) defined in the call to
make.mark.model
setup.parameters(
model,
parameters = list(),
nocc = NULL,
check = FALSE,
number.of.groups = 1
)The return value depends on the argument check. If it is TRUE
then the return value is a vector of the names of the parameters used in the
specified type of model. For example, if model="CJS" then the return
value is c("Phi","p"). This is used by the function
valid.parameters to make sure that parameter specifications
are valid for the model (i.e., specifying recovery rate r for "CJS" would
give an error). If the function is called with the default of
check=FALSE, the function returns a list of parameter specifications
which is a modification of the argument parameters which adds
parameters not specified and default values for all types of parameters that
were not specified. The list length and names of the list elements depends
on the type of model. Each element of the list is itself a list with varying
numbers of elements which depend on the type of parameter although some
elements are the same for all parameters. Below the return value list is
shown generically with parameters named p1,...,pk.
p1 | List of specifications for parameter 1 |
p2 | List of specifications for parameter 2 |
| . | |
| . | |
| . | |
pk | List of specifications for parameter k |
The elements for each parameter list all include:
begin | 0 or 1; beginning time for the first |
| parameter relative to first occasion | |
num | 0 or -1; number of parameters relative to |
| number of occassions | |
type | type of PIM structure; either "Triang" or "Square" |
formula | formula for parameter
model (e.g., ~time) |
link | link function for parameter
(e.g., "logit") |
and may include:
share | only valid for p in closed capture models; |
| if TRUE p and c models shared | |
mix | only valid for closed capture heterogeneity |
| models; if TRUE mixtures are used | |
rows | only valid for closed capture heterogeneity models |
fixed | fixed values specified by user and |
| not used modified in this function |
type of model ("CJS", "Burnham" etc)
list of model parameter specifications
number of occasions (value only specified if needed)
if TRUE only the vector of parameter names is returned
par.list
number of groups defined for data
Jeff Laake
The primary difference in setting up models for MARK is the number and types
of parameters that are included in the model. This function sets up the
list of parameters used in the model and defines values for each parameter
that affect how the PIM and design data are structured in the input file for
program MARK. Some of the values of the parameter list are user specified
such as formula, link,fixed so this function only adds
to the list of values that are not specified by the user. That is, it takes
the input argument parameters and adds list elements for parameters
not specified by the user and adds default values for each type of parameter
and then returns the modified list. The structure of the argument
parameters and the return value of this function are the same as the
structure of the argument parameters in make.mark.model
and argument model.parameters in mark. They are lists
with an element for each type of parameter in the model and the name of each
list element is the parameter name (e.g., "p", "Phi","S", etc). For each
parameter there are a list of values (e.g., formula, link, num etc as
defined below). Thus parameters is a list of lists.
setup.model,valid.parameters