hzar.make.fitRequest: Generate a hzar.fitRequest with the specified attributes.
In hzar: Hybrid Zone Analysis using R

Description Usage Arguments Details Value Note Author(s) See Also

This method is meant to generate an arbitrary hzar.fitRequest object to pass to hzar.doFit. Note that this method does not check its arguments for validity. Use hzar.first.fitRequest.old.ML or hzar.next.fitRequest for a more convenient method for generating hzar.fitRequest objects.

hzar.make.fitRequest(modelParameters,
                     covMatrix,
                     clineLLfunc,
                     mcmcParameters,
                     mcmcRaw = NULL,
                     fit.run = FALSE,
                     fit.success = FALSE)

`modelParameters`	A named list of at least length 2. See details for format.
`covMatrix`	A covariance matrix for the gaussian proposal distribution as described in `MCMCmetrop1R`. Should be a square matrix of dimension equal to the number of free parameters, which can be generated by `hzar.cov.rect` or `hzar.cov.mcmc`. Although NULL is acceptable, it is extremely likely that hzar.doFit will crash.
`clineLLfunc`	A function of theta that returns a log likelihood. It is best to use the results of `hzar.make.clineLLfunc.old.ML`, `hzar.make.clineLLfunc.old.bayes`, or `hzar.make.LLfunc.null`.
`mcmcParameters`	The parameters controling the operation of the mcmc process. Use the results from `hzar.make.mcmcParam`.
`mcmcRaw`	The mcmc object created by a successful run of `MCMCmetrop1R`. Useful if you wish to import old mcmc objects for use with hzar.
`fit.run`	Has this particular request been run? Note that this does not update automatically; the result of `hzar.doFit` is a new object with mcmcRaw, fit.run, and fit.success updated as appropriate. Primariy affects the behavior of `hzar.next.fitRequest`.
`fit.success`	Has this particular request been run successfully? Note that this does not update automatically; the result of `hzar.doFit` is a new object with mcmcRaw, fit.run, and fit.success updated as appropriate. Primariy affects the behavior of `hzar.next.fitRequest`.

For modelParameters, the list must have the following entries:

$initA named list with the initial values of the free parameters. Used as theta.init in MCMCmetrop1R.
$tuneA named list with the tuning values of the free parameters. Used as tune in MCMCmetrop1R.

A hzar.fitRequest object. A list with values:

`$modelParam`	modelParameters from above.
`$cM`	covMatrix from above.
`$llFunc`	clineLLfunc from above.
`$mcmcParam`	mcmcParameters from above.
`$mcmcRaw`	mcmcRaw from above.

and with attributes:

`"fit.run"`	fit.run from above.
`"fit.success"`	fit.success from above.

Although modelParameters only needs to contain $init and $tune, modelParam will sometimes contain $fixed, $lower and $upper. These are artifacts of hzar.make.clineLLfunc.old.ML and can be safely ignored.

Graham Derryberry asterion@alum.mit.edu

hzar.first.fitRequest.old.ML hzar.next.fitRequest hzar.cov.mcmc hzar.cov.rect hzar.make.clineLLfunc.old.ML hzar.make.clineLLfunc.old.bayes hzar.make.LLfunc.null hzar.make.mcmcParam MCMCmetrop1R