Runs estimation of parameters for Reca models. Invokes eca.estimate
.
Arguments
- RecaData
RecaData
as returned fromPrepareRecaEstimate
- Nsamples
number of MCMC samples that will be made available for
eca.predict
. See documentation foreca.estimate
,- Burnin
number of MCMC samples run and discarded by
eca.estimate
before any samples are saved. See documentation foreca.estimate
.- Thin
controls how many iterations are run between each samples saved. Defaults to 0. This may be set to account for autocorrelation introduced by Metropolis-Hastings simulation. see documentation for
eca.estimate
- ResultDirectory
a directory where Reca may store temp-files
eca.estimate
andeca.predict
. See details.- Lgamodel
The length age relationship to use for length-age fits (options: "log-linear", "non-linear": Schnute-Richards model). See documentation for
eca.estimate
. Defaults to log-linear- Delta.age
see documentation for
eca.estimate
. Defaults to 0.001.- Seed
see documentation for
eca.estimate
. Defaults to random seed.- UseCachedData
if TRUE Parameterization is not run, but any previous runs for exactly the same arguments are returned.
Value
RecaParameterData
results from Reca Model Parameterization.
Details
eca.estimate
performs Markov-chain Monte Carlo (MCMC) simulations to determine maximum likelihood of parameters for the given samples.
This is computationally intensive and run time may be noticable. For a given model configuration running time is mainly determined by the parameters 'Nsample', 'Burnin' and 'Thin'.
Seed
If 'Seed' is not provided a random seed is chosen. This is stored in the returned data (RecaParameterData$GlobalVariables$Seed). This seed is passed to Reca, but not all versions of Reca has provided exact reproducability for a given seed, so the behaviour is dependent on the installed Reca-version.
Caching
The argument 'UseCachedData' allows previously computed parameterization to be returned in stead of parameterizing again. If no previous run is located in the 'ResultDirectory', or the arguments or data that are passed to Reca differs from the previous run, execution will halt with an error when 'UseCachedData'. In this respect it may also be useful to note a counter intuitive aspect of the argument 'Seed'. If 'Seed' was not provided for the previous run, the arguments will be considered equal if the seed is set to the value returned on the previous run (RecaParameterData$GlobalVariables$Seed).
ResultDirectory files:
Various report functions may use output of this function with the function eca.predict
which samples the posterior distributions of parameters.
Communication between eca.estimate
and eca.predict
is managed by writing and reading files,
and a directory for storing intermediate calculations must be provided with the parameter 'ResultDirectory'.
For multi-chain analysis, a different directory should be provided for each chain.
The result directory will be created if it does not exist.
Be aware that this breaks with the general design of StoX and somewhat limits the transferrability of StoX projects between computers.
See also
PrepareRecaEstimate
for model configuration, and data preparation for this function, and
RunRecaModels
for obtaining predictions / estimates from the Reca-models.