MizerParams-class.Rd

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% Please edit documentation in R/MizerParams-class.R
\docType{class}
\name{MizerParams-class}
\alias{MizerParams-class}
\title{A class to hold the parameters for a size based model.}
\description{
Although it is possible to build a \code{MizerParams} object by hand it is
not recommended and several constructors are available. Dynamic simulations
are performed using \code{\link[=project]{project()}} function on objects of this class. As a
user you should never need to access the slots inside a \code{MizerParams} object
directly.
}
\details{
The \linkS4class{MizerParams} class is fairly complex with a large number of
slots, many of which are multidimensional arrays. The dimensions of these
arrays is strictly enforced so that \code{MizerParams} objects are consistent
in terms of number of species and number of size classes.

The \code{MizerParams} class does not hold any dynamic information, e.g.
abundances or harvest effort through time. These are held in
\linkS4class{MizerSim} objects.
}
\section{Slots}{

\describe{
\item{\code{metadata}}{A list with metadata information. See \code{\link[=setMetadata]{setMetadata()}}.}

\item{\code{mizer_version}}{The package version of mizer (as returned by
\code{packageVersion("mizer")}) that created or upgraded the model.}

\item{\code{extensions}}{A named vector of strings where each name is the name of
and extension package needed to run the model and each value is a string
giving the information that the remotes package needs to install the
correct version of the extension package, see https://remotes.r-lib.org/.}

\item{\code{time_created}}{A POSIXct date-time object with the creation time.}

\item{\code{time_modified}}{A POSIXct date-time object with the last modified time.}

\item{\code{w}}{The size grid for the fish part of the spectrum. An increasing
vector of weights (in grams) running from the smallest egg size to the
largest maximum size.}

\item{\code{dw}}{The widths (in grams) of the size bins}

\item{\code{w_full}}{The size grid for the full size range including the resource
spectrum. An increasing vector of weights (in grams) running from the
smallest resource size to the largest maximum size of fish. The
last entries of the vector have to be equal to the content of the w slot.}

\item{\code{dw_full}}{The width of the size bins for the full spectrum. The last
entries have to be equal to the content of the dw slot.}

\item{\code{w_min_idx}}{A vector holding the index of the weight of the egg size
of each species}

\item{\code{maturity}}{An array (species x size) that holds the proportion of
individuals of each species at size that are mature. This enters in the
calculation of the spawning stock biomass with \code{\link[=getSSB]{getSSB()}}. Set
with \code{\link[=setReproduction]{setReproduction()}}.}

\item{\code{psi}}{An array (species x size) that holds the allocation to reproduction
for each species at size, \eqn{\psi_i(w)}. Changed with
\code{\link[=setReproduction]{setReproduction()}}.}

\item{\code{intake_max}}{An array (species x size) that holds the maximum intake for
each species at size. Changed with \code{\link[=setMaxIntakeRate]{setMaxIntakeRate()}}.}

\item{\code{search_vol}}{An array (species x size) that holds the search volume for
each species at size. Changed with \code{\link[=setSearchVolume]{setSearchVolume()}}.}

\item{\code{metab}}{An array (species x size) that holds the metabolism
for each species at size. Changed with \code{\link[=setMetabolicRate]{setMetabolicRate()}}.}

\item{\code{mu_b}}{An array (species x size) that holds the external mortality rate
\eqn{\mu_{ext.i}(w)}. Changed with \code{\link[=setExtMort]{setExtMort()}}.}

\item{\code{ext_encounter}}{An array (species x size) that holds the external encounter rate
\eqn{E_{ext.i}(w)}. Changed with \code{\link[=setExtEncounter]{setExtEncounter()}}.}

\item{\code{pred_kernel}}{An array (species x predator size x prey size) that holds
the predation coefficient of each predator at size on each prey size. If
this is NA then the following two slots will be used. Changed with
\code{\link[=setPredKernel]{setPredKernel()}}.}

\item{\code{ft_pred_kernel_e}}{An array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the encounter rate integral. If this is NA
then the \code{pred_kernel} will be used to calculate the available
energy integral. Changed with \code{\link[=setPredKernel]{setPredKernel()}}.}

\item{\code{ft_pred_kernel_p}}{An array (species x log of predator/prey size ratio)
that holds the Fourier transform of the feeding kernel in a form
appropriate for evaluating the predation mortality integral. If this is NA
then the \code{pred_kernel} will be used to calculate the integral.
Changed with \code{\link[=setPredKernel]{setPredKernel()}}.}

\item{\code{rr_pp}}{A vector the same length as the w_full slot. The size specific
growth rate of the resource spectrum.}

\item{\code{cc_pp}}{A vector the same length as the w_full slot. The size specific
carrying capacity of the resource spectrum.}

\item{\code{resource_dynamics}}{Name of the function for projecting the resource
abundance density by one timestep.}

\item{\code{other_dynamics}}{A named list of functions for projecting the
values of other dynamical components of the ecosystem that may be modelled
by a mizer extensions you have installed. The names of the list entries
are the names of those components.}

\item{\code{other_encounter}}{A named list of functions for calculating the
contribution to the encounter rate from each other dynamical component.}

\item{\code{other_mort}}{A named list of functions for calculating the
contribution to the mortality rate from each other dynamical components.}

\item{\code{other_params}}{A list containing the parameters needed by any mizer
extensions you may have installed to model other dynamical components of
the ecosystem.}

\item{\code{rates_funcs}}{A named list with the names of the functions that should be
used to calculate the rates needed by \code{project()}. By default this will be
set to the names of the built-in rate functions.}

\item{\code{sc}}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
The community abundance of the scaling community}

\item{\code{species_params}}{A data.frame to hold the species specific parameters.
See \code{\link[=species_params]{species_params()}} for details.}

\item{\code{given_species_params}}{A data.frame to hold the species parameters that
were given explicitly rather than obtained by default calculations.}

\item{\code{gear_params}}{Data frame with parameters for gear selectivity. See
\code{\link[=setFishing]{setFishing()}} for details.}

\item{\code{interaction}}{The species specific interaction matrix, \eqn{\theta_{ij}}.
Changed with \code{\link[=setInteraction]{setInteraction()}}.}

\item{\code{selectivity}}{An array (gear x species x w) that holds the selectivity of
each gear for species and size, \eqn{S_{g,i,w}}. Changed with
\code{\link[=setFishing]{setFishing()}}.}

\item{\code{catchability}}{An array (gear x species) that holds the catchability of
each species by each gear, \eqn{Q_{g,i}}. Changed with
\code{\link[=setFishing]{setFishing()}}.}

\item{\code{initial_effort}}{A vector containing the initial fishing effort for each
gear. Changed with \code{\link[=setFishing]{setFishing()}}.}

\item{\code{initial_n}}{An array (species x size) that holds the initial abundance of
each species at each weight.}

\item{\code{initial_n_pp}}{A vector the same length as the w_full slot that describes
the initial resource abundance at each weight.}

\item{\code{initial_n_other}}{A list with the initial abundances of all other
ecosystem components. Has length zero if there are no other components.}

\item{\code{resource_params}}{List with parameters for resource.}

\item{\code{A}}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
Abundance multipliers.}

\item{\code{linecolour}}{A named vector of colour values, named by species.
Used to give consistent colours in plots.}

\item{\code{linetype}}{A named vector of linetypes, named by species.
Used to give consistent line types in plots.}

\item{\code{ft_mask}}{An array (species x w_full) with zeros for weights larger than
the maximum weight of each species. Used to efficiently minimize
wrap-around errors in Fourier transform calculations.}
}}

\seealso{
\code{\link[=project]{project()}} \code{\link[=MizerSim]{MizerSim()}}
\code{\link[=emptyParams]{emptyParams()}} \code{\link[=newMultispeciesParams]{newMultispeciesParams()}}
\code{\link[=newCommunityParams]{newCommunityParams()}}
\code{\link[=newTraitParams]{newTraitParams()}}
}