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project.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/project.R
\name{project}
\alias{project}
\title{Project size spectrum forward in time}
\usage{
project(
object,
effort,
t_max = 100,
dt = 0.1,
t_save = 1,
t_start = 0,
initial_n,
initial_n_pp,
append = TRUE,
progress_bar = TRUE,
...
)
}
\arguments{
\item{object}{Either a \linkS4class{MizerParams} object or a
\linkS4class{MizerSim} object (which contains a \code{MizerParams} object).}
\item{effort}{The effort of each fishing gear through time. See notes below.}
\item{t_max}{The number of years the projection runs for. The default value
is 100. This argument is ignored if an array is used for the \code{effort}
argument. See notes below.}
\item{dt}{Time step of the solver. The default value is 0.1.}
\item{t_save}{The frequency with which the output is stored. The default
value is 1. This argument is ignored if an array is used for the \code{effort}
argument. See notes below.}
\item{t_start}{The the year of the start of the simulation. The simulation
will cover the period from \code{t_start} to \code{t_start + t_max}.
Defaults to 0. Ignored if an array is used for the \code{effort}
argument or a \code{MizerSim} for the \code{object} argument.}
\item{initial_n}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} The initial abundances of
species. Instead of using this argument you should set \code{initialN(params)}
to the desired value.}
\item{initial_n_pp}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} The initial abundances
of resource. Instead of using this argument you should set
\code{initialNResource(params)} to the desired value.}
\item{append}{A boolean that determines whether the new simulation results
are appended to the previous ones. Only relevant if \code{object} is a
\code{MizerSim} object. Default = TRUE.}
\item{progress_bar}{Either a boolean value to determine whether a progress
bar should be shown in the console, or a shiny Progress object to implement
a progress bar in a shiny app.}
\item{...}{Other arguments will be passed to rate functions.}
}
\value{
An object of class \linkS4class{MizerSim}.
}
\description{
Runs the size spectrum model simulation.
The function returns an object of type
\linkS4class{MizerSim} that can then be explored with a range of
\link{summary_functions}, \link{indicator_functions} and
\link{plotting_functions}.
}
\note{
The \code{effort} argument specifies the level of fishing effort during the
simulation. If it is not supplied, the initial effort stored in the params
object is used. The effort can be specified in four different ways:
\itemize{
\item A single numeric value. This specifies the effort of all fishing gears
which is constant through time (i.e. all the gears have the same constant
effort).
\item A named vector whose names match with existing gear names.
The values in the vector specify the constant fishing effort for those
fishing gears, i.e. the effort is constant through time. The
effort for gears that are not included in the effort vector is set to 0.
\item A numerical vector which has the same length as the number of fishing
gears. The values in the vector specify the
constant fishing effort of each of the fishing gears, with the ordering
assumed to be the same as in the MizerParams object.
\item A numerical array with dimensions time x gear. This specifies the
fishing effort of each gear at each time step. The first dimension, time,
must be named numerically and increasing. The second dimension of the array
must be named and the names must correspond to the gear names in the
\code{MizerParams} object. The value for the effort for a particular time
is used during the interval from that time to the next time in the array.
}
If effort is specified as an array then the smallest time in the array is
used as the initial time for the simulation. Otherwise the initial time is
set to the final time of the previous simulation if \code{object} is a
\code{MizerSim} object or to \code{t_start} otherwise. Also, if the effort is
an array then the \code{t_max} and \code{t_save} arguments are ignored and the
simulation times will be taken from the effort array.
If the \code{object} argument is of class \code{MizerSim} then the initial
values for the simulation are taken from the final values in the
\code{MizerSim} object and the corresponding arguments to this function will
be ignored.
}
\examples{
\donttest{
params <- NS_params
# With constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# With constant fishing effort which is different for each gear
effort <- c(Industrial = 0, Pelagic = 1, Beam = 0.5, Otter = 0.5)
sim <- project(params, t_max = 20, effort = effort)
# With fishing effort that varies through time for each gear
gear_names <- c("Industrial","Pelagic","Beam","Otter")
times <- seq(from = 1, to = 10, by = 1)
effort_array <- array(NA, dim = c(length(times), length(gear_names)),
dimnames = list(time = times, gear = gear_names))
effort_array[,"Industrial"] <- 0.5
effort_array[,"Pelagic"] <- seq(from = 1, to = 2, length = length(times))
effort_array[,"Beam"] <- seq(from = 1, to = 0, length = length(times))
effort_array[,"Otter"] <- seq(from = 1, to = 0.5, length = length(times))
sim <- project(params, effort = effort_array)
}
}