getCommunitySlope.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/summary_methods.R
\name{getCommunitySlope}
\alias{getCommunitySlope}
\title{Calculate the slope of the community abundance}
\usage{
getCommunitySlope(sim, species = NULL, biomass = TRUE, ...)
}
\arguments{
\item{sim}{A \linkS4class{MizerSim} object}

\item{species}{The species to be selected. Optional. By default all target
species are selected. A vector of species names, or a
numeric vector with the species indices, or a logical vector indicating for
each species whether it is to be selected (TRUE) or not.}

\item{biomass}{Boolean. If TRUE (default), the abundance is based on biomass,
if FALSE the abundance is based on numbers.}

\item{...}{
  Arguments passed on to \code{\link[=get_size_range_array]{get_size_range_array}}
  \describe{
    \item{\code{min_w}}{Smallest weight in size range. Defaults to smallest weight in
the model.}
    \item{\code{max_w}}{Largest weight in size range. Defaults to largest weight in the
model.}
    \item{\code{min_l}}{Smallest length in size range. If supplied, this takes
precedence over \code{min_w}.}
    \item{\code{max_l}}{Largest length in size range. If supplied, this takes precedence
over \code{max_w}.}
  }}
}
\value{
A data.frame with four columns: time step, slope, intercept and the
coefficient of determination R^2.
}
\description{
Calculates the slope of the community abundance through time by performing a
linear regression on the logged total numerical abundance at weight and
logged weights (natural logs, not log to base 10, are used). You can specify
minimum and maximum weight or length range for the species. Lengths take
precedence over weights (i.e. if both min_l and min_w are supplied, only
min_l will be used). You can also specify the species to be used in the
calculation.
}
\examples{
# Slope based on biomass, using all species and sizes
slope_biomass <- getCommunitySlope(NS_sim)
slope_biomass[1, ] # in 1976
slope_biomass[idxFinalT(NS_sim), ] # in 2010

# Slope based on numbers, using all species and sizes
slope_numbers <- getCommunitySlope(NS_sim, biomass = FALSE)
slope_numbers[1, ] # in 1976

# Slope based on biomass, using all species and sizes between 10g and 1000g
slope_biomass <- getCommunitySlope(NS_sim, min_w = 10, max_w = 1000)
slope_biomass[1, ] # in 1976

# Slope based on biomass, using only demersal species and 
# sizes between 10g and 1000g
dem_species <- c("Dab","Whiting", "Sole", "Gurnard", "Plaice",
                 "Haddock", "Cod", "Saithe")
slope_biomass <- getCommunitySlope(NS_sim, species = dem_species, 
                                   min_w = 10, max_w = 1000)
slope_biomass[1, ] # in 1976
}
\seealso{
Other functions for calculating indicators: 
\code{\link{getMeanMaxWeight}()},
\code{\link{getMeanWeight}()},
\code{\link{getProportionOfLargeFish}()}
}
\concept{functions for calculating indicators}
\concept{summary_function}