Description Usage Arguments Value See Also Examples

Plots Mean Maximum Length (MML), the Large Fish Indicator (LFI), Typical Length (TyL) and the Length Quantiles (LQ) of the whole community or a subset of the species.

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plot_indicators(inputs, outputs, ...)
## S4 method for signature 'LeMans_param,LeMans_outputs'
plot_indicators(inputs, outputs, species, time_steps, prob, length_LFI, ...)
## S4 method for signature 'LeMans_param,missing'
plot_indicators(inputs, N, species, time_steps, prob, length_LFI, ...)
## S4 method for signature 'missing,LeMans_outputs'
plot_indicators(
wgt,
mid,
l_bound,
u_bound,
Linf,
species,
outputs,
time_steps,
species_names = NULL,
prob,
length_LFI,
...
)
## S4 method for signature 'missing,missing'
plot_indicators(
wgt,
mid,
l_bound,
u_bound,
Linf,
N,
species,
time_steps,
species_names = NULL,
prob,
length_LFI,
MML,
TyL,
LFI,
LQ,
units = "cm",
...
)
plot_LFI(inputs, outputs, ...)
## S4 method for signature 'LeMans_param,LeMans_outputs'
plot_LFI(
inputs,
outputs,
species,
time_steps,
species_names,
length_LFI,
LFI,
...
)
## S4 method for signature 'LeMans_param,missing'
plot_LFI(inputs, N, species, time_steps, species_names, length_LFI, LFI, ...)
## S4 method for signature 'missing,LeMans_outputs'
plot_LFI(
wgt,
l_bound,
u_bound,
outputs,
species,
time_steps,
species_names,
length_LFI,
LFI,
...
)
## S4 method for signature 'missing,missing'
plot_LFI(
wgt,
l_bound,
u_bound,
N,
species,
time_steps,
species_names,
length_LFI,
LFI,
units = "cm",
...
)
plot_MML(inputs, outputs, ...)
## S4 method for signature 'LeMans_param,LeMans_outputs'
plot_MML(inputs, outputs, species, species_names, time_steps, MML, ...)
## S4 method for signature 'LeMans_param,missing'
plot_MML(inputs, N, species, time_steps, species_names, MML, ...)
## S4 method for signature 'missing,LeMans_outputs'
plot_MML(wgt, Linf, outputs, species, time_steps, species_names, MML, ...)
## S4 method for signature 'missing,missing'
plot_MML(
wgt,
Linf,
N,
species,
time_steps,
species_names,
MML,
units = "cm",
...
)
plot_TyL(inputs, outputs, ...)
## S4 method for signature 'LeMans_param,LeMans_outputs'
plot_TyL(inputs, outputs, species, time_steps, species_names, TyL, ...)
## S4 method for signature 'LeMans_param,missing'
plot_TyL(inputs, N, species, time_steps, species_names, TyL, ...)
## S4 method for signature 'missing,LeMans_outputs'
plot_TyL(wgt, mid, outputs, species, time_steps, species_names, TyL, ...)
## S4 method for signature 'missing,missing'
plot_TyL(
wgt,
mid,
N,
species,
time_steps,
species_names,
TyL,
units = "cm",
...
)
plot_LQ(inputs, outputs, ...)
## S4 method for signature 'LeMans_param,LeMans_outputs'
plot_LQ(inputs, outputs, species, time_steps, species_names, LQ, prob, ...)
## S4 method for signature 'LeMans_param,missing'
plot_LQ(inputs, N, species, species_names, time_steps, LQ, prob, ...)
## S4 method for signature 'missing,LeMans_outputs'
plot_LQ(
wgt,
u_bound,
outputs,
species,
time_steps,
species_names,
LQ,
prob,
...
)
## S4 method for signature 'missing,missing'
plot_LQ(
wgt,
u_bound,
N,
species,
time_steps,
species_names,
LQ,
prob,
units = "cm",
...
)
``` |

`inputs` |
A |

`outputs` |
A |

`...` |
Additional arguments. |

`species` |
A numeric value or vector or a character string or vector denoting the species to be used to calculate the indicators. This option is only required if |

`time_steps` |
A numeric vector denoting the time steps to be used to calculate and/or plot the indicators. The default is |

`prob` |
A numeric value or vector between 0 and 1 denoting the LQ(s) to be calculated. This option is only required if |

`length_LFI` |
A numeric value or vector representing the threshold(s) to be used to calculate the LFI. This option is only required if |

`N` |
An array with dimensions |

`wgt` |
A matrix with dimensions |

`mid` |
A numeric vector of length |

`l_bound` |
A numeric vector of length |

`u_bound` |
A numeric vector of length |

`Linf` |
A numeric vector of length |

`species_names` |
A character vector of length |

`MML` |
A numeric vector representing the outputs of the function |

`TyL` |
A numeric vector representing the outputs of the function |

`LFI` |
A numeric vector or matrix representing the outputs of the function |

`LQ` |
A numeric vector or matrix representing the outputs of the function |

`units` |
A character string denoting the units of length used in the model. The default is |

`plot_indicators`

returns a set of four line plots depicting changes in the MML, LFI, TyL and LQ(s) of the community (including only the selected species) over time.

`plot_LFI`

returns a line plot depicting the LFI of the community (including only the selected species) over time.

`plot_MML`

returns a line plot depicting the MML of the community (including only the selected species) over time.

`plot_TYL`

returns a line plot depicting the TyL of the community (including only the selected species) over time.

`plot_LQ`

returns a line plot depicting the LQ(s) of the community (including only the selected species) over time.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ```
# Set up and run the model
NS_params <- LeMansParam(NS_par, tau=NS_tau, eta=rep(0.25, 21), L50=NS_par$Lmat, other=1e12)
effort <- matrix(0.5, 10, dim(NS_params@Qs)[3])
model_run <- run_LeMans(NS_params, years=10, effort=effort)
# Calculate the indicators
tmp <- get_indicators(NS_params, model_run)
MML <- tmp$MML
LFI <- tmp$LFI
TyL <- tmp$TYL
LQ <- tmp$LQ
# Plot the indicators
plot_indicators(MML=MML, LFI=LFI, TyL=TyL, LQ=LQ)
# Plot the LFI
plot_LFI(LFI=LFI)
# Plot MML
plot_MML(MML=MML)
# Plot the TyL
plot_TyL(TyL=TyL)
# Plot the LQs
plot_LQ(LQ=LQ)
``` |

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