plot_indicators | R Documentation |
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.
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.
get_indicators
# 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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