get_annual_catch | R Documentation |
Get annual catch for each species, the Catch Per Unit Effort (CPUE) or the Catch Per Gear (CPG)
get_annual_catch(inputs, outputs, ...) ## S4 method for signature 'missing,missing' get_annual_catch( Catch, years = (dim(Catch)[3] + (inc_first - 1)) * phi_min, phi_min = 0.1, inc_first = FALSE ) ## S4 method for signature 'LeMans_param,missing' get_annual_catch( inputs, Catch, years = (dim(Catch)[3] + (inc_first - 1)) * inputs@phi_min, inc_first = FALSE ) ## S4 method for signature 'LeMans_param,LeMans_outputs' get_annual_catch( inputs, outputs, years = (dim(outputs@Catch)[3] + (inc_first - 1)) * inputs@phi_min, inc_first = FALSE ) ## S4 method for signature 'missing,LeMans_outputs' get_annual_catch( outputs, years = (dim(outputs@Catch)[3] + (inc_first - 1)) * phi_min, phi_min = 0.1, inc_first = FALSE ) get_CPUE(inputs, outputs, ...) ## S4 method for signature 'LeMans_param,LeMans_outputs' get_CPUE(inputs, outputs, effort, years = nrow(effort), inc_first = FALSE) ## S4 method for signature 'LeMans_param,missing' get_CPUE(inputs, Catch, effort, years = nrow(effort), inc_first = FALSE) ## S4 method for signature 'missing,LeMans_outputs' get_CPUE( outputs, Qs, effort, years = nrow(effort), phi_min = 0.1, inc_first = FALSE ) ## S4 method for signature 'missing,missing' get_CPUE( Catch, Qs, effort, years = nrow(effort), phi_min = 0.1, inc_first = FALSE ) get_CPG(inputs, outputs, ...) ## S4 method for signature 'LeMans_param,LeMans_outputs' get_CPG(inputs, outputs, effort, years = nrow(effort), inc_first = FALSE) ## S4 method for signature 'LeMans_param,missing' get_CPG(inputs, Catch, effort, years = nrow(effort), inc_first = FALSE) ## S4 method for signature 'missing,LeMans_outputs' get_CPG( outputs, Qs, effort, years = nrow(effort), phi_min = 0.1, inc_first = FALSE ) ## S4 method for signature 'missing,missing' get_CPG( Catch, Qs, effort, years = nrow(effort), phi_min = 0.1, inc_first = FALSE )
inputs |
A |
outputs |
A |
... |
Additional arguments. |
Catch |
An array with dimensions |
years |
A numeric value representing the number of years included in |
phi_min |
A numeric value representing the time step of the model. |
inc_first |
A logical statement indicating whether the first time step of |
effort |
A matrix with dimensions |
Qs |
An array of dimensions |
get_annual_catch
returns a matrix with dimensions years
and length(species)
where the i,j
th element represents the total catch (g) of the j
th species
in the i
th year.
get_CPUE
returns a matrix with dimensions tot_time
and nfish
where the i,j
th element represents the CPUE in the i
th time step for the j
th species.
get_CPG
returns an array with dimensions nfish
, dim(Qs[3])
and the number of time steps, where the i,j,k
th element denotes the total catch of the i
th species by the j
th gear in the k
th time step.
# 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) # Get annual catch get_annual_catch(inputs=NS_params, outputs=model_run) # Calculate the CPUE get_CPUE(inputs=NS_params, outputs=model_run, effort=effort) # Calculate Catch Per Gear (CPG) get_CPG(inputs=NS_params, outputs=model_run, effort=effort)
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