get_annual_catch {LeMaRns} | R Documentation |
Get annual catch for each species, catch per unit effort or catch per gear
Description
Get annual catch for each species, the Catch Per Unit Effort (CPUE) or the Catch Per Gear (CPG)
Usage
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
)
Arguments
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 |
Value
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.
Examples
# 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)