LimeSimulation class
LimeSimulation.Rdit generates two dataframes containing information about the estimated vs real catch as well as the estimated unfished vs fished population. It does not apply any depletion threshold for the unfished population.
Value
A list of dataframes with the expected catch and fished/unfished population
a dataframe with the real standarised relative real and standarised expected catch
a dataframe with the unfished and fished population
Public fields
catch_datalist of long and wide dataframes
mid_pointsvector of modelled lengths by LIME
agesinteger vector
estimated_catchestimated catch three-dimensional matrix
fished_populationestimated fished population matrix
fished_populationestimated fished population matrix
unfished_populationestimated unfished population matrix
Methods
Method new()
Initialise the class
Usage
LimeSimulation$new(
catch_data,
mid_points,
ages,
estimated_catch,
fished_population,
unfished_population
)Method run()
Generates the model fitting information (relative catch at length and relative fished and unfished population at age)
Method build_catch_df()
Builds a catch dataframe with the relative and expected catch. Both data are standarised (divided by their total sum)
Method build_population_df()
Builds a population dataframe with expected unfished and fished population. Both data are standarised (divided by their total sum). The expected values are relative to age rather than length.