create_survey_diet: Create survey diet observations from Atlantis output

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Create survey diet observations from Atlantis output

Description

Create survey diet observations from Atlantis output

Usage

create_survey_diet(dat, time, species, boxes, effic, selex)

Arguments

dat	A data.frame of numbers at age containing the following columns: species agecl polygon layer time atoutput The data.frame is generated from either create_survey or create_fishery_subset.
time	The timing of the survey (a vector indicating specific time steps, which are typically associated with years) i.e., seq(365,10*3650,365) would be an annual survey for 10 years
species	The predator species to sample in the survey (a vector)
boxes	A matrix with two columns: 1) polygon: box ID's that are sampled 2) survArea: area sampled in that box
effic	Efficiency for each species: a matrix with nrow=length(species). Columns: species: the species name. Matches names in species efficiency:
selex	Selectivity at age. A dataframe defining selectivity at age for each species. Columns are: species: the species name. Matches names in species agecl: the age class that selectivity represents selex: the proportion selected relative to fully selected age classes (between 0 and 1)
spex	The specifications of Atlantis model (box-specific area, habitat, etc.) for now, from load_boxarea a dataframe with polygon and area column names

Details

The function takes consumption-at-age data from an Atlantis scenario where the data was read in from Atlantis output using load_detailed_diet_comp. One does not need to use these functions to create dat, rather you must only ensure that the structure of dat is the same. Currently, the function subsets the data by polygon and time, and sums over layers. An efficiency (effic) parameter is applied that determines that proportion of fully selected fish that are captured by the survey, then selectivity-at-age is applied. This function works for specific defined species, specific defined polygons, and specific defined time.

Value

Returns a matrix similar to the input matrix, with atoutput tons of prey consumed columns: species, agecl, polygon, layer, time, atoutput –will sum over layers, but enter NA as layer to indicate all layers

Author(s)

Poseidon

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.