datalowSA: datalowSA a set of functions to assist with data-poor...

In haddonm/datalowSA: A Package to Faciliate Application of Data poor Stock Assessments

datalowSA a set of functions to assist with data-poor assessments

Description

The datalowSA package provides three categories of functions analytical functions that enable the production of data-poor model-assisted stock assessments, utility functions that assist with data manipulation and extracting informaiton from output objects, and plotting functions that facilitate the illustration of the results of the assessments. In addition there are example data sets with which to illustrate the methods.

Analytical functions

central

generates three estimates of central tendency

doproject

generates constant catch projections after running cMSY

fillell

runs the checks on SRA to find success and failure

fillell2

runs the checks on SRA to find success and failure, but but adds the criteria that the end depletion must be lower than the start

Level4MSY

generates an MSY estimate from catches and F estimates

run_cMSY

The main function for conducting a modified Catch-MSY analysis.

sraMSY

Is called by run_cMSY and it calls oneSRA for as many iterations or replicates as entered. It produces large arrays of the biomass trajectories from each SRA along with whether or not each trajectory meets the acceptance criteria or not. Not exported but can be read using r4tier5:::sraMSY

oneSRA

Is called by sraMSY. It takes in the vector of initial biomass depletions plus the randomly generated set of population model parameters and runs the SRA for each of the combinations of parameters and initial depletion levels. Not exported but can be read using r4tier5:::oneSRA

pulloutStats

summaries the results from the Catch-MSY analysis by generating the mean, minimum, maximum, and quantiles of the resulting r, K, and MSY values.

Utility functions

gettier5data

gets the columns of data required for Tier5, the input data.frame must contain at least year and catch, but can also contain species

gettraject

extracts the plausible biomass trajectories from the output of cMSY

halftable

halves the height of a tall narrow data.frame

makedeplet

converts the biomass trajetories into a depletion matrix

pulloutStats

summaries results from the Catch-MSY analysis

datalowSA

A brief description of all functions in datalowSA

summarycMSY

makes tables of msy, r, K, meanr, meanK, and all picks

tier4to5

generates a Tier5 formatted dataset from a tier4 dataset

whichsps

generates a listing of which species are in the tier4 data

Plotting functions

plotMSY6

generates 6 graphs illustrating the array of rK parameter combinations and whether they were successful or not. That plot is coloured by how many trajectories across the initial depletion range were successful.

plottrajectory

plots out the predicted biomass trajectories from those parameter combinations that have been accepted. It can either put all trajectories on one plot or generate a separate plot for each rK parameter set. Each individual biomass trajectory represents a set of population model parameters and a single initial depletion. It is possible to only print a specified number of parameter sets rather than all of them.

Data sets

fishdat

A dataset containing the fish data.frame, the glb list, and the props data.frame set up ready for use with datalowSA. In particular it can be used with fitASPM, fitSPM, run_cMSY, and DBSRA. see ?fishdat

dataspm

A dataset containing the fish data.frame, the glb list, and the props data.frame set up ready for use with datalowSA. In particular it can be used with the SPM functions, as well as the ASPM functions. see ?dataspm

invert

A dataset containing the fish data.frame as a 31 x 7 matrix, the glb and props data.frames are set to NULL. The fish data.frame has both the standardized cpue as well as the unstandardized geom, that is the geometric mean cpue. This is particularly set up to be used with the SPM functions but also the Catch-MSY routines. see ?invert

plaice

A dataset containing the fish, glb, props, agedata, and lendata for North sea plaice. Data taken from Beverton and Holt (1957). The primary use of this data set is to illustrate the use of catch curves.

sps

A dataset containing 9 columns of typical scalefish fisheries data

Vignettes

To learn more about datalowSA, start with the vignette: browseVignettes(package = "datalowSA")

haddonm/datalowSA documentation built on Nov. 5, 2023, 6:40 p.m.