datalowSA | R Documentation |
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.
generates three estimates of central tendency
generates constant catch projections after running cMSY
runs the checks on SRA to find success and failure
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
generates an MSY estimate from catches and F estimates
The main function for conducting a modified Catch-MSY analysis.
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
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
summaries the results from the Catch-MSY analysis by generating the mean, minimum, maximum, and quantiles of the resulting r, K, and MSY values.
gets the columns of data required for Tier5, the input data.frame must contain at least year and catch, but can also contain species
extracts the plausible biomass trajectories from the output of cMSY
halves the height of a tall narrow data.frame
converts the biomass trajetories into a depletion matrix
summaries results from the Catch-MSY analysis
A brief description of all functions in datalowSA
makes tables of msy, r, K, meanr, meanK, and all picks
generates a Tier5 formatted dataset from a tier4 dataset
generates a listing of which species are in the tier4 data
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.
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.
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
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
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
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.
A dataset containing 9 columns of typical scalefish fisheries data
To learn more about datalowSA, start with the vignette:
browseVignettes(package = "datalowSA")
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