One directory corresponds to a single stock, which in turn has the following directory structure ./Stock/cfg Assessment configuration options ./Stock/data Input data (in Lowestoft VPA format) used by the stock assessments ./Stock/res Output data (graphs, tables) produced by the stock assessment. Not stored in repository
In addition, the "_Common" folder contains all of the shared modules, including the appropriate R packages ./_Common Source folder for common code module and associated scripts ./_Common/Pkgs Source folder for appropriate R packages The script "UpdatePackages.r" in the ./_Common/Pkgs folder can be used to bring all of the required packages up to date systematically.
The file "./_Common/HAWG Common assessment module.r" provides a common and standardised set of code for generating the outputs for a "standard" HAWG stock assessment. To take advantage of this code, the user should first source the module into their code eg source(file.path("..","_Common","HAWG Common assessment module.r"))
This script has two roles: it checks that the user has the correct version of the required packages installed, and it then provides the user with access to the common functions, detailed below. The user can then proceed with their stock assessment in the normal manner, and, when appropriate, call these functions to produce the standard set of graphs of tables. The user is then free to continue after this point, and perform extra analysises, including short term forecasts and the like.
For an example of this in action, see "WBSS Assessment.r"
All code is designed to be run with the ./Stock/ directory as the working directory. Changes from this will cause code to break - I wish there was a nice way around this, but there isn't really, unfortunately. All paths should be setup relative to this directory.
do.summary.plots(stck,ica.obj) Generates the standard set of summary plots and diagnostic figures Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc ica.obj FLICA Output of an FLICA stock assessment
do.retrospective.plots(stck,idxs,ctrl,n.retro.yrs) Performs a classic retrospective analysis and sends the results to retro.plots() for plotting. Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc idxs FLIndices Contains the tuning indices ctrl FLICA.control Contains the FLICA assessment setting parameters n.retro.yrs integer Number of years for which to perform the retrospective analysis
retro.plots(stck,idxs,ctrl) Plots the results of a retrospective analysis, showing retrospective results of SSB, Fbar and Recruits, the perception of individual cohorts, and the retrospective perception of individual age groups Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc idxs FLIndices Contains the tuning indices ctrl FLICA.control Contains the FLICA assessment setting parameters
do.SRR.plot(stck) Plots a basic stock-recrutiment relationship by joing the dots for sequential years, and labelling each point with the corresponding year Argument Class Description stck FLStock Result of an assessment, containing stock.n etc
catch.coh(stck) Plots the proportion of a cohort in the catch as a stacked line plot Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc
stacked.age.plot(stck,"slot") Plots the proportion of any slot with age-groups of a stock as a stacked line plot Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc "slot" slot refers to the exact slot you want to use of the stck object
stacked.age.plot(idxs,"index") Plots the propotion of the age-groups in the tuning index as a stacked line plot Argument Class Description idxs FLIndices Contains the tuning indices "index" slot refers to the exact slot you want to use of the idxs object
Plots the ratio between mature and inmature biomass of a stock
Argument Class Description
stck FLStock Contains the information about the stock eg m, catch numbers etcPlots the indices per yearclass versus each other
Argument Class Description
idxs FLIndices Contains the tuning indices
"index" slot refers to the exact slot you want to use of the idxs objectPlots the weight at age in the catch connecting similar ages over the years
Argument Class Description
stck FLStock Contains the information about the stock eg m, catch numbers etc
start integer Year of start of timeseries
end integer Year of end of timeseriescatch.curves(stck,start,end) Plots the log catch ratios in 3 different ways Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc start integer Year of start of timeseries end integer Year of end of timeseries
ref.pts(stck,model,factor) Plots the yield-recruit curves including reference points, and fits a SR-model Argument Class Description stck FLStock Contains the information about the stock eg m, catch numbers etc model character SR-model you want to use factor integer transformation value to reduce size of stock numbers to be able to fit SR
cor.tun(idxs) Plots the correlation within indices Argument Class Description idxs FLIndices Contains the tuning indices
The common assessment module does not specify the type of output format - this is left up to the user to decide. If no device is configured, all of the graphs will be displayed in the graphics window. If the user wishes to save the graphs, eg to windows metafiles, png or PDF, they should configure the output device before sourcing the common module, and close it afterwards. Note that use of the stockassessment.org website requires the generation of png files eg
png("figures - %02d.png",units = "px", pointsize = 10, bg = "white")