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GYM User's Manual - Australian Antarctic Division

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1. Graphing Options The graphing options will display the dataset graphically in either MathSoft Axum or MathSoft S Plus This can work on most Axum and S Plus versions after 4 0 There are currently two graphing options either a graph embedded into this application or a graph shown in software application Graph embedded inthis Selecting this option will bring up an Axum Choose Graph application and Plot window You need to select what type of graph you want Creating multiple graphs can be done by selecting to Add New Graph Another editing option includes double clicking on a graph to get access to the Axum S Plus Standard Editing Menus When you have finished editing these you need to press Escape There is also an option that allows you to clear all plots To Save or Print the graph using this option you need to use Object Linking Embedding OLE To do this you need to right click on the graph where upon a small box with two options appears This will allow you to Edit or to Open If you select Open it will put the graph into Axum S Plus where you can continue to edit the graph When you select Exit and return to the original application a Save prompt will appear Once you have selected to Save the graph it will update the original graph in the GYM application Graph shown in This option will start up Axum S Plus and a Choose Graph Application and Plot window will appear This option gives you full use of the standar
2. View form description see detailed help or Add For make notes Delete Row Edit Row Step 2 Set dates to monitor stock Step 3 Set dates to dd mm dd rari monitor fishable 1 iz 1 i biomass Spawning season from Spawning Form i i 7 fi 7 Use Defaults Clear Close Day Month Year Monitor all years in projection Monitoring fishable biomass Step 4 Save inputs The first calendar date entered into this form must be greater than or equal to the first day of year 0 as set above In addition the value entered must be between 1 and 31 inclusive The value entered must be between 1 and 12 inclusive The value entered must be equal to or between the initial year specified above and 2099 This option enables the stock to be monitored in every year on the same day specified in the first year Enter the calendar dates at the beginning and end of the period in which the fishable vulnerable biomass is monitored This 1s Important for the integration of CPUE into the assessment such that the period needs to coincide with the time for which the CPUE 1s standardised 57 Part 3 Using the GYM Generalised Yield Model GYM User s Manual General Output Details Form When the GYM simulation is complete all information is delivered in the form of outputs which are in turn saved in the selected database The General Output Details Form details all of the output types and
3. Age based selectivity Age Selectivity Relative Fishing effort Date Effort This is only available for years in the known catch series If turned off then the fields for entering the selectivity functions will be absent 1 e the fishery in that year had the same selectivity as the previous year When turned on new parameters for selectivity can be entered to be applied that year All aspects of these parameters are available It is advisable that this be turned on for the first year of the catch history and parameters be entered explicitly Otherwise the forward projection parameters will be applied in the early years of the catch history until the variation in selectivity is applied As for maturity the length based fishing selectivity can be incorporated by entering in the following parameters Uncertainty can be incorporated in this length based function by specifying a range of values for the length at which the fish are 50 recruited to the fishery Minimum of the range for length when 50 of that length are recruited to the fishery Maximum of the range for length when 50 of that length are recruited to the fishery Length range over which recruitment to the fishery increases from 0 to Age based fishing selectivity can also be incorporated by entering an array of ages and selectivity into the string grid The age must be in years The values entered for selectivity must be numeric To incorporate the sea
4. directory epi se ing se input 1 7 2003 3 51 contents Recruitment input 288 2003 2 4 1 Fisheries infor input 003 351 This section of the 1 Simulation ch input This section 1 Characteristic input P E main screen 17 Initial populati input displays the inputs Evaluation of i manages all of the baa enag a m and results forms Scenarios in a tree 1 Monitoring of input 162003 3 51 for the selected a 1 General outp input 1 7 2003 3 54 i d ire cto ry e Post processi post processing 1 7 2003 3 51 S cenario GY Root Directory The GY root directory connects the Directory and its components to the Database Folder A Folder can contain other Folders and or Scenarios and is used to differentiate between the different data levels in the directory Once a Folder has been created it can contain an unlimited number of Scenarios and additional Folders Instructions for initiating several key Folder actions follow Creating a New Folder A new folder can be created by e Right click the mouse e Selecting New Folder from the right pull down menu NOTE Any number of New Folders and new Scenarios can be created under one single folder Renaming A Folder can be renamed by e Right click the mouse e Select rename from the right pull down menu Alternatively you can also rename a Folder by e Clicking the mouse pausing then re clicking the mouse e Then use the standard wi
5. see de la Mare 1994 for full details of this method The two latter functions can include a stock recruitment relationship This form 1s divided into two tabs The Recruitment function tab contains the details of the known recruitment vector and the three functions above The left part of the tab 1s where the lognormal and proportional recruitment functions can be parameterised The right part of the tab is where the recruitment vector can be specified and whether it is to be used a time series Within the Survey Data tab you can incorporate a time series of surveys with estimates of abundance at age from each survey These are then used to generate the vector of recruitments and for estimating the parameters of the log normal recruitment function 42 Part 3 Using the GYM Generalised Yield Model GYM User s Manual ig Recruitment Step 1 Set the recruitment function used in the absence of estimate of recruitment in a given year A time View form seres of recruliments can be nominated Cae description see detailed help or Recruitment Function make notes Select recruitment function Use log normal distribution Update from Survey Data f Lise vector Use vector in unknown years Recruitment related to M Recruitment Parameters Recruitment Vector Mean recruitment Use Recruitment SEs in bootstrap a 5B0 for recruitment depletion m Log normal function Min coefficient of variation Max coefficient of variat
6. 01 ri cial at age input 1 6 2003 4 02 ae Gq Long lived 02 fl Maturity input 1 6 2003 4 04 aes Gig Lono lived 03 7 Spawning season input 17672003 4 05 Recruitment input 2162003 2 4 ri Fishenes information input 17672003 4 24 ad Simulation characteristics input 1 6 2003 4 10 ri Characteristics of a trial input 14722003 3 51 i Initial population structure input 2 16 2003 2 3 MA Evaluation of wield input Ve 22003 3 55 ii Estimating BO im gamma cal input Ve 22003 3 55 Monitoring of stack input 14722003125 ri General output details input 1722003 12 5 vi Post processing options post processing 162003 3 59 E Summary results 371272003 5 1 Results Percentile The Results Percentile form shows the percentiles used in the assessment against the CCAMLR decision rules Results Summary The Results Summary form shows the summary of results of the assessments relative to the CCAMLR decision rules and provides for a degree of flexibility in the application of those rules Results Biomass The Results Biomass form shows the general characteristics of the population from the PG file described below obtained for the Scenario and displayed in a grid format In addition these results can be viewed by test or by trial Results SBO Median The Results SBO Median form shows all of the SBO median results from the Scenario in a grid format In addition these results c
7. 2 5 shows the consequences of surveying the pre exploitation biomass at different times of the year to estimate By and the subsequent estimation of y above Clearly the peak in biomass at the end of summer illustrated in Figure 2 4 needs to be factored into the assessment procedure so that the same estimate of yield will arise from the assessment irrespective of when the survey is undertaken Thus some attention needs to be given during the setup process to ensure that all parameters are correctly aligned on the temporal scale 17 Part 2 Introduction to the GYM Generalised Yield Model GYM User s Manual Figure 2 5 Effect of time of the year on estimation of y for Antarctic krill projection year begins on 1 November 0 20 0 15 Gamma 0 10 0 05 0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 1 0 Fraction of Year 2 3 WHY USE THE GENERALISED YIELD MODEL The Generalised Yield Model provides a very flexible simulation environment for examining and assessing the importance of different biological and fishery parameters in governing the population dynamics of a stock It also provides a range of options for taking account of many of the uncertainties in the assessment process The outputs of the GYM are extensive and can be utilised from within the scenario manager or imported directly into your favoured data manipulation and statistical software 18 Part 2 Introduction to the GYM Generalised Yield Model GYM User s
8. A E 4 1 4 6 INSTALLATION OPTIONS suits iisa nnne a iia ia aaie i aaia 4 1 4 7 SYM POR DOS aoe E E 5 FOJE LE SAO opa 5 1 5 UPGRADING sir RS 5 1 6 LEARNING HOW TO USE GYM rcssconzeceavonatazacnninatenincntaedenctesedeagnenadencuaieceneseecednaseaaenenaeis 6 TUTORIAL A 1 OVERVIEW OF THE GYM USER INTERFACE occcoccccnccncccccnccoccncnocncno 6 TUTORIAL A 2 SEEING HOW GYM WORKS occoocccccocccococccoccccncconcconcnononcnononononononcnnnnnnos 6 PART 2 INTRODUCTION TO THE GENERALISED YIELD MODEL 8 2 1 WHAT IS THE GENERALISED YIELD MODEL cococcnccncnncncccncnccncnoccncnncnccnncnononononononos 8 2 2 OVERVIEW OF THE GENERALISED YIELD MODEL ooocccoccncnncnnnccncccncnccnncnononononanoss 8 2 2 1 Background and Rationale for the development of the GYM ooocccoccccccncccnccn 8 2 2 2 Developing the approach for Antarctic Krill ooccccocccccconncccnnncconncnononos 13 2 2 3 Applying the rules in krill asSSESSMON oocccooonccccnncccnncccnnnocnononnonanncnanonanonnnnnnos 14 2 2 4 Generalising this approach for other fish Species ccooocccccccnccccncccnnncconononanonnns 15 2 2 9 A population projection model cooocccocnccccnconcncnocnnnoncnnnnnonononanonncncnnrnnnncnnnnnnnos 16 2 3 WHY USE THE GENERALISED YIELD MODEL oocccoccccnnccncnccnnccccncccccncconononononcnonnss 18 PART 3 USING THE GENERALISED YIELD MODEL cccceccseeeeeeeeeeeeeeneees 20 3 1 INTRODUC HON sra iia 2
9. EE TEN Al TTT TT MIO IM MM MMM Spawning Biomass 40000 0 M1 1111 I 1999 2001 2003 2005 2007 2009 2011 2013 2015 2017 2019 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2020 Year Part 2 Introduction to the GYM 12 Generalised Yield Model GYM User s Manual 2 2 2 Developing the approach for Antarctic Krill Constable et al 2000 describe the development of the assessment method for Antarctic krill adopted by CCAMLR It was agreed that the general objectives for krill the most important prey species in the Antarctic would be e to keep krill biomass at a level higher than would be the case for single species harvesting considerations and in so doing to ensure sufficient escapement of krill to meet the reasonable requirements of predators e given that krill dynamics have a stochastic component to focus on the lowest biomass that might occur over a future period rather than on the average biomass at the end of that period as might be the case in a single species context and e to ensure that any reduction of food to predators which may arise out of krill harvesting is not such that land breeding predators with restricted foraging ranges are disproportionately affected compared with predators in pelagic habitats These concepts resulted in rules for deciding pr
10. Export Options e Graphing Options e Evaluation Options These methods transform the datasets into MathSoft Axum graphs grids tables MathSoft S Plus graphs and grids tables and Excel spreadsheets Once the data has been transformed further analysis can be conducted These options are beneficial as they allow the user to easily transform simulation results into useful forms within the GYM program or directly export the results to familiar software programs for further analysis Part 4 Specifications of the GYM 74 Specifications for the Generalised Yield Model GYM Preview and Export Options The preview and export options allow you to view the dataset in a grid format and also to export the dataset as a Comma Separated Value File that can be imported into a Microsoft Excel spreadsheet Grid Preview This option will display a grid containing all of the data selected from the datasets You are able to group the fields by selecting the column heading and dragging it to the blank space directly above the grid Export to a CSV File in This option will convert the dataset to a Coma Separated Excel Value File CSV File in Excel When you select this option a save as dialogue box will appear You need to follow the prompts and when the export has completed an Export Successful Box will appear This data will be converted into a format accessible by Excel Further analysis can then be conducted on the dataset within the Excel program
11. If strong year classes are present then the population may be able to support catches above the precautionary level for one or more years Consequently the use of long term annual yields may result in foregoing increased catches when the stock is abundant While no strategies for short term adjustments to catch limits have been evaluated as yet a procedure has been used in the interim to enable short term assessments of yield of mackerel icefish de la Mare et al 1998 This requires a recent survey of the status of the stock including its age structure and biomass followed by an assessment of yield based on the predator criterion The short term assessments provide estimates of catches over two years ahead that result in 75 of the stock escaping the fishery at the end Two years corresponds to the time a cohort remains in the fishery This approach can be incorporated into a scenario of the Generalised Yield Model 2 2 5 A population projection model The Generalised Yield Model is an age structured population model The basic demographic features of the model are illustrated in Figure 2 4 where the population age structure is combined with growth and maturity data to estimate the overall biomass of the population as well as the spawning stock The removal of catches from the population can be modelled in a number of ways including by fishing mortality constant catches over time or by specifying a time series of catches The amount of catch taken
12. Manual PART 3 USING THE GENERALISED YIELD MODEL 3 1 INTRODUCTION The GYM User Interface was designed for straightforward data entry and movement throughout the GYM program It allows users to enter inputs easily into files through forms control the simulation and analyse outputs within a familiar file management environment Part 3 describes each individual menu option file form and window component of the GYM User Interface e Menu and Options This section describes each Menu and their options e Structure of Inputs This section outlines the two methods available for data input into the model describing in detail the Parameter Input Forms associated with the user interface e Running the Simulation This section outlines how to run a simulation and describes the options and forms that control the simulation e Controlling Outputs This section describes the results or outputs of the GYM simulation e Post Processing Analysis This section details the Post Processing Analysis options available within GYM 3 2 STRUCTURE OF MENUS AND OPTIONS In addition to displaying the directory structure the GYM main screen provides access to the four key menus and the additional features within right click menus Table 1 Table 1 List of Menus and Addition Features of the GYM User interface The GYM Directory This directory accommodates the folders and scenarios The File Menu The File Menu controls the import and export
13. Structure or Biomass Input the calendar date day and month to which the known age structure and or biomass relate Biomass to scale This is the biomass to which the age structure needs to be scaled If no scaling is required then set this to zero CV for scale If the CV is greater than zero then the biomass for scaling the age structure will be sampled from a log normal distribution Data Grid for known age structure Insert the age abundance and CV of the age structure The abundance at age will be determined from a log normal distribution if the CV is greater than zero 54 Part 3 Using the GYM Generalised Yield Model GYM User s Manual Evaluation of Yield Form In a single test the model can project the stock forward using three different options These options involve evaluating the yield by setting a constant value for each year of the future projection period where those values could be e Catches a constant catch e Gammas a constant catch determined as a proportion of the estimate of total biomass in the year prior to exploitation e Fishing Mortalities a constant annual F Once the type has been selected the values that are to be tested are put into an array fai Evaluation of yield Step 1 View form description see TI Enter the type of evaluation as catches gammas or fishing detailed help or make mortalities and values to be tested as constant values over projection period T
14. Windows NT 16 mb RAM Pentium 233 256 colours Netscape Navigator Internet Explorer is also recommended for full functionality of on line Help and for access to the web based Tutorials in development The following is the recommended minimum for installation o Windows NT4 98 2000 or later o 128Mb RAM o Pentium HI 1GHz or AMD equivalent Part 1 Getting Started Generalised Yield Model GYM User s Manual and Specifications 1 4 1 GYM WITH GRAPHIC USER INTERFACE recommended When using the GYM in conjunction with the graphical user interface Scenario Manager for the first time it is important to ensure that all associated files are correctly in place The scenario manager requires a number of run time files that provide grid functionality etc For this reason the first time you install GYM you install from CD ROM or download the full installation executable from the internet The installation software is capable of installing version 501 and later versions of the scenario manager the required simulator kernel and the documentation Installation can be performed from either CD ROM or downloading from the internet The installation program on the CD ROM setup exe includes all of the required run time dependencies The AAD internet site permits download of the same installation software as on the CD ROM 1 4 2 DATABASE RUN TIME REQUIREMENTS The scenario manager utilises an Access database for storing scenario parame
15. button Edit Row Editing the row allows you to input data or to change the data currently in a particular row in the string grid Information and Help The top panel of each Parameter Input Form contains all Options information and help details lg Scenario base information Descriptor This form displays the key identifying details of the Scenario and enables users to enter any additional details Descriptor A brief description of the function of the Parameter Input Form is contained in an open window Help Additional Help material is stored in the Help Icon This can be located by selecting the Help Icon on the right hand side of the top panel Notes Users can enter and store their own notes in the Note window This can be located by selecting the Note Icon on the right hand side of the top panel 30 Part 3 Using the GYM Generalised Yield Model GYM User s Manual 3 3 STRUCTURE OF INPUTS Data can be entered into the GYM using two methods Firstly the user interface has been designed to permit direct data entry into boxes within the Parameter Input Forms of a Scenario The second method involves entering data in the form of text Input Files or modifying existing text Input Files It should be noted that GYM was originally designed for use without a user interface but since 2000 a comprehensive user interface has been developed and continually updated The present GYM user interface is designed to hide struct
16. class formulation in order to minimise bias in the size Of the plus class in the initial population fg Age structure Step 1 View form This form controls the age structure of the stock at years description see detailed help or make notes First age class in stock Step 2 Enter ages years Last age class in stock Oldest age in last class Use Defaults Clear Step 3 Save inputs ar First age class in stock This is the first age for recruitment in the simulation The unit used in the model for this parameter is Year therefore only a whole number can be entered into the field Values entered must be greater than or equal to 0 and less than or equal to 80 Last age class in stock The last age class in stock is the last age to be used in the projections year Values entered must be whole numbers and greater than or equal to 0 and less than or equal to 80 Oldest age in last class This is the age of the oldest fish to be used in setting up the plus class of the initial population structure Values entered must be whole numbers and greater than or equal to the last age class in stock and less than or equal to 80 How to initiate a Plus A plus class can be initiated by having the value for the class Oldest age in last class greater than the value for the Last age class in stock When present the plus class is a sum to infinity of numbers at each age greater than or equal to the La
17. dataset for viewing analysis 3 Selecting what software to view analyse dataset The GYM contains options for the dataset to be viewed or analysed as graphics tables or spreadsheets from within the program Specifications for the Generalised Yield Model GYM Step 1 1 Add Scenario im Post processing analysis Untitled X Bi gt j A o Y New Open Save Delete Add Sc Results Remowe Data Help Current analysis definition name Defining scenario results Date scenario execubed EEE rai ahy ih Leb ied xj Analysis or view esport iz to be performed using the following datasets from scenario exect 0 ih E umeni snakes definition name heining sceratio maur Chobe snare aeut lar TOP 423 Table 30 Thal 3 Gains Sho 14 1508 Cument seeria in anales definition Scenario settings in this arabis Step 1 2 View details ci diri Select results Wagi Moshe capone SEO ratos red ere Paicentde wargi sr Simulator outputs Piscantlss Flaw S20 median data Step 2 Set Add 8 scenaria s resuts Hom ihe ioafbar ta begin you CE constraints HARSIDIMAUVOR OR those resus Once you have selected the scenario s to use in analysis sel Preview and export options f Grid preview Comma Separated Value file Excel Graphing Options C MathSoft Axum MathSoft SPlus Step 3 Graph embedded in this application Select f Graph shown in Application viewing Ev
18. date The area of the survey in units consistent with the other surveys and the assessments e g km This value is the total observed density of fish in the survey 45 Part 3 Using the GYM Generalised Yield Model GYM User s Manual Total expected This value is the total expected density following the fitting density of mixture distributions to length density distributions If the observed and expected densities are unknown then these could each be set to 1 String grid Age Values to be entered must be greater than or equal to 0 Density Values to be entered must be greater than or equal to 0 SE Values to be entered must be greater than or equal to 0 Fisheries Information Form The GYM models the fishing mortality in the same way as natural mortality and maturity patterns The fishing patterns vulnerability and effort may vary through the course of a fishery Fishing vulnerability selectivity can be developed using a length based relationship an age based ogive or a combination of the two These patterns are kept constant during the future projection but can be varied each year through a period of known catches Multiple fisheries and years within the fisheries can be added to develop a comprehensive picture of the historical fishing mortality on the population The Fisheries Information Form provides for inputting the details of the known catch history and the vulnerability and fishing effort patterns for the fut
19. describes its functionality for fisheries stock assessments Part 3 Using the Generalised Yield Model Using the Generalised Yield Model describes what GYM can do how to use the User Interface of GYM including the purposes and use of all options menus forms and files that are encountered when using GYM This provides users an outline of the process for generating a fish stock harvesting strategy scenario Part 4 Specifications for the Generalised Yield Model The Specifications for the Generalised Yield Model provides the detail of the population model used in the projection program and outlines the methods the model uses for assessing key population parameters Part 5 Worked Examples of the Generalised Yield Model The Worked Examples section provides examples that illustrate how the Generalised Yield Model Version GYM501 works and the methods used show how to validate different aspects of the program 1 3 REGISTRATION To ensure that we provide you with quality software and continue to offer technical support please register yourself as an Australian Antarctic Division AAD Marine Eco Software User by filling out the registration form available on the AAD website http www aad gov au marine eco software The benefits of registering include updates on all GYM developments and dates for version releases 1 4 INSTALLATION In order to install and operate GYM the minimum computer configuration needs to be at least Windows 98 or
20. estimates to be incorporated Thus the simulation model is used to calculate a distribution of possible population sizes both in the absence of fishing and at various fishing mortalities These distributions are used to determine the proportion y of an estimate of the unexploited biomass By from a hydroacoustic survey that can be caught each year de la Mare 1996 Each of the many simulations starts with a biomass of krill which is divided into a number of age classes This biomass of krill is then estimated to give By by drawing from a statistical distribution that reflects the properties of the biomass survey estimates In each simulation year the biomass is recalculated by adding an amount for annual growth and deducting an amount corresponding to natural mortality The biomass of each year s recruits is added and the constant annual catch of yB is deducted Variability in the simulated population biomass in each year arises because the recruitment varies from one year to the next Annual recruitment is drawn from a statistical distribution that reproduces the statistical properties of the estimates of proportional recruitment obtained from the length compositions collected during krill surveys de la Mare 1994a 1994b The value for y 1s selected which gives a statistical distribution of the outcomes of all simulations that meet the criteria Fig 2 3 The model is run with y 0 1 e no catches to observe the distribution of unexpl
21. execution log Settings The settings window displays the locations of the data directory and three primary files Database File Kernel File Lookup Table Generator File used by GYM If the files are incorrectly identified the correct files can either be manually entered or by clicking on the button to the right you are able to browse for them Once each file has been selected then you 25 Part 3 Using the GYM Generalised Yield Model GYM User s Manual need to save the settings The Settings Window will also appear when you first start the program or if the directory or files can t be found These buttons allow you to w Settings browse within your hard drive for l the location of files Export Data Directory C Program Files Generalized Yield Model Database File Name Bla ela ete neralised Yield Model Gy501 mdb Kemel File Mame C Program Files Generalised Yield Model GYM5071 ex Reset Advanced Save Lancel Export data directory This is the location that input and output files will be sent If necessary this can be in a separate directory to where the program files are stored Database File Name This file is typically located in the directory the application was installed in and has a mdb extension Kernel File Name This is the main program and is typically named after the GY version Its extension is exe 3 2 5 THE HELP MENU Through the continuing processes of refining and s
22. first two criteria in the decision rule For example Patagonian toothfish as a large predator is unlikely to constitute much of the diet of seals and birds Therefore the species is considered in a single species context and the second criterion is applied at the 50 level rather than at the 75 level An unusual case is the mackerel icefish which is a prey species and therefore should have the predator criterion applied as for krill However it fails to meet the recruitment criterion even without fishing because of its high recruitment variability de la Mare et al 1998 and for stocks around South Georgia because of sporadic years with high natural mortality owing to predation by fur seals when krill abundance is low Agnew et al 1998 Modifications to the decision rules have been proposed to overcome this problem de la Mare et al 1998 Agnew et al 1998 In addition to reviewing the structure of the decision rule for each species the manner in which assessments are undertaken is contingent on the state of available knowledge and methodologies Assessing long term annual yields provides a means of incorporating many uncertainties in a single assessment so represents a precautionary approach In particular precautionary catch limits take account of the periods in which the stock has naturally fallen to a low level As they are based on a constant catch over a twenty thirty year period there is no need for annual reassessments
23. from individual cohorts at different times during the year can be controlled as well 16 Part 2 Introduction to the GYM Generalised Yield Model GYM User s Manual Figure 2 4 Population characteristics of Antarctic krill used in the Generalised Yield Model assessment of Krill in Area 48 following the CCAMLR 2000 acoustic survey SC CAMLR 2000 including projected numbers at age given a mean natural mortality rate of 0 8 yr top panel the von Bertalanffy growth curve with seasonal growth over summer panel 2 the conversion to weight from length at age approximate in this assessment panel 3 the average maturity and fishing selectivity ogives and the biomass at age given the numbers and weight at age bottom panel solid red line The spawning biomass at age 1s shown in the bottom panel as the dotted black line 1 0 Numbers 0 5 0 0 60 Length 30 mm ol 6 Weight 3 0 1 Maturity 0 1 Selectivity 0 Biomass 0 6 Cohort red Spawning black oe 0 2 0 0 0 1 2 3 4 5 6 T 8 An important part of setting up the Generalised Yield Model is to establish the timing of the different biological features such as growth and spawning Figure 2 4 illustrates how krill have a seasonal growth pattern The relationship between this pattern the seasonal pattern of fishing and natural mortality and the timing of recruitment will affect the relationship between estimates of biomass from surveys and estimates of yield Figure
24. is in reference to the status of the spawning biomass during a trial relative to the pre exploitation reference level either median spawning biomass or the spawning biomass in the year prior to the known catch series The depletion level say 0 2 is the status below which the stock is considered depleted and recruitment will be impaired Seed for random number Stochastic models require a random seed value to initiate the generator random number generator Specifying the seed gives the user control over the random number series The number set as the seed will initiate the random number generators path The default value is 24189 Reset seed to this number Selecting this option will mean that the seed value for each for each test test is the value entered in the above parameter As tests are affected by the starting value of the seed for the random number generator the use of the same seed will result in the random number sequence being the same in each test This enables the user to compare the effects of changes in parameters between tests 51 Part 3 Using the GYM Generalised Yield Model GYM User s Manual Characteristics of a Trial Form The Characteristics of a Trial Form sets the majority of the general characteristics that control the trial simulation and length of the projection The parameters incorporated on this form primarily focus on setting the initial spawning biomass attributes of the population There are two m
25. maturity at length is incorporated by specifying a range minimum maximum for length when 50 of that length are mature If there is no uncertainty then minimum maximum Minimum length Minimum of the range for length when 50 of that length 50 are mature are mature 40 Part 3 Using the GYM Generalised Yield Model GYM User s Manual Maximum length 50 are mature Range over which maturity occurs Age Based Age and Length Based Maximum of the range for length when 50 of that length are mature Length range over which maturity increases from 0 to 1 This option is used when the proportion of fish at age a that are mature is known or if maturity 1s age dependent Data is entered directly into the string grid under the columns age and the maturity where the latter is the proportion mature This option is a combination of the two previous options see Age based and Length based Spawning Season Form The status of the spawning stock in a given year is estimated from the average spawning biomass over the spawning season This requires the start and end times of the spawning season to be provided as calendar dates iyi Spawning season This form sets the spawning season of the stock using dates Date when spawning begins Date when spawning ends Step 1 View form description see detailed help or make notes day month Step 2 7 Enter in dates i E Step 3 Use Detaults C
26. of data and offers an exit point The Batch Menu The Batch Menu controls the execution of the scenarios by the model including selecting and adding scenarios to a batch to be run The View Menu The View Menu allows the user to consult the settings of the program view graphics of key demographic parameters of the population and perform post processing analysis The Help Menu The help menu provides advice for users when using GYM Additional Features All additional options and features of GYM are incorporated within this section including options from the mouse right click pull down menu 20 Part 3 Using the GYM Generalised Yield Model GYM User s Manual 3 2 1 THE GYM DIRECTORY The GYM directory offers a management directory that stores all Scenarios under levels of folders This follows the familiar Microsoft Explorer structure The directory contains three main components e GY Root Directory e Folder e Scenario Generalized Yield Model G02 natural mortality File Batch View Help GY root E Examples general input 1 7 2003 3 53 G01 advancing ages 1 Files input 1 7 2003 3 52 G02 natural mortality 1 Age structure input 1 7 2003 3 51 GO3 natural and fishing mortalities N EA a atural mortal input 1 7 2003 3 52 GYM Scenario G04 lookup table Krill 3 pe 4 7 0003 351 Examples long lived species Management Longived 01 1 weight at age er Ue Scenario gt Tive inpu li 5
27. scripts are available to help with this purpose 3 5 CONTROLLING OUTPUTS The main outputs generated by the simulation are saved in the Microsoft Access database selected in Settings The output types are selected by the user in the General Output Details Form prior to the simulation The main outputs from the GYM simulation are formatted as Results and Output Files The simulation also generates the Input Files from the data saved within the Parameter input Forms these can also be saved within the database if desired see Input Files Ultimately the outputs chosen will depended on what analysis or graphing the user intends to perform on the data after the simulation 3 5 1 RESULTS A scenario with results has its icon changed to an R results from an I input The raw data are displayed in Result forms shown with an R in the form icon which are located at the bottom of the form list for a Scenario 65 Part 3 Using the GYM Generalised Yield Model GYM User s Manual r Generalized Yield Model G01 advancing ages _ o x File Batch wiew Help Gir root Modified Examples general l 1 Scenario base information input 1 6 2003 4 01 GOI advancing ages T Files input 1 6 2003 4 01 o gt 17 GOZ natural mortality ye ri Age structure input 17672003 3 59 a G0 natural andiena mortalities 1 Natural mortality input 1 6 2003 4 17 E m Fg ri Length at age input 14642003 4 04 ae ig Lona lived
28. the nominated survey times lt Root filename gt PS Characteristic Test Trial Year Inc Total biomass Total Number Spawn Biomass Spawn Number Vulnrbl BMS Vulnrbl Number Basic Description Catch Gamma or F being tested Number of the trial within a scenario Year within a trial Fraction of the year at the beginning of the increment in which survey falls Total biomass Total number in the population Spawning biomass Spawning number Vulnerable biomass Vulnerable number Population characteristics for each increment in the year lt Root filename gt PI Characteristic Test Trial Year Inc Total biomass Total Number Spawn biomass Spawn Number Vulnrbl BMS Vulnrbl Number F x effort Catch M Basic Description Catch Gamma or F being tested Number of the trial within a scenario Year within a trial Fraction of t