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 General

 Model List

Population Simulator

Line Art Drawing of a Fish

Length Based Population Simulator
(POPSIM-L)

 

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About

Version 8.0 (December 2013)

Research Model

 

The Length Based Population Simulator (POPSIM-L) is a general data simulator designed to allow users to create populations with known underlying parameters and error structure. The program can be used to reveal the limitations of alternative estimation methods. These considerations are particularly important where model misspecification can lead to widely varying results. This simulator should have general utility for examining tradeoffs among model dimensionality, degree of fit, and generality.


The user specifies the coefficients of a von Bertalanffy growth equation.  This is applied in creating the initial population as normally distributed based on user specified proportion at age. The growth equation is also used in creating growth projection matrices for each age class.  All inputs are by sex.


Maturity and fishery selectivity are specified as length based functions.  The user specifies the fully recruited fishing mortality and natural mortality in each year of the model.  The population is developed using a length by age matrix for each year as a forward projecting model.  Mortality is applied and then growth projection.  The user may specify recruitment either as a vector of annual recruitment or Beverton-Holt, Ricker or Shepherd stock recruitment functions.  Alternatively, the user may specify either a 1-stage or 2-stage empirical cumulative distribution function

.

The user may specify “surveys” of abundance based on applying log-normal error to the “true” populations in each year. Both “East Coast” (age-specific) and “West Coast” (age-aggregated) tuning indices can be created from the survey information.

 

Catch samples are developed by random sampling at length and application of age-length keys.  Age-length keys can have user defined ageing imprecision applied.


The resulting stochastic realizations can be used to automatically generate datasets for input to VPA/ADAPT, CSA, ASPIC, ASAP, and SCALE.   Because the “surveys” with error are independent of how they are applied as indices of abundance in the estimation model, the same random error is being applied on each realization independent of the model being evaluated.  Thus, multiple models can be compared in their relative ability to recover the “true state of nature”.


POPSIM can be used to verify that the estimation models can recover the true parameters and the limitations of various models when their underlying assumptions are violated. The simulator is designed to allow users to rapidly compare the relative merits of alternative modeling approaches. The user interface allows for complete graphical analysis of input and output data.

 

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Version History

 

POPSIM-L (January 2014) is a continuation of earlier versions of POPSIM based on both age and length characteristics of the population. The approach used to generate tuning indices has been simplified.

Compatible with

               VPA/ADAPT                         Version 3.3

               CSA                                      Version 4.2.2

               ASPIC                                   Version 5.34.9

               ASAP                                    Version 3.0.14

               SCALE                                  Version 1.0.11


PopSim Version 7.0.0 (October, 2010)

  • User may create a simulated population consisting of multiple fleets

  • Has an improved sampling approach on simulated surveys of abundance that randomly varies the number of survey samples on each iteration for each survey in every year

  • Has been updated to interface with Stock Synthesis version 3.11b, note that earlier versions of SS3 are not compatiible with this version of PopSim


PopSim Version 6.1.2 (May, 2010)

  • User may specify Multiple Ageing Precision Matrices

  • User may specify Optional Harvest Strategy


PopSim Version 5.4 (October, 2009)

  • Allows the user to set up a simulated  population by specifying both sexes independently. 

  • Males and females can be specified independently over the model time horizon for the following properties:

           Natural Mortality

           Growth Equation

           Length Weight Equation
           Maturity

  • Improved Survey Sampling

  • Calculation of Surplus Production for simulated population

  • Export Simulated Population as R Object

  • Uses the Microsoft .NET Framework which updates the look and feel of the graphical interface.

  • The user may compare the performance of the following estimator models (Versions refer to Calculation Engine):

          VPA/ADAPT                           (Version 3.0)

          CSA                                       (Version 3.1)

          ASPIC                                    (Version 5.34)

          ASAP                                     (Version 2.0)

          Stock Synthesis 3                   (Version 3.03a)

          SCALE                                   (Version 1.0)

          AIM                                        (Version 2.1)

          STATCAM                              (Version 1.4)

 

PopSim Version 4.8 (February 2008)

  • A bug fix to prevent a divide-by-zero error when there are zero catch samples in one or more markets. This can happen when there are low market landings and / or sampling. 

  • A bug fix to prevent a rounding error in a table in the PopSim report file that reports the number of fish samples in each market by year.

 

PopSim Version 4.7 (February 2008)

  • Improved interface with AIM

  • A bug fix for the application of length weight equation parameters in samples.

 

PopSim Version 4.6 (February 2008)

  • PopSim will now support testing of ASAP (version 2.0).

  • There was also a change to the handling of Market categories to insure that market distribution of intermediate markets with high standard deviations do not inadvertently overlap in to the tails of the largest or smallest market categories.

 

PopSim Version 4.5 (January 2008)

  • A separate growth projection matrix is created from the von Bertalanffy equation for all age classes.

  • A simulated population with multiple realizations of catch & surveys with error is created.

  • Can read PopSim version 4.0 and higher input files.

  • The following models are supported: AIM, ASPIC, CSA, SCALE, SS2, VPA

 

PopSim Version 4.0 (October 2007)

  • This is a major revision of PopSim.

  • Catch with error is created by randomly drawing samples within "Market Categories" and expanding to match landings.

  • Fishery selectivity, maturity, discards, etc., are defined in terms of length based functions.

  • The following models are supported: ASPIC, CSA, SCALE, SS2, VPA

 

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Older Version Changes 

 

PopSim Version 3.5.2 (April 2006) 

  • For the CSA template, added the ability to override the simulated population's natural mortality values with user-specified values.

  • Fixed a bug which wrote the CSA template incorrectly if the user did not enter values for the Weights in the Objective Function.

 

PopSim Version 3.5.1 (February 2006)

  • Added two additional statistical quantities, RMS Error and the C.V. of the RMS Error, to the results from the analysis of error applied to the simulated population.

  • Added the ability to capture error messages and output to the command window to a log file and have the log file viewed in the graphical interface.

  • Added the ability to create a VPA template for data with no plus group.

  • Fixed a bug which forced users to enter values of 1.0 or less for Natural Mortality in the age-based input data.

  • Fixed a bug that wrote the input file incorrectly when the session begins with a case where the option to apply error to the catch is turned off.

  • Disallowed the user to use input files with periods in the file name or folder name with CSA due to limitations in the CSA calculation engine.

  

PopSim Version 3.5 (December 2005)

  • Added the ability to use length-based input data.

  • Added an additional output file (*.AUX5) when performing a statistical analysis of the applied error which re-sorts the Indices with error.

  • Fixed a bug that didn't plot data properly in the multi-line plots when the lines are not all the same age.

  • Fixed a bug in the Simulated Population plots that showed the Average Biomass data when user selects to show SSB data.

  • Fixed a bug that didn't enable the "Jump To Fishery" boxes for the Simulated Population data grids.

  • Fixed a bug that didn't read PopSim version 2 input files properly.

  • Fixed a bug that the Grid Edit form's Continuous Edit by Row didn't function properly in the Catch CV Correlation Coefficients grid.

  • Fixed a bug in the CSA Template form that disallowed some valid post-recruitment Indices.

  • Added the ability to paste data into grids if the copied data came from Quattro Pro or a text file.

  • Improved handling of very small or very large numbers in generating and plotting statistical reports.

  • Fixed a bug that sometimes caused the iterative calculations to fail if the first year and last year of the template file did not correspond to the first and last year of the input data file.

 

PopSim Version 3.1 (April 2005)

  • For applying error to catch, different CV's can be used per age and fishery, with a matrix of correlation coefficients.

  • Indices can span a subset of model years.

  • A report on the distribution of error applied to Catch, Yield and Indices can be created.

  • Improvements to the graphic interface including a start page summarizing the input and output files available for viewing and shortcuts to some menu items.

  • Improved ability to mix and match input files and template files.

 
PopSim Version 3.0
Allows a more comprehensive specification of input to VPA/ADAPT, ASPIC, ASAP, and CSA. Can now launch multiple realizations of these models with user defined variability and compare how well the estimator models recover the "true state of nature" as defined by the original POPSIM forward projection.
 
Changes to the input data include:

  • Added the ability to have multiple fisheries.

  • Instead of using the proportion of the year at which spawning occurs, the input data uses the proportion of the year for F and M before spawning. 

  • Allow the option to use fishing mortality selectivity parameters.

  • Weight in Stock can be subdivided into Jan-1 stock weights and Spawning Stock Biomass weights.

  • Allow a different random number seed for applying error to recruitment, catch and indices.

  • For applying error to indices, a grid of correlation coefficients can be specified.

  • A selectivity function can be applied to each index's overall catchability.

  
Added functionality to the graphic interface include:

  • Ability to export data from grids.

  • Incorporation of separate forms for input and output, accessible via the Windows menu, allows users to quickly and easily find the needed item with fewer tabs to sort through.

  • Ability to scan in results from a previously completed model without having to re-run the model again.

  • Ability to quickly save plots to a file in a batch instead of one at a time. Ability to select default light and dark background color schemes as well as user customized schemes.

  • Ability to view an error log file using a text editing software package of your choice or continue to use the viewer that comes with PopSim.

  • Ability to turn on or off the "Do you want to save data now?" prompts.

  

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website last modified May 16, 2016

 
 

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