The Length BasedPopulation
(POPSIM-L) is a general data simulator designed to allow users to
create populations with known underlying parameters and error structure.
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
general utility for examining tradeoffs among model dimensionality, degree
fit, and generality.
The user specifies the coefficients of a von Bertalanffy growth
equation. This is applied in creating the initial population as
distributed based on user specified proportion at age. The growth equation
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
natural mortality in each year of the model. The population is
a length by age matrix for each year as a forward projecting model.
Mortality is applied and then growth projection. The user may
recruitment either as a vector of annual recruitment or Beverton-Holt,
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”
and “West Coast” (age-aggregated) tuning indices can be created from the
Catch samples are developed by random sampling at length and application
have user defined ageing imprecision applied.
The resulting stochastic realizations can be used to automatically
datasets for input to VPA/ADAPT,
ASAP, and SCALE.Because the “surveys” with
independent of how they are applied as indices of abundance in the
model, the same random error is being applied on each realization
of the model being evaluated. Thus, multiple models can be compared
their relative ability to recover the “true state of nature”.
POPSIM can be used to verify that the estimation models can recover the
parameters and the limitations of various models when their underlying
assumptions are violated. The simulator is designed to allow users to
compare the relative merits of alternative modeling approaches. The user
interface allows for complete graphical analysis of input and output data.
(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
PopSim Version 7.0.0 (October, 2010)
User may create a simulated population consisting of multiple
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,
Allows the user to set up a simulated population by
both sexes independently.
Males and females can be specified independently over the model
time horizon for the following properties:
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
of the graphical interface.
The user may compare the performance of the following estimator
models (Versions refer to Calculation Engine):
PopSim Version 4.8 (February
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.
A bug fix for the application of length weight
equation parameters in samples.
PopSim Version 4.6 (February
PopSim will now support testing of ASAP
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
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.
For the CSA template, added the ability to override the
population's natural mortality values with user-specified values.
Fixed a bug which wrote the CSA template incorrectly if
user did not enter values for the Weights in the Objective Function.
3.5.1 (February 2006)
additional statistical quantities, RMS Error and the C.V. of the RMS
Error, to the results from the analysis of error applied to 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.
ability to create a VPA template for data with no plus group.
bug which forced users to enter values of 1.0 or less for Natural
Mortality in the age-based input data.
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.
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.
3.5 (December 2005)
ability to use length-based input data.
additional output file (*.AUX5) when performing a statistical
of the applied error which re-sorts the Indices with error.
bug that didn't plot data properly in the multi-line plots when the
lines are not all the same age.
a bug in
the Simulated Population plots that showed the Average Biomass data
when user selects to show SSB data.
that didn't enable the "Jump To Fishery" boxes for the Simulated
Population data grids.
bug that didn't read PopSim version 2
input files properly.
bug that the Grid Edit form's
Continuous Edit by Row didn't function properly in the Catch CV
Correlation Coefficients grid.
a bug in
the CSA Template form that disallowed some valid post-recruitment
Added the ability to
paste data into grids if
the copied data came from Quattro Pro or a text file.
handling of very small or very large numbers in generating and
bug that sometimes caused the
iterative calculations to fail if the first year and last year of
template file did not correspond to the first and last year of the
input data file.
PopSim Version 3.1 (April
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
shortcuts to some menu items.
Improved ability to mix and match input files and template
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
Changes to the input data include:
Added the ability to have multiple fisheries.
Instead of using the proportion of the year at which
the input data uses the proportion of the year for F and M before
Allow the option to use fishing mortality selectivity
Weight in Stock can be subdivided into Jan-1 stock weights
Stock Biomass weights.
Allow a different random number seed for applying error to
catch and indices.
For applying error to indices, a grid of correlation
A selectivity function can be applied to each index's
Added functionality to the graphic interface include:
Ability to export data from grids.
Incorporation of separate forms for input and output,
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
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
as well as user customized schemes.
Ability to view an error log file using a text editing
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