The Age BasedPopulation
Simulator (POPSIM-A) 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 weights, maturity, natural mortality, fishery
selectivity, and discard fraction at age.The program supports multiple fleets and flexible harvest
The user specifies the fully recruited fishing mortality and natural
mortality in each year of the model. The population is developed as
length by age matrix for each year as a forward projecting model.
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 from a multinomial age
The resulting stochastic realizations can be used to automatically
generate datasets for input to VPA/ADAPT,
and ASAP.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.
(January 2014) is a major change in the underlying structure
from the original POPSIM approach, which was length and age based.
Removal of length attributes speeds the calculations and allows easier
understanding of application to age-based models.
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:
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):
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.
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
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.
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
Added the ability to create a VPA template for data with no plus
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
Disallowed the user to use input files with periods in the file
name or folder name with CSA due to limitations in the CSA
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
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
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
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
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
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
Ability to turn on or off the "Do you want to save data now?"