The Population
Simulator (POPSIM) 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.

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 as 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 using either Beverton-Holt or Ricker
stock recruitment functions.

The user may specify “surveys” of abundance based
on applying log-normal error to the “true”
populations in each year. The program will use the survey
data as needed to create indices for use in testing estimation
models.

Catch samples are developed by sampling by user defined market
categories from the “true” Catch data.
The user can specify length-weight equation coefficients for the true
Catch as different from the Samples. The user also specifies
the sampling rate by market categories and error levels used in
creating simulated landings by market. 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, SS2,
SCALE and AIM. 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 Visual Basic user interface allows for complete
graphical analysis of input and output data.

POPSIM 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.

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.

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.

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.