is a statistical catch-at-age model. It is a likelihood-based
assessment model for joint analyses of age-specific fishery and survey
data. Age-structured population stock dynamics are modeled
using standard forward-projection methods for statistical catch-at-age
analyses. The population dynamics model is fit to observed fishery and
survey data using an iterative maximum likelihood estimation
The calculation engine was developed by Dr. Jon Brodziak, NMFS
Pacific Islands Fishery Science Center, using AD Model Builder.
Replaces 1.3.1 and includes significant updates to the calculation engine with associated GUI changes.
can select fishery selectivity and survey selectivity functions to be
either parametric or nonparametric. If fishery selectivity is parametric
then either a 3-parameter Thompson or a 2-parameter logistic curve is
estimated Otherwise, a nonparametric selectivity value will be estimated
for each age group from 1 up to the number of estimated ages. In either
case, the selectivity vector is normalized to have a maximum value of 1.
can specify whether a smoothing function should be applied to fishery
can specify a natural mortality at age multiplier. This multiplier times
the estimate of the fully-vulnerable natural mortality rate determines the
natural mortality at age vector. One can also choose to fix or estimate
the fully-vulnerable natural mortality rate. If the fully-vulnerable
natural mortality rate is estimated, one needs to specify the coefficient
of variation of the lognormal prior distribution for fully-vulnerable
can apply a penalty function to shrink recruitment deviations to be near
themean recruitment estimate
starting in the terminal year of the assessment time horizon and proceeding
backwards for a fixed number ofyears, nshrinkage; this is the number of recent years for which
incomplete observations of cohort strength may lead one to shrink
estimates towards their mean value.
can apply the bootstrap to construct bootstrap replicates of the
population numbers at age vector in the terminal year plus one, analogous
to the Toolbox VPA program. These bootstrap replicates are written to file
and can be input to the Toolbox AGEPRO module.
can choose to add a small nonnegative constant to the argument of natural
log functions to ensure that there is no numeric overflow if the argument
becomes close to zero during the parameter optimization.
can set mean recruitment or mean fishing mortality to be fixed constants
instead of estimated parameters. One can set annual recruitment deviations
or fishing mortality deviations to be fixed constant vectors instead of
estimated parameter vectors.
can use the fit_survey_index flag to determine whether to fit each survey
index. This simplifies the choice of including or excluding a given survey
can change the optimization phases for estimating parameters to fit recruitment,
fishing mortality, survey, fishery, and natural mortality processes.
outputs incude time series of predicted catch, population, spawning, and
exploitable biomass at age, similar to VPA outputs, along with the
fraction of unfished spawning biomass realized in each year.
STATCAM Version 1.3.1
Replaces Beta Version 1.3
Recruitment year is now set to Start Year - Number of Ages
+1 (Formerly +2).
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.