MATLAB
Modeling YY "supermales" for invasive species control with coupled differential equations and an individual-based model. |
Quantify irregularity in the spatial distribution of spawning fish in real time using quantiles |
Spatially explicit modeling of fish inhabiting stream networks (as opposed to 2D space) is tricky. Here are the basics of computing on a stream network using matrix algebra.
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Growth of fish can be used to describe environmental conditions. Here are some maximum likelihood estimates of growth parameters and multi-model comparisons.
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Population Viability Analysis is a tool for assessing the probability of persistence. Bayesian analysis of spawner-recruit data are used to drive this PVA. |
R
North Fork John Day Spring Chinook PVA. Data for spawners, migrants, and survival across two life stages permit this multistage life-cycle PVA. Includes effect of warming. Uses maximum likelihood methods.
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Simultaneous estimation of juvenile steelhead abundance at 83 population units using 2-occasion mark-recapture data. Uses data augmentation, covariates, and Bayesian methods.
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A mixture of distributions is used to estimate catch rates when only a portion of stocked fish are marked. Uses data simulation and Bayesian analysis.
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Beverton-Holt relationship with female spawners. Uses maximum likelihood method and AIC to assess how many asymptotes are needed down the Oregon coast.
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Animal abundance is estimated by combining mark-recapture data and ancillary count data in an index site. Uses maximum likelihood and Bayesian methods.
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Harvest rates can be indexed to biological reference points derived from Ricker recruitment parameters. Uses Bayesian estimates for derived parameters and multi-model assessment with WAIC.
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JAGS
model1.txt | |
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model2.txt | |
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