Stock assessment methods for data-limited fisheries
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DESCRIPTION Bump version Dec 23, 2016
NAMESPACE
README.Rmd
README.md
datalimited.Rproj

README.md

Stock assessment methods for data-limited fisheries

Build Status DOI

Installation

Before installing datalimited, you will need to install JAGS and have a C++ compiler set up.

The R package datalimited can then be installed from GitHub with:

# install.packages("devtools")
devtools::install_github("datalimited/datalimited")

The package implements the methods used in Rosenberg et al. (2014) including the following:

  • Catch-MSY based on Martell and Froese (2013); see ?cmsy
  • Catch-only method with sample importance resampling based on asconcellos and Cochrane (2005); see ?comsir
  • Panel regression in the style of Costello et al. (2012); see ?prm
  • State-space catch-only model from Thorson et al. (2013); see ?sscom

An example with cmsy()

library("datalimited")
set.seed(1)
x <- cmsy(blue_gren$yr, ct = blue_gren$ct, reps = 2e4)
names(x)
#> [1] "theta"       "biomass"     "bmsy"        "msy"         "mean_ln_msy"
#> [6] "bbmsy"
par(mfrow = c(2, 2))
plot(blue_gren$yr, blue_gren$ct, type = "o", xlab = "Year", 
  ylab = "Catch (t)")
plot(blue_gren$yr,  apply(x$biomass, 2, median)[-1], type = "o",
  ylab = "Estimated biomass", xlab = "Year")
hist(x$bmsy)
plot(x$theta$r, x$theta$k, col = "#00000030")

library("ggplot2")
ggplot(x$bbmsy, aes(year, bbmsy_q50)) + geom_line()  +
    geom_ribbon(aes(ymin = bbmsy_q25, ymax = bbmsy_q75), alpha = 0.2) +
    geom_ribbon(aes(ymin = bbmsy_q2.5, ymax = bbmsy_q97.5), alpha = 0.1) +
    geom_hline(yintercept = 1, lty = 2) + theme_light()

Citation

To cite the package, cite the authors of the original assessment method (shown below), Rosenberg et al. (2014), and:

citation("datalimited")
#> 
#> To cite package 'datalimited' in publications use:
#> 
#>   Sean C. Anderson, Jamie Afflerbach, Andrew B. Cooper, Mark
#>   Dickey-Collas, Olaf P. Jensen, Kristin M. Kleisner, Catherine
#>   Longo, Giacomo Chato Osio, Daniel Ovando, Carolina Minte-Vera,
#>   Coilin Minto, Iago Mosqueira, Andrew A. Rosenberg, Elizabeth R.
#>   Selig, James T. Thorson and Jessica C. Walsh (2016).
#>   datalimited: Stock Assessment Methods for Data-limited
#>   Fisheries. R package version 0.1.0.
#>   https://github.com/datalimited/datalimited
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {datalimited: Stock Assessment Methods for Data-limited Fisheries},
#>     author = {Sean C. Anderson and Jamie Afflerbach and Andrew B. Cooper and Mark Dickey-Collas and Olaf P. Jensen and Kristin M. Kleisner and Catherine Longo and Giacomo Chato Osio and Daniel Ovando and Carolina Minte-Vera and Coilin Minto and Iago Mosqueira and Andrew A. Rosenberg and Elizabeth R. Selig and James T. Thorson and Jessica C. Walsh},
#>     year = {2016},
#>     note = {R package version 0.1.0},
#>     url = {https://github.com/datalimited/datalimited},
#>   }

References

Costello, C., D. Ovando, R. Hilborn, S. D. Gaines, O. Deschenes, and S. E. Lester. 2012. Status and solutions for the world’s unassessed fisheries. Science 338:517-520.

Martell, S., and R. Froese. 2013. A simple method for estimating MSY from catch and resilience. Fish and Fisheries 14:504-514.

Rosenberg, A. A., M. J. Fogarty, A. B. Cooper, M. Dickey-Collas, E. A. Fulton, N. L. Gutiérrez, K. J. W. Hyde, K. M. Kleisner, C. Longo, C. V. Minte-Vera, C. Minto, I. Mosqueira, G. C. Osio, D. Ovando, E. R. Selig, J. T. Thorson, and Y. Ye. 2014. Developing new approaches to global stock status assessment and fishery production potential of the seas. FAO Fisheries and Aquaculture Circular, Rome, Italy.

Thorson, J. T., C. Minto, C. V. Minte-Vera, K. M. Kleisner, and C. Longo. 2013. A new role for effort dynamics in the theory of harvested populations and data-poor stock assessment. Canadian Journal of Fisheries and Aquatic Sciences 70:1829–1844.

Vasconcellos, M., and K. Cochrane. 2005. Overview of World Status of Data-Limited Fisheries: Inferences from Landings Statistics. Pages 1-20 in G. H. Kruse, V. F. Gallucci, D. E. Hay, R. I. Perry, R. M. Peterman, T. C. Shirley, P. D. Spencer, B. Wilson, and D. Woodby, editors. Fisheries Assessment and Management in Data-Limited Situations. Alaska Sea Grant, University of Alaska Fairbanks.