A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (< http://www.fao.org/docrep/W5449E/W5449E00.htm>), as well as other more recent methods.
TropFishR is a collection of fisheries models based on the FAO Manual "Introduction to tropical fish stock assessment" by Sparre and Venema (1998, 1999). Not only scientists working in the tropics will benefit from this new toolbox. The methods work with age-based or length-frequency data and assist in the assessment of data poor fish stocks. Overall, the package comes with 30 functions, 19 data sets and 10 s3 methods. All objects are documented and provide examples that allow reproducing the examples from the FAO manual. In addition, the package includes the Length-based Bayesian biomass estimator method (LBB) by Froese et al. (2018), which allows to estimate reference levels (e.g. B/B0) based on yearly length-frequency data.
You can find detailed descriptions of new features, bug fixes, other changes of specific package versions here.
First, install the Gibbs sampler JAGS for your Operating System from this web site.
Then, download the released version of TropFishR from CRAN:
Or the development version from GitHub:
Please use the R command
citation("TropFishR") to receive information on
how to cite this package.
The tutorial demonstrates the use of the main functions of TropFishR for a single-species stock assessment with length-frequency data. The lfqDataTutorial gives a brief description of LFQ data and illustrates how files with raw length measurements (e.g. excel files) can be imported into R and trimmed for the use with TropFishR. The ELEFANTutorial demonstrates the ELEFAN functions available in TropFishR in detail and discusses best practices. The LBBmanual introduces the Length-based Bayesian biomass estimator method (LBB) by Froese et al. (2018) and demonstrates its usage within TropFishR.
In case you have questions or find bugs, please write an email to Tobias Mildenberger or post on TropFishR/issues. If you want to be updated with the development of the package or want to discuss with TropFishR users and developers, follow the project on ResearchGate.