ShinyTropFish

- This app allows you to conduct a length-based stock assessment of your own data without requiring any R knowledge -


Disclaimer: The results of your analysis will be hosted up to 1 week on the server before being deleted. We do not take any responsibility over your data or results. It is possible to download the application and run if offline. Please see the "About" tab for further information.







Load your data



Please arrange your length measurements in an csv or txt file in the format explained in detail in this tutorial. Make sure that the headers of your data are called: 'length', 'dates', and 'frequency'.





Example data




Explore your data






Overall LFQ plots:

Number of length measurements per month:



Estimate growth parameters


Find more information and a user manual about Electronic LEngth Frequency ANalysis (ELEFAN) in this tutorial. Please be aware of the the best practices of this method listed in the above tutorial.







LFQ restructuring







ELEFAN settings



Growth



Fitted parameters:


LFQ plot:


GA fitness plot:


Cohort plot:





Recruitment



Estimates:


Plot:


Estimate mortality rates


Fitted parameters:



LCCC plot:


Selectivity plot:


GOTCHA parameters:


GOTCH catch curve:



Estimate reference levels


YPR



Fitted parameters:


Yield per recruit plot:


Yield per recruit plot (F vs Lc):


Biomass per recruit plot (F vs Lc):





LB-SPR



Fitted parameters:







All results



All parameters






Growth




LFQ plot:


GA fitness plot:


Cohort plot:




Recruitment







Mortality rates






Gotcha parameters:




Reference levels



YPR





Yield per recruit

Biomass per recruit


LB-SPR










Scientific articles:


Mildenberger TK, Taylor MH, Kokkalis A, Pauly D. 2019, Fish stock assessment with length-frquency data: A novel app and best practices. Fisheries Research. doi:... COMING

Mildenberger TK, Taylor MH, Wolff M. 2017, TropFishR: an R package for fisheries analysis with length‐frequency data. Methods Ecol Evol, 8: 1520-1527. doi:10.1111/2041-210X.12791

Taylor MH, Mildenberger TK. 2017, Extending electronic length frequency analysis in R. Fish Manag Ecol. 2017;24:330–338. https://doi.org/10.1111/fme.12232



Tutorials:


Mildenberger, TK. 2018. Length-frequency data for TropFishR. Link

Taylor, MH. 2018. Using the TropFishR ELEFAN functions. Link

Mildenberger, TK. 2017. Single-species fish stock assessment with TropFishR. Link





ShinyTropFish


Shiny app for Tropical Fisheries Analysis in R. The click-based user interface for the R package TropFishR. 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.



Version


Version number: v0.1 (Beta)



News


This is the beta version of ShinyTropFish. You can find detailed descriptions of new features, bug fixes, other changes of specific package versions concerning ShinyTropFish and concerning TropFishR



Installation for offline use


This application can be used offline. Please download the package from GitHub with devtools::install_github("tokami/ShinyTropFish") and run the R commands: require(ShinyTropFish) and runApp("apps/").



Citation


Please cite this application as: Mildenberger TK, Taylor MH, Kokkalis A, Pauly D. 2019, Fish stock assessment with length-frquency data: A novel app and best practices. Fisheries Research. doi:... COMING



Questions/Issues


In case you have questions or find bugs, please write an email to Tobias Mildenberger or post on ShinyTropFish/issues . If you want to be updated with the development of the application and underlying R package (TroFishR) or want to discuss with ShinyTropFish and TropFishR users and developers, follow the project on ResearchGate .



Developer team


Tobias K. Mildenberger

Creator, Author, Maintainer
DTU AQUA
National Institute of Aquatic Resources
Technical University of Denmark
Kemitorvet
2800 Kgs. Lyngby
Denmark

Marc H. Taylor

Author
Thuenen Institute of Sea Fisheries
Herwigstrasse 31
27572 Bremerhaven
Germany

Alexandros Kokkalis

Author
DTU AQUA
National Institute of Aquatic Resources
Technical University of Denmark
Kemitorvet
2800 Kgs. Lyngby
Denmark

Daniel Pauly

Author
Institute for the Oceans and Fisheries
The University of British Columbia
2202 Main Mall
Vancouver, British Columbia
Canada