class: center, middle, inverse, title-slide # Fisheries Collapse ### Carl Boettiger --- # Unit III: Global Fisheries Collapse? --- ## Introduction - [Atlantic Cod History](https://www.youtube.com/watch?v=3fCX6XKzbUY) - ["End of the Line" Trailer](https://www.youtube.com/watch?v=H6WOvY_C-_I) --- ## Atlantic Cod History <iframe width="560" height="315" src="https://www.youtube.com/embed/3fCX6XKzbUY" frameborder="0" allowfullscreen ></iframe> --- ## End of the Line <iframe width="560" height="315" src="https://www.youtube.com/embed/H6WOvY_C-_I" frameborder="0" allowfullscreen ></iframe> --- ## Cod Collapse <img src="http://berkeley.carlboettiger.info/espm-88b/fish/img/codcollapse.jpg" width=600> Source: http://www.millenniumassessment.org/documents/document.356.aspx.pdf --- ## Global fisheries trends <img src="http://berkeley.carlboettiger.info/espm-88b/img/worm2006.png" width=700 height = 400> ### Source: [Worm et al. 2006 _Science_](http://doi.org/10.1126/science.1132294) --- ## Media version - [New York Times: "Study Sees 'Global Collapse' of Fish Species"](http://www.nytimes.com/2006/11/03/science/03fish.html?_r=0) - [BBC declares: 'Only 50 years left' for sea fish](http://news.bbc.co.uk/2/hi/science/nature/6108414.stm) ![](http://graphics8.nytimes.com/images/2006/11/02/us/1103-nat-webFISH.gif) --- ## The Database [RAM Legacy Stock Assessment Database](http://ramlegacy.marinebiodiversity.ca/ram-legacy-stock-assessment-database) <img src="ram-2011.png" width=700> ```r library("tidyverse") library("readxl") ``` --- ## Reading in the tables ```r download.file("https://depts.washington.edu/ramlegac/wordpress/databaseVersions/RLSADB_v3.0_(assessment_data_only)_excel.zip", "ramlegacy.zip") path <- unzip("ramlegacy.zip") sheets <- readxl::excel_sheets(path) ram <- lapply(sheets, readxl::read_excel, path = path) names(ram) <- sheets ## Name the available tables: names(ram) ``` ``` ## [1] "area" "assessment" ## [3] "assessmethod" "assessor" ## [5] "biometrics" "bioparams" ## [7] "bioparams_ids_views" "bioparams_units_views" ## [9] "bioparams_values_views" "management" ## [11] "stock" "taxonomy" ## [13] "timeseries" "timeseries_ids_views" ## [15] "timeseries_units_views" "timeseries_values_views" ## [17] "tsmetrics" ``` --- ## Exploring the Database: a bird's eye view - "Tidy Data": Codd's Third Normal form: > Each row must describe the Key, the Whole Key, and Nothing But the Key (so help me Cobb) --- ## What is a Stock Assessment? - From the Assessment Table, id: http://www.afsc.noaa.gov/REFM/docs/2010/GOApop.pdf - From said pdf, methods (in 2009 assessment): http://www.afsc.noaa.gov/refm/docs/2009/GOApop.pdf > When treated this way, our stock assessment is a large Bayesian model, which includes informative (e.g., lognormal natural mortality with a small CV) and noninformative (or nearly so, such as a parameter bounded between 0 and 10) prior distributions. In the model presented in this SAFE report, the number of parameters estimated is 134. -- http://www.afsc.noaa.gov/refm/docs/2009/GOApop.pdf pg 757 --- ## Task 1: Investigating Cod Collapse <img src="http://berkeley.carlboettiger.info/espm-88b/fish/img/codcollapse.jpg" width=600>