Shrimp Mortality

View the rendered methods document here: https://rethinkpriorities.github.io/shrimp_mortality/

About

This is the supplemental methods document and files for our report on Pre-slaughter Mortality of Farmed Shrimp. It contains all of the data and code used for the analyses in the report. The files render a quarto book that details the method and code we used. The book has three chapters covering:

1. Modeling shrimp pre-slaughter mortality using survival curves
2. Comparing our estimates to others found in the literature
3. Comparing our estimates to mortality estimates for other farmed taxa and wild shrimp.

We focus on the most farmed species, Penaeus vannamei, Penaeus monodon, and Macrobrachium rosenbergii. Often data for the latter included Macrobrachium nipponese, so we group them under the label Macrobrachium.

How to use

If you want to read through the methods document and see all of the code, view the rendered methods document.

If you would like to run the code yourself locally, download all of the files in the repository. Open the shrimp_pre-slaughter_mortality.Rproj file to begin. This will automatically set the working directory and warn if any packages need to be installed.

Folders

• docs contains the rendered html files and other site files.

• chapters contains the .qmd files (Quarto markdown files) where the method and code are written.

• data contains the .csv data files used in the analyses. It contains three subfolders:

  • comparison data files for comparing shrimp mortality to the mortality of other species
  • guesstimate data from Waldhorn and Autric's (2023) Guesstimate model used to build our survival curves model
  • survival_curves contains data created in the Survival Curves model chapter (Chapter 1) and used in subsequent chapters

data files

File name __________________________________	Description ____________________________________________________________________
wild_shrimp.csv	Spreadsheet showing how we calculated wild shrimp mortality from the numbers in Table 11.1 of Dall et al., 1991.
comparison folder
cross-species_data.csv	Data we collected from the literature on mortality rates, slaughter age, and slaughter weight of other farmed species, including chickens, carnivorous fish, insects, and non-shrimp crustaceans (lobsters, crabs, etc.).
guesstimate folder
die_on_farm_samples.csv	Raw Guesstimate model estimates (5000 samples) for the number of shrimp who die on farms (including pre-slaughter mortality) by species.
macrobrachium_days_lived.csv monodon_days_lived.csv vannamei_days_lived.csv	Raw Guesstimate model estimates (5000 samples) for the number of days lived on average for each life stage (larval, postlarval, juvenile-subadult) of each species analyzed. Each species is in a separate file.
macrobrachium_mortality_rates.csv monodon_mortality_rates.csv vannamei_mortality_rates.csv	Raw Guesstimate model estimates (5000 samples) for the mortality rates of each life stage (larval, postlarval, juvenile-subadult) of each species. Each species is in a separate file.
slaughtered_samples.csv	Raw Guesstimate model estimates (5000 samples) for the number of shrimp slaughtered in 2020 by species. The file includes estimates for "other penaeids," but that data is not analyzed here.
survival_curves folder
bystage_farmed_shrimp_model_probs.csv	Data estimated in the Survival Curves chapter for the probability of a shrimp dying in each life stage. All three taxa are in one file.
macro_model_slaughter_probs.csv monodon_model_slaughter_probs.csv vannamei_model_slaughter_probs.csv	Data estimated in the Survival Curves chapter for the probability of a shrimp reaching slaughter age. Each species is in a separate file. 'macro' refers to Macrobrachium.
macro_totalfarmed_days.csv monodon_totalfarmed_days.csv vannamei_totalfarmed_days.csv	Data estimated in the Survival Curves chapter for the length of the farming cycle for each species. Each species is in a separate file. 'macro' refers to Macrobrachium.