README.md

FishLife

Estimate fish traits for all marine fish species globally

Visualize predictions

A graphical user interface (GUI) is available online

Example usage

Load the package

# Install and load package
devtools::install_github("james-thorson/FishLife")
library( FishLife )

Vignette available

Please see the FishLife vignette for details on how to extract predictions frmo the package, update predictions using new data, or replicate the analysis using a new data set.

vignette("tutorial","FishLife")

Get predictions for a given taxon

I also show a few simple examples of life-history predictions using FishLife, as archived in the package.

# Get basic plot for Lutjanus campechanus (in database, so prediction is informed by species-specific data)
Plot_taxa( Search_species(Genus="Lutjanus",Species="campechanus")$match_taxonomy )

# Get basic plot for Sebastes cortezi (not in database, so uses predictive distribution for genus Sebastes)
Plot_taxa( Search_species(Genus="Sebastes",Species="cortezi")$match_taxonomy )

# Get basic plot for Family Scombridae 
Plot_taxa( Search_species(Family="Scombridae")$match_taxonomy )

Description of package

Please cite if using the software

• Thorson, J. T., S. B. Munch, J. M. Cope, and J. Gao. 2017. Predicting life history parameters for all fishes worldwide. Ecological Applications. 27(8): 2262–2276. https://onlinelibrary.wiley.com/doi/10.1002/eap.1606/full

Further reading

Evaluating accuracy of data and life-history predictions in FishBase

• Thorson, J. T., J. M. Cope, and W. S. Patrick. 2014. Assessing the quality of life history information in publicly available databases. Ecological Applications 24:217–226. https://onlinelibrary.wiley.com/doi/10.1890/12-1855.1/abstract