Estimate growth, size, maturity, mortality, stock-recruit, and population-dynamics parameters for all fish species globally
A graphical user interface (GUI) is available online
# Install and load package
devtools::install_github("james-thorson/FishLife")
library( FishLife )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")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 and extract values for Family Scombridae
( Predictions = Plot_taxa(Search_species(Family="Scombridae")$match_taxonomy) )You can also see the full set of parameters calculated for each taxon, either for internal use of anticipated to be useful for users:
head(FishLife::FishBase_and_RAM$beta_gv)These can similarly be extracted and plotted:
params = matrix( c("K","M", "G","ln_MASPS"), ncol=2, byrow=TRUE)
Plot_taxa( Search_species(Genus="Lutjanus",Species="campechanus")$match_taxonomy, params=params )
while other values (e.g., slope at the origin for the Beverton-Holt stock recruit curve) can then be calculated from the set of available parameters.
By default FishLife uses the most-recent version published. This currently includes both growth, size, maturity, and mortality parameters from FishBase, as well as stock-recruit parameters estimated using the RAM Legacy stock-recruit database. To use earlier versions, use the Database argument in each function:
# Get basic plot for Lutjanus campechanus (in database, so prediction is informed by species-specific data)
Plot_taxa( Search_species(Genus="Lutjanus",Species="campechanus")$match_taxonomy, Database="FishBase" )or expliclty use the updated database using:
Plot_taxa( Search_species(Genus="Lutjanus",Species="campechanus")$match_taxonomy, Database="FishBase_and_RAM" )`- Thorson, J. T. In press. Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data-integrated life-history model. Fish and Fisheries.
- 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
- 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
Presentation of research program available online