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# FishLife
Estimate growth, size, maturity, mortality, stock-recruit, and population-dynamics parameters for all fish species globally
A package for phylogenetic comparative methods (PCM) and phylogenetic trait imputation (PTI) using phylogenetic factor analysis and/or phylogenetic structural equation models.

The package also includes results for these analyses applied to all fishes fishes globally, estimating:
* life history parameters (growth, maturity, mortality);
* juvenile productivity (stock-recruit parameters);
* life-cycle characteristics (generation time and intrinsic growth rate);
* spawning, behavioral, reproductive, and foraging traits;
* morphometric characteristics;
as described below

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7590994.svg)](https://doi.org/10.5281/zenodo.7590994)

# Database of results
The FishLife package also includes results for three prior analyses, which can be used to extract life-history predictions for all fishes:
* [Thorson et al. 2023](https://doi.org/10.1111/2041-210X.14076): This includes life-history parameters based on data from FishBase, morphometric information from [FishShapes]([url](http://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.3829)), and spawning, behavioral, reproductive, and trophic traits. Results are accessed using `data(FishBase, package="FishLife_and_Mophometrics")`, or `Plot_taxa(..., Database = FishLife::FishBase_and_Mophometrics)`
* [Thorson 2020]([url](https://doi.org/10.1111/faf.12427)): This includes life-history parameters based on data from FishBase as well as stock-recruit information from the RAM Legacy database, and combines these to get life-cycle predictions. Results are accessed using `data(FishBase, package="FishLife_and_RAM")`, or `Plot_taxa(..., Database = FishLife::FishBase_and_RAM)`
* [Thorson et al. 2017]([url](http://onlinelibrary.wiley.com/doi/10.1002/eap.1606/full)): This includes life-history parameters based on data from FishBase, and is accessed using `data(FishBase, package="FishLife")`, or `Plot_taxa(..., Database = FishLife::FishBase)`

# Visualize predictions

A graphical user interface (GUI) is available [online](https://james-thorson.shinyapps.io/FishLife/)
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Description of package
=============
### Please cite if using the software
* 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., Maureaud, A.A., Frelat, R., Mérigot, B., Bigman, J.S., Friedman, S.T., Palomares, M.L.D., Pinsky, M.L., Price, S.A., Wainwright, P., 2023. Identifying direct and indirect associations among traits by merging phylogenetic comparative methods and structural equation models. Methods Ecol. Evol. n/a. https://doi.org/10.1111/2041-210X.14076

### Previous software versions and analytical descriptions
* Thorson, J.T., 2020. Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data-integrated life-history model. Fish Fish. 21, 237–251. https://doi.org/10.1111/faf.12427
* 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. http://onlinelibrary.wiley.com/doi/10.1002/eap.1606/full

Further reading
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