README.md

In NOAA-EDAB/LeMANS: length-based multispecies analysis by numerical simulation (LeMANS)

LeMANS (Length-based Multispecies Analysis by Numerical Simulation)

Details of the model can be found in the following publications:

• Hall et al. (2006). A length-based multispecies model for evaluating community responses to fishing. Can. J. Fish. Aquat. Sci. 63:1344-1359. doi: https://doi.org/10.1139/f06-039

• Rochet et al. (2011). Does selective fishing conserve community biodiversity? Prediction from a length-based multispecies model. Can. J. Fish. Aquat. Sci. 68:469-486. doi: https://doi.org/10.1139/F10-159

Originally coded in MATLAB

Commments/questions/bugs should be documented at https://github.com/NOAA-EDAB/LeMANS/issues

Features

• Each component of the model (M1, M2, F, suitability, size preference etc) has been modularized such that a users code block can be substitued.

• original data files (used in Rochet et al. (2011)) are bundled with the package.

• The code is substantially faster (~9 times) than the original MATLAB implementation

• It serves as a framework for extending the model

Usage

Installation

# build the package from github with vignettes
remotes::install_github("NOAA-EDAB/LeMANS",build_vignettes = TRUE)

If you don't have remotes installed you will see an error "there is no package called 'remotes'"; if that happens install devtools with install.packages("remotes").

If installation of LeMANS fails, it could be due to the Rcpp package. Try to install Rcpp first.

Help

# view the documentation on usage
browseVignettes("LeMANS")

The code was developed with a similar structure to the MATLAB code. Supporting data files are lazily loaded and ready to use.

• rochet_GB_foodweb - Predator-prey matrix (binary). Predator (column), prey (row)
• rochet_GB_initialValues - number of individuals per tow for each species/sizeclass combination
• rochet_GB_parameterValues - carrying capacity (k), Maximum length (Linf) + for each species
• rochet_GB_species - lists common name, scientific name, and guild each species is a member of.
• rochet_GB_modelSetup - A list containing species independent parameter values (otherFood, Falpha, FL50)

To run the model with parameter values described in the Rochet et al paper simply type:

results <- key_run(Ffull=0.4, nYrs=50, rochet_GB_modelSetup, rochet_GB_parameterValues, rochet_GB_initialValues, rochet_GB_foodweb, rochet_GB_species)

To plot the catch output aggregated over sizeClass:

plot_key_run(results$catch/1E6, ylabel = "catch (millions individuals)", is.aggregated=T, speciesNames=rochet_GB_species, scale="free")

Contact

| andybeet | ----------------------------------------------------------------------------------------------- | |

Legal disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

NOAA-EDAB/LeMANS documentation built on Feb. 7, 2021, 11:01 p.m.