Tools for loading Stock Synthesis (SS3) models into FLR. Used in conditioning of Operating Models based on SS3 by considering structural uncertainty in input parameters and assumptions. A grid of SS3 runs can be created and results loaded on objects of various classes, ready for use in FLR.
To install this package, and all its dependencies, start R and enter:
install.packages("ss3om", repos=structure(
c(CRAN="https://cloud.r-project.org/", FLR="https://flr-project.org/R")))
or directly from the github repository by first updating to the latest version of r4ss:
remotes::install_github("r4ss/r4ss")
remotes::install_github("flr/ss3om")
Different FLR objects can be loaded from a folder containing the output of an SS3 run.
dir <- system.file("ext-data", "herring", package="ss3om")
To create an FLStock object from a model run, we can call readFLSss3,
stk <- readFLSss3(dir)
plot(stk)
and to extract and convert the stock-recruit relationship, you can use
srr <- readFLSRss3(dir)
plot(her)
Copyright (c) 2016-2022 European Union & Iago Mosqueira. Released under the EUPL 1.2.
You are welcome to:
- Submit suggestions and bug-reports at: https://github.com/flr/ss3om/issues
- Send a pull request on: https://github.com/flr/ss3omn/
- Maintainer: Iago Mosqueira (WMR) iago.mosqueira@wur.nl