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Companion package for MARSS that allows you to use TMB to fit MARSS models

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marssTMB

{marssTMB} is in active development and not all code has been tested. Also the following are not allowed currently: R or Q with 0s on the diagonal, R or Q with "equalvarcov", B estimation. Time-varying parameters has been coded but not tested.

To use

Install MARSS 3.11.6 (development version)

install.packages('MARSS', repos = c('https://atsa-es.r-universe.dev', 'https://cloud.r-project.org'))

Install marssTMB

install.packages('marssTMB', repos = c('https://atsa-es.r-universe.dev', 'https://cloud.r-project.org'))

Fit a MARSS model

See the Quick Start Guide to get started. Call MARSS() with method="TMB"

library(MARSS)
y <- t(harborSealWA); dat <- dat[2:4, ]
MARSS(y, method="TMB")

Note R and Q can only be diagonal, unconstrained or fixed. equalvarcov is not available nor are zeros allowed on the diagonal as is available with the Kalman filter + EM and BFGS algorithm in MARSS(). But TMB is very fast. Also be aware that {marssTMB} is still in early development and you should check your answers against method="kem" and method="BFGS".

Developer notes

Install {TMBtools} package which is being used to help with set-up.

Rebuilding

  • Add or edit models in src as hpp files. See TMBtools documentation on how to make a cpp file into a hpp file.
  • Run TMBtools::export_models() whenever changes are made to any hpp files
  • Rebuild the package
  • Add helper files (includes) to inst/include/marssTMB and then put a #include marssTMB/newfile.hpp in your hpp file.
  • Build package and documentation with pkgdown::build_site()

NOAA 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.